Methods and systems for fluid transport and optical assembly

Abstract

Disclosed herein are examples of systems and methods for processing a plurality of particles in a solution. The system comprising: a sample unit to receive and hold a container comprising a sample, a tube to travel and extend through a first opening of the sample unit and into the container, wherein the tube is further to direct the plurality of cells to flow out of the container for processing by a microfluidic cartridge; and a pressurizer line to extend through a third opening of the sample unit, wherein the pressurizer line is to direct a pressurizing fluid into the sample unit to thereby pressurize the sample unit.

Description

METHODS AND SYSTEMS FOR FLUID TRANSPORT AND OPTICAL ASSEMBLYCROSS-REFERENCE

[0001] This application claims the benefit of U.S. Provisional Application No. 63 / 536,680, filed September 5, 2023, U.S. Provisional Application No. 63 / 539,611, filed September 21, 2023, and Application Serial No. NL 2036033, filed October 13, 2023, which applications are incorporated herein by reference.BACKGROUND

[0002] The analysis of a particle, such as a cell, can be performedby examining properties such as fluorescent images or sequencing data. This examination can help determine the type or state of the cell, such as identifying cell type. Additionally, the properties of cells may also be analyzed to diagnose diseases and other conditions. Such analysis may include an evaluation of cell morphology. This process can involve directing the cells through a flow channel or a channel of a cartridge under fluidic guidance through a microscope imaging field. The images captured can then be processed to further evaluate cell morphology. While numerous devices, systems, and methods have been used to process and analyze cells in the past, there remains an unmet need for a more effective approach to open the avenue for new technologies.SUMMARY

[0003] In an aspect, the present disclosure provides a system comprising: a sample unit to receive and hold a container comprising a sample, which sample comprises a plurality of particles in a solution; a tube to travel and extend through a first opening of the sample unit and into the container, wherein the tube is further to direct the plurality of cells to flow out of the container for processing by a microfluidic cartridge; and a pressurizer line to extend through a third opening of the sample unit, wherein the pressurizer line is to direct a pressurizing fluid into the sample unit to thereby pressurize the sample unit. In some embodiments, the sample unit comprises a sealed interior volume for enclosing the container. In some embodiments, the tube extends along a first longitudinal axis, and the washing fluid line extends along a second longitudinal axis different from the first longitudinal axis. In some embodiments, the first longitudinal axis and the second longitudinal axis are substantially perpendicular to one another. In some embodiments, the first opening is located at a distal end portion of the sample unit, and the second opening is located at a side portion of the sample unit. In some embodiments, the washing solution source is to direct the washing solution through the washing fluid line towards the tube within the sample unit. In some embodiments, the microfluidic cartridge comprises a sorting junction to sort the plurality ofparticles using at least particle types. In some embodiments, the sample unit comprises a housing having a plurality of sections that are to move relative to one another along a vertical axis of the sample unit, wherein the first opening and the second opening are disposed over a same section. In some embodiments, the housing comprises a seal at a contact surface between the plurality of sections. In some embodiments, the pressurizingfluid is a compressed gas. In some embodiments, the pressurizing fluid source is in fluidic communication with the pressurizer line. In some embodiments, the pressurizing fluid is used to create pressure within the sample unit so as to direct flow of the plurality of particles from the container and through the tube. In some embodiments, the motor unit comprises a rotatable shaft to impart a rotational motion to the container when the container is held within the sample unit, to thereby generate a substantially uniform suspension of particles in the container. In some embodiments, the motor unit is disposed within the sample unit. In some embodiments, the motor unit is disposed outside of the sample unit. In some embodiments, the tube is to travel and extend to an inner volume of the container. In some embodiments, the tube is disposed within the inner volume of the container, a distance between (i) a distal end of the tube and (ii) a bottom surface of the container ranges between about 0.1 millimeters (mm) and about 1 mm. In some embodiments, a length of the tube ranges between about 1 inch and about 6 inches. In some embodiments, an inner diameter of the tube ranges between about 1 / 500 inch and about 1 / 100 inch. In some embodiments, an outer diameter of the tube ranges between about 1 / 100 inch and about 1 / 10 inch. In some embodiments, the system further comprises a washing fluid line to extend through a second opening of the sample unit, wherein the washing fluid line is to direct a washing solution to clean the tube within the sample unit in-between two or more sample processingruns. In an aspect, the present disclosure provides a method for sample processing, the method comprising: moving a container or a sample unit relative to each other thereby causing the container to be secured in the sample unit, wherein the container comprises a sample, which sample comprises a plurality of particles in a solution; directing the plurality of particles to flow through a tube and out of the container for processing by a microfluidic cartridge, wherein the tube extends through a first opening of the sample unit and is disposed in the container; and prior to or sub sequent to (b), directing a washing solution to flow through a washing fluid line to clean the tube within the sample unit, wherein the washing fluid line extends through a second opening of the sample unit. In some embodiments, (b) is performed when the container is enclosed within a sealed interior volume of the sample unit. In some embodiments, in (b) the tube extends through the first opening along a first longitudinal axis, and in (c) the washing fluid line extends along a second longitudinal axis different from the first longitudinal axis. In some embodiments, the first longitudinal axis and the secondlongitudinal axis are substantially perpendicular to one another. In some embodiments, the first opening is located at a distal end portion of the sample unit, and the second opening is located at a side portion of the sample unit. In some embodiments, (c) comprises directing the washing solution from a washing solution source, through the washing fluid line, and towards the tube disposed within the sample unit. In some embodiments, the sample unit comprises a housing comprising a plurality of sections, wherein the first opening and the second opening are disposed over a same section, and wherein the method further comprises moving the plurality of sections relative to one another along a vertical axis of the sample unit to close or seal the sample unit. In some embodiments, the housing comprises a seal at a contact surface between the plurality of sections. In some embodiments, the pressurizer line extends through a third opening of the sample unit. In some embodiments, the pressurizing fluid is a pressurized gas. In some embodiments, the pressurizing fluid is directed from a pressurizing fluid source in fluidic communication with the pressurizer line. In some embodiments, the motor unit is disposed within the sample unit. In some embodiments, the motor unit is disposed outside of the sample unit. In some embodiments, the tube is disposed within the inner volume of the container, a distance between (i) a distal end of the tube and (ii) a bottom surface of the container ranges between about 0.2 millimeters (mm) and about 1 mm. In some embodiments, a length of the tube ranges between about 1 inch and about 6 inches. In some embodiments, an inner diameter of the tube ranges between about 1 / 500 inch and about 1 / 100 inch. In some embodiments, an outer diameter of the tube ranges between about 1 / 100 inch and about 1 / 10 inch. In an aspect, the present disclosure provides a system comprising: a platform to hold a container comprising a sample, which sample comprises a plurality of particles in a solution; a top portion disposed above the platform; a vertical actuator coupled to at least one of the platform or the top portion, wherein the vertical actuator is to direct a relative movement between the platform and the top portion, to bring the platform and the top portion into contact with one another to enclose the container on the platform; a motor unit coupled to the platform, wherein the motor unit comprises a rotatable shaft to impart a rotational motion to the container, to thereby generate a substantially uniform suspension of particles in the container; and a joint that partially couples the top portion and the vertical actuator to each other, wherein the joint is to permit a relative movement between the top portion and the vertical actuator, to thereby de-couple the rotational motion of the container from the vertical actuator. In some embodiments, the relative movement between the top portion and the vertical actuator has at least two degrees-of-freedom. In some embodiments, the relative movement between the top portion and the vertical actuator is via at least three degrees-of-freedom. In some embodiments, the joint comprises a ball-and-socket joint. In some embodiments, the vertical actuator is coupledto the top portion. In some embodiments, the vertical guide rail is to limit movement of the top portion along an axis that is different from a vertical axis of the vertical guide rail, to provide an alignment between the top portion and the platform during their relative movement. In some embodiments, the base comprises at least one damper to de-couple rotational motion of the motor unit from the base. In some embodiments, the at least one damper comprises a plurality of dampers. In some embodiments, the at least one damper comprises a spring damper. In some embodiments, the motor unit is coupled to a bottom surface of the platform. In an aspect, the present disclosure provides a method for sample processing, the method comprising: securing a container on a platform and below a top portion, wherein the container comprises a sample, which sample comprises a plurality of particles in a solution; moving the platform and the top portion relative to one another using a vertical actuator to (i) bring the platform and the top portion into contact with one another and (ii) enclose the container on the platform; imparting a rotational motion to the container using a motor unit comprising a rotatable shaft, to thereby generate a substantially uniform suspension of particles in the container, wherein the top portion and the vertical actuator are partially coupled to one another via a joint, wherein the joint permits a relative movement between the top portion and the vertical actuator, to de-couple the rotational motion of the container from the vertical actuator during (c). In some embodiments, the relative movementbetween the top portion andthe vertical actuator is via at least two degrees-of-freedom. In some embodiments, the relative movementbetween the top portion andthe vertical actuator is via at leastthree degrees-of-freedom. In some embodiments, thejointcomprises a ball-and-socket joint. In some embodiments, the vertical actuator is coupled to the top portion. In some embodiments, the top portion is coupled to a vertical guide rail, wherein, in (b), the vertical guide rail (i) limits movement of the top portion along an axis that is different from a vertical axis of the vertical guide rail and (ii) provides an alignment between the top portion and the platform during their relative movement. In an aspect, the present disclosure provides a system comprising: a sample unit comprising a bottom portion, wherein the bottom portion is disposed within an inner volume of the sample unit and to hold a container comprising a sample, which sample comprises a plurality of particles in a solution; a motor unit coupled to the platform and disposed within the inner volume of the sample unit, wherein the motor unit comprises a rotatable shaft configured impart a rotational motion to the container when the container is disposed over the platform, thereby to generate a substantially uniform suspension of particles in the container; and a pressurizer line to extend through an opening of the sample unit, wherein the pressurizer line is to direct a pressurizing fluid into the sample unit, thereby to pressurize the inner volume of the sample unit. In some embodiments, the motor unit is coupled to a bottom surface of the platform.In some embodiments, the pressurizing fluid is a pressurized gas. In some embodiments, the pressurizing fluid source is in fluidic communication with the pressurizer line. In some embodiments, the tube is further to direct the plurality of particles to flow out of the container for processing by a microfluidic cartridge. In some embodiments, a pressure exerted by the pressurizing fluid is sufficient to pressurize the sample unit and direct flow of the plurality of particles from the container andthrough the tube. In some embodiments, the microfluidic cartridge comprises a cell sorting junction to sort the plurality of particles using at least particle types. In an aspect, the present disclosure provides a method for sample processing, the method comprising: securing a container on a platform of a sample unit, wherein the platform is disposed within an inner volume of the receptable, and wherein the container comprises a sample, which sample comprises a plurality of particles in a solution; imparting, using a motor unit coupled to the platform, a rotational motion to the container when the container is disposed over the platform, to generate a substantially uniform suspension of particles in the container, wherein the motor unit is disposed within the inner volume of the sample unit; and directing a pressurizing fluid into the sample unit through a pressurizer line to pressurize the inner volume of the sample unit, wherein the pressurizer line is extended through an opening of the sample unit. In some embodiments, the motor unit is coupled to a bottom surface of the platform. In some embodiments, the pressurizing fluid is a pressurized gas. In some embodiments, the pressurizing fluid is directed from a pressurizing fluid source in fluidic communication with the pressurizer line. In some embodiments, the tube is extended through an additional opening of the sample unit and disposed in the container. In some embodiments, a pressure exerted by the pressurizing fluid is sufficient to pressurize the sample unit and direct flow of the plurality of particles from the container and through the tube. In some embodiments, the motor unit comprises a rotatable shaft configured to impart a rotational motion to the container when the container is disposed over the platform; and a controller coupled to the motor unit, wherein the controller is to direct the motor unit to impart the rotational motion to the container, to generate a substantially uniform suspension of particles in the container, wherein the rotational motion comprises: a first rotation along a direction at a first speed; and a second rotation along a different direction at a second speed, wherein the first speed or the second speedis between about200 rotations per minute (RPM) and about 1,000 RPM In some embodiments, the direction and the different direction are opposite to one another. In some embodiments, each of the first speed and the second speed is between about 200 RPM and about 1,000 RPM. In some embodiments, the first speed or the second speed is greater than or equal to about 400 RPM. In some embodiments, the first speed or the second speed is greater than or equalto about500 RPM. In some embodiments, the rotational motion further comprises: athirdrotation along the direction at a third speed, wherein the first speed and the third speed are different; or a fourth rotation along the additional direction at a fourth speed, wherein the second speed and the fourth speed are different. In some embodiments, the rotational motion comprises the third rotation and the fourth rotation. In some embodiments, the rotational motion comprises, in a sequential order, the first rotation, the third rotation, the second rotation, and the fourth rotation. In some embodiments, each of the third speed and the fourth speed is between about 200 RPM and about 1,000 RPM. In some embodiments, each of the third speed and the fourth speed is greater than or equal to about 400 RPM. In some embodiments, each of the third speed and the fourth speed is greater than or equal to about 500 RPM. In an aspect, the present disclosure provides a method for sample processing, the method comprising: holding a container on a platform, wherein the container comprises a sample, which sample comprises a plurality of particles in a solution; imparting, using a motor unit coupled to the platform, a rotational motion to the container when the container is disposed over the platform, to generate a substantially uniform suspension of particles in the container, wherein the rotational motion comprises: a first rotation along a direction at a first speed; and a second rotation along a different direction at a second speed, wherein the first speed or the second speed is between about 200 rotations per minute (RPM) and about 1,000 RPM. In some embodiments, the direction and the different direction are opposite to one another. In some embodiments, each of the first speed and the second speed is between about 200 RPM and about 1,000 RPM. In some embodiments, the first speed or the second speed is greater than or equal to about 400 RPM. In some embodiments, the first speed or the second speed is greater than or equal to about 500 RPM. In some embodiments, the rotational motion further comprises: a third rotation along the direction at a third speed, wherein the first speed and the third speed are different; or a fourth rotation along the additional direction at a fourth speed, wherein the second speed and the fourth speed are different. In some embodiments, the rotational motion comprises the third rotation and the fourth rotation. In some embodiments, the rotational motion comprises, in a sequential order, the first rotation, the third rotation, the second rotation, and the fourth rotation. In some embodiments, each of the third speed and the fourth speed is between about 200 RPM and about 1,000 RPM. In some embodiments, each of the third speed and the fourth speed is greater than or equal to about 400 RPM. In some embodiments, each of the third speed and the fourth speed is greater than or equal to about 500 RPM. In an aspect, the present disclosure provides an apparatus comprising: a cartridge receiving region to receive a cartridge; an emission assembly including: a first light source, and a set of optical elements to redirect light from the first light source to illuminate a first fluid channel of the cartridge with a first beam of light and a second fluid channel of the cartridgewith a second beam of light; and a collection assembly to receive light transmitted from the emission assembly through the first fluid channel and through the second fluid channel, the collection assembly to generate signals indicating presence of one or more particles in the first fluid channel or in the second fluid channel. In some embodiments, the first light source comprises a laser. In some embodiments, the laser comprises a collimated diode laser. In some embodiments, the first beam of light illuminates the first fluid channel with an illumination footprint having an elliptical shape, and the second beam of light illuminates the second fluid channel with an illumination footprint having an elliptical shape. In some embodiments, the first fluid channel has a width, the second fluid channel has a width, the first beam of light illuminates an entirety of the width of the first fluid channel, and the second beam of light illuminate s an entirety of the width of the second fluid channel. In some embodiments, the emission assembly further includes a demagnifying telescope interposed between the first light source and the set of optical elements. In some embodiments, the emission assembly further includes a half wave plate interposed between the first light source and the set of optical elements. In some embodiments, the set of optical elements includes a Wollaston prism. In some embodiments, the set of optical elements includes a telescope to expand the first beam of light and the second beam of light. In some embodiments, the set of optical elements includes a focusing lens to focus the first beam of light and the second beam of light as expanded by the telescope. In some embodiments, the set of optical elements includes atleasttwo mirrors. In some embodiments, the atleasttwo mirrors move via one or both of translational adjustment or tilt adjustment to thereby reposition the first beam of light or the second beam of light relative to the cartridge. The apparatus of any of claims 96 through 107, the set of optical elements to provide separation of the first beam of light from the second beam of light by approximately 250 micrometers. In some embodiments, the cartridge has a third fluid channel and a fluid junction, the third fluid channel leading into the fluid junction, and the first fluid channel and the second fluid channel each leading out of the fluid junction. In some embodiments, the cartridge further includes a first valve and a second valve, the first valve to selectively permit communication of fluid from the third fluid channel to the first fluid channel via the fluid junction, and the second valve to selectively permit communication of fluid from the third fluid channel to the second fluid channel via the fluid junction. In some embodiments, the emission assembly further comprises a second light source, the second light source providing alignment illumination to the cartridge. In some embodiments, the second light source illuminates the cartridge with white light. In some embodiments, the apparatus further comprises a processor, the processor to process signals from the collection assembly to thereby determine a number of particles communicated through one or both of the first fluid channel or the second fluid channel.In some embodiments, the collection assembly includes a first photosensor to generate a signal indicating presence of one or more particles in the first fluid channel. In some embodiments, the collection assembly further including a second photosensor to generate a signal indicating presence of one or more particles in the second fluid channel. In some embodiments, the collection assembly further includes a beam splitter, the beam splitter to split light received from the first fluid channel and from the second fluid channel, the beam splitter to direct light received from the first fluid channel toward the first photosensor, and the beam splitter to direct light received from the second fluid channel toward the second photosensor. In some embodiments, the beam splitter comprises a polarizing beam splitter, the polarizing beam splitter to split light received from the first fluid channel and from the second fluid channel via polarization. In some embodiments, the collection assembly includes a camera, the camera to capture an image of the first fluid channel and the second image channel to verify alignment of the first beam of light with the first fluid channel and to verify alignment of the second beam of light with the second fluid channel. In some embodiments, the collection assembly further includes a firstbeam splitter, the first beam splitter to direct light received from the first fluid channel and from the second fluid channel simultaneously along a first path and a second path, the first path leading toward the camera, the second path leading toward a combination of a first photosensor a second photosensor, the first photosensor to generate a signal indicating presence of one or more particles in the first fluid channel, and the second photosensor to generate a signal indicating presence of one or more particles in the second fluid channel. In some embodiments, the collection assembly further includes a second beam splitter, the second beam splitter to split light received along the second path, the second beam splitter to direct light received from the first fluid channel toward the first photosensor, and the second beam splitter to direct light received from the second fluid channel toward the second photosensor. In some embodiments, the firstbeam splitter comprises a beam splitter cube. In some embodiments, the first path is longer than the second path. In some embodiments, the apparatus further comprises: a movable cartridge receiving stage, and a processor, the processor to provide movement of the movable cartridge receiving stage in response to an image captured by the camera indicating misalignment of the first beam of light with the first fluid channel or misalignment of the second beam of light with the second fluid channel. In an aspect, the present disclosure provides a method comprising: activating a single light source; communicating light from the single light source through an emission assembly, the emission assembly including optical elements redirecting light from the first light source to illuminate a first fluid channel of a cartridge with a first beam of light and a second fluid channel of the cartridge with a second beam of light; communicating fluid through the cartridge, the fluidcontaining particles; and receiving signals from a collection assembly, the collection assembly receiving light transmitted from the emission assembly through the first fluid channel and through the second fluid channel, the received signals indicating presence of one or more particles in the first fluid channel or in the second fluid channel. In an aspect, the present disclosure provides an apparatus comprising: a cartridge receiving region to receive a cartridge, the cartridge including: a first fluid channel, a second fluid channel, a third fluid channel, a fluid junction, the third fluid channel leading into the fluid junction, the first fluid channel and the second fluid channel each leading out of the fluid junction, a first valve, the first valve to selectively permit communication of fluid from the third fluid channel to the first fluid channel via the fluid junction, and a second valve, the second valve to selectively permit communication of fluid from the third fluid channel to the second fluid channel via the fluid junction; and an optical assembly, to generate signals indicating presence of one or more particles in the first fluid channel, the optical assembly further to generate signals indicating presence of one or more particles in the second fluid channel. In an aspect, the present disclosure provides a method comprising: driving fluid through a cartridge, the cartridge including: a first fluid channel, a second fluid channel, a third fluid channel, a fluid junction, the third fluid channel leading into the fluid junction, the first fluid channel and the second fluid channel each leading out of the fluid junction, a first valve, the first valve to selectively permit communication of fluid from the third fluid channel to the first fluid channel via the fluid junction, and a second valve, the second valve to selectively permit communication of fluid from the third fluid channel to the second fluid channel via the fluid junction; and using an optical assembly to count one or both of: a number of particles flowing through the first fluid channel, or a number of particles flowing through the second fluid channel. In an aspect, the present disclosure provides an apparatus comprising: a cartridge receiving region to receive a cartridge; an emission assembly, the emission assembly to illuminate at least one fluid channel of the cartridge with at least one beam of light; and a collection assembly, the collection assembly to receive light transmitted from the emission assembly through the at least one fluid channel, the collection assembly including: a camera, the camera to capture an image of the at least one fluid channel to verify alignment of the at least one beam of light with the at least one fluid channel, at least one photosensor, the at least one photosensor to generate signals indicating presence of one or more particles in the at least one fluid channel, and a beam splitter, the beam splitter to direct light received from the at least one fluid channel simultaneously along a first path and a second path, the first path leading toward the camera, the second path leading toward the at least one photosensor. In an aspect, the present disclosure provides a method comprising: illuminating at least one fluid channel of a cartridge with at least one beam of light; receiving light transmittedfrom the emission assembly through the at least one fluid channel; splitting the received light along a first path and along a second path, the first path leading toward a camera, the second path leading toward at least one photosensor; capturing an image with the camera to verify alignment of the at least one beam of light with the at least one fluid channel; and generating one or more signals with the at least one photosensor to indicate presence of one or more particles in the at least one fluid channel.INCORPORATION BY REFERENCE

[0004] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. To the extent publications and patents or patent applications incorporated by reference contradict the disclosure contained in the specification, the specification is intended to supersede and / or take precedence over any such contradictory material.BRIEF DESCRIPTION OF THE DRAWINGS

[0005] The novel features of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative implementations, in which the principles of the disclosure are utilized, and the accompanying drawings (also “Figure” and “FIG.” herein), of which:

[0006] FIG. 1 illustrates an ecosystem according to one implementation of the disclosure;

[0007] FIG. 2 illustrates a system, such as a sample unit, according to one implementation of the disclosure.

[0008] FIG. 3 illustrates a front view of the sample unit according to one implementation of the disclosure.

[0009] FIG. 4 illustrates an angled view of the sample unit according to one implementation of the disclosure.

[0010] FIG. 5A illustrates, in one example, the sample unit according to the disclosure in an open configuration.

[0011] FIG. 5B illustrates, in one example, the sample unit according to the disclosure in a closed configuration.

[0012] FIG. 6A illustrates, in one example, an isolated view of the sample unit according to the disclosure and a portion of the actuator unit according to the disclosure.

[0013] FIG. 6B illustrates, in one example, an angled view of the sample unit comprising acleaning port.

[0014] FIG. 6C illustrates, in one example, an angled view of the sample unit comprising a pressure inlet.

[0015] FIG. 7 illustrates a sample unit according to one implementation of the disclosure.

[0016] FIG. 8 illustrates, in one example, a side view of a bottom portion of the sample unit and a guide unit according to one implementation of the disclosure.

[0017] FIG. 9 illustrates, in one example, a side view of a bottom portion of the sample unit and a motor according to one implementation of the disclosure.

[0018] FIG. 10 illustrates, in one example, a view of the top portion and the actuator extension according to one implementation of the disclosure.

[0019] FIG. 11 illustrates, in one example, a view of a coupling unit according to one implementation of the disclosure.

[0020] FIG. 12 illustrates, in one example, an angled view of the actuator extension according to one implementation of the disclosure.

[0021] FIG. 13A illustrates a view of the sample unit in fully closed configuration.

[0022] FIG. 13B illustrates a view of the sample unit in a partially open configuration.

[0023] FIG. 13C illustrates a view of the sample unit in a closed configuration.

[0024] FIG. 14 illustrates an actuator unit according to one implementation of the disclosure.

[0025] FIG. 15A illustrates a base unit according to one implementation of the disclosure.

[0026] FIG. 15B shows an open view of a damper according to one implementation of the disclosure.

[0027] FIG. 16 illustrates a view of a base unit and a positional monitor according to one implementation of the disclosure.

[0028] FIG. 17A illustrates a top-down view of a base unit comprising a positional sensor according to one implementation of the disclosure.

[0029] FIG. 17B illustrates an angled view of a base unit comprising a positional sensor according to one implementation of the disclosure.

[0030] FIG. 18A illustrates a schematic of a tubing between the sample holder and a cartridge according to one implementation of the disclosure.

[0031] FIG. 18B illustrates a schematic of a tubing between the sample holder and a cartridge according to one implementation of the disclosure in an alternate configuration.

[0032] FIG. 19 illustrates a schematic of a sample unit with tubing according to one implementation of the disclosure.

[0033] FIG. 20 illustrates a sample unit in an open configuration according to oneimplementation of the disclosure.

[0034] FIG. 21 illustrates a sample unit in a closed configuration according to one implementation of the disclosure.

[0035] FIG. 22 illustrates a portion of the sample unit according to one implementation of the disclosure.

[0036] FIG. 23 illustrates the sample unit and a portion of an actuator unit according to one implementation of the disclosure.

[0037] FIG. 24 illustrates a base unit of the cell storage module according to one implementation of the disclosure.

[0038] FIG. 25 A illustrates a portion of the actuator unit when the sample unit is in an open configuration according to one implementation of the disclosure.

[0039] FIG. 25B illustrates a portion of the actuator unit when the sample unit is in a closed configuration according to one implementation of the disclosure.

[0040] FIG. 26 illustrates an actuator unit according to one implementation of the disclosure.

[0041] FIG. 27 illustrates a sample unit under pressure according to one implementation of the disclosure.

[0042] FIG. 28 illustrates a sealing mechanism when the sample unit is in an open configuration according to one implementation of the disclosure.

[0043] FIG. 29 illustrates a sealing mechanism when the sample unit is in a closed configuration according to one implementation of the disclosure.

[0044] FIG. 30A illustrates a system for preparing a sample according to one implementation of the disclosure.

[0045] FIG. 30B illustrates a system for sorting a sample according to one implementation of the disclosure.

[0046] FIG. 31 illustrates a workflow for sorting and imaging cells according to one implementation of the disclosure.

[0047] FIG. 32 illustrates a computer system in communication with the system according to one implementation of the disclosure.

[0048] FIG. 33 depicts a schematic view of an example of a cell analysis system according to one implementation of the disclosure.

[0049] FIG. 34 depicts a perspective view of an example of a cartridge that may be used in examples of the cell analysis system of FIG.33 accordingto one implementation of the disclosure.

[0050] FIG. 35 depicts an exploded perspective view of the cartridge of FIG. 34 accordingto one implementation of the disclosure.

[0051] FIG. 36 depicts a perspective view of an example underside of a first layer of the cartridge of FIG. 34 according to one implementation of the disclosure.

[0052] FIG. 37 depicts a perspective view of an example underside of a second layer of the cartridge of FIG. 34 according to one implementation of the disclosure.

[0053] FIG. 38 depicts a top plan view of the cartridge of FIG. 34 according to one implementation of the disclosure.

[0054] FIG. 39 depicts an enlarged top plan view of an example of a primary sorting region of the cartridge of FIG. 34 according to one implementation of the disclosure.

[0055] FIG. 40 depicts a further enlarged top plan view of the primary sorting region of FIG. 39 according to one implementation of the disclosure.

[0056] FIG. 41 A depicts a cross-sectional view of the primary sorting region of FIG. 39, taken along line 9-9 of FIG. 40, with an example of a first valve in an open state and an example of a second valve in an open state according to one implementation of the disclosure.

[0057] FIG. 41B depicts a cross-sectional view of the primary sorting region of FIG. 39, taken along line 9-9 of FIG. 40, with the second valve in a closed state and the first valve in the open state according to one implementation of the disclosure.

[0058] FIG. 41C depicts a cross-sectional view of the primary sorting region of FIG. 39, taken along line 9-9 of FIG. 40, with the second valve in the open state and the first valve in a closed state according to one implementation of the disclosure.

[0059] FIG. 42 depicts a schematic side view of an example optical emission assembly and an example optical collection assembly thatmay be incorp oratedinto the cell analysis system of BIG. 33 according to one implementation of the disclosure.

[0060] FIG. 43 depicts a perspective view of the optical emission assembly of FIG. 42 according to one implementation of the disclosure.

[0061] FIG. 44 depicts an exploded view of the optical emission assembly of FIG. 44, with a frame omitted according to one implementation of the disclosure.

[0062] FIG.45 depicts a perspective view of an example laser telescopeassembly of the optical emission assembly of FIG. 44 according to one implementation of the disclosure.

[0063] FIG. 46 depicts a cross-sectional view of the laser telescope assembly of FIG.45, taken along line 14-14 of FIG. 45 according to one implementation of the disclosure.

[0064] FIG. 47 depicts a perspective view of an example Wollaston prism assembly of the optical emission assembly of FIG. 44 according to one implementation of the disclosure.

[0065] FIG. 48 depicts a cross-sectional view of the Wollaston prism assembly of FIG. 47, taken along line 16-16 of FIG. 47 according to one implementation of the disclosure.

[0066] FIG. 49 depicts a perspective view of an example prism telescope assembly of the optical emission assembly of FIG. 44 according to one implementation of the disclosure.

[0067] FIG. 50 depicts a cross-sectional view of the prism telescope assembly of FIG. 49, taken along line 18-18 of FIG. 49 according to one implementation of the disclosure.

[0068] FIG. 51 depicts a perspective view of an example mirror assembly of the optical emission assembly of FIG. 44 according to one implementation of the disclosure.

[0069] FIG. 52 depicts another perspective view of the mirror assembly of FIG. 51 according to one implementation of the disclosure.

[0070] FIG. 53 depicts a perspective view of an example focus lens assembly of the optical emission assembly of FIG. 44 according to one implementation of the disclosure.

[0071] FIG. 54 depicts a cross-sectional view of the focus lens assembly of FIG. 53, taken along line 22-22 of FIG. 53 according to one implementation of the disclosure.

[0072] FIG. 55 depicts another perspective view of the focus lens assembly of FIG. 53 according to one implementation of the disclosure.

[0073] FIG. 56 depicts a cross-sectional view of the focus lens assembly of FIG. 53, taken along line 24-24 of FIG. 55 according to one implementation of the disclosure.

[0074] FIG. 57 depicts a perspective view of an example dual mirror assembly of the optical emission assembly of FIG. 44 according to one implementation of the disclosure.

[0075] FIG. 58 depicts another perspective view of the dual mirror assembly of FIG. 57 according to one implementation of the disclosure.

[0076] FIG. 59 depicts another perspective view of the dual mirror assembly of FIG. 57 according to one implementation of the disclosure.

[0077] FIG. 60 A depicts a side elevation view of the dual mirror assembly of FIG. 57, in an example first stage of adjustment along a first horizontal dimension according to one implementation of the disclosure.

[0078] FIG. 60B depicts a side elevation view of the dual mirror assembly of FIG. 57, in an example second stage of adjustment along the first horizontal dimension according to one implementation of the disclosure.

[0079] FIG. 61 A depicts a side elevation view of the dual mirror assembly of FIG. 57, in an example first stage of adjustment along a second horizontal dimension according to one implementation of the disclosure.

[0080] FIG. 61B depicts a side elevation view of the dual mirror assembly of FIG. 57, in an example second stage of adjustment along the second horizontal dimension according to one implementation of the disclosure.

[0081] FIG. 62 depicts a perspective view of the optical collection assembly of FIG. 42 according to one implementation of the disclosure.

[0082] FIG. 63 depicts an exploded view of the optical collection assembly of FIG. 42 according to one implementation of the disclosure.

[0083] FIG. 64 depicts a cross-sectional view of the optical collection assembly of FIG. 42, taken along line 32-32 of FIG. 62 according to one implementation of the disclosure.

[0084] FIG. 65 depicts an exploded view of an example mirror assembly of the optical collection assembly of FIG. 42 according to one implementation of the disclosure.

[0085] FIG. 66 depicts another perspective view of the optical collection assembly of FIG. 42 according to one implementation of the disclosure.

[0086] FIG. 67 depicts a cross-sectional view of the optical collection assembly of FIG. 42, taken along line 35-35 of FIG. 66 according to one implementation of the disclosure.

[0087] FIG. 68 depicts a perspective view of an example optical sensor assembly of the optical collection assembly of FIG. 42 according to one implementation of the disclosure; and

[0088] FIG. 69 depicts a graph showingan example plotofan optical signal indicatingpassage of a particle through an optical cell detector provided by the optical emission assembly and optical collection assembly of FIG. 42 according to one implementation of the disclosure.DETAILED DESCRIPTION

[0089] The following detailed description of certain examples will be better understood when read in conjunction with the appended drawings. To the extent that the figures illustrate diagrams of the functional blocks of various examples, the functional blocks are not necessarily indicative of the division between hardware components. Thus, for example, one or more of the functional blocks (e.g., processors or memories) may be implemented in a single piece of hardware (e.g., a general purpose signal processor or random access memory, hard disk, or the like). Similarly, the programs may be stand-alone programs, may be incorporated as subroutines in an operating system, may be functions in an installed software package, and the like. It should be understood that the various examples are not limited to the arrangements and instrumentality shown in the drawings.

[0090] Throughout this specification and the claims which follow, unless the context requires otherwise, the word “comprise,” and variations such as “comprises” and “comprising” means various components may be co-jointly employed in the methods and articles (e.g., compositions and apparatuses including device and methods). For example, the term “comprising” will be understood to imply the inclusion of any stated elements or steps but not the exclusion of anyother elements or steps. In general, any of the apparatuses and methods described herein should be understood to be inclusive, but all or a sub -set of the components and / or steps may alternatively be exclusive and may be expressed as “consisting of’ or alternatively “consisting essentially of’ the various components, steps, sub -components, or sub-steps. Furthermore, references to “one example” are not intended to be interpreted as excluding the existence of additional examples that also incorporate the recited features. The use of “including,” “comprising,” “having,” or “in which,” and variations thereof, herein is meant to encompass the items listed thereafter and equivalents thereof as well as additional items.

[0091] While various implementations of the disclosure havebeen shown and described herein, it will be obvious to those skilled in the art that such implementations are provided by way of example only. Numerous variations, changes, and substitutions may occur to those skilled in the art without departing from the disclosure. It should be understood that various alternatives to and combinations of the implementations of the disclosure described herein may be employed.

[0092] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the present disclosure belongs. In case of conflict, the present application including the definitions will control. Also, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular.

[0093] As used herein, the singular forms “a,” “an,” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise. As used herein, the term “and / or” includes any and all combinations of one or more of the associated listed items and may be abbreviated as “ / ”.

[0094] When used in the claims, the term “set” should be understood as one or more things which are grouped together. Similarly, when used in the claims “based on” should be understood as indicating that one thing is determined at least in part by what it is specified as being “based on.” Where one thing is required to be exclusively determined by another thing, then that thing will be referred to as being “exclusively based on” that which it is determined by.

[0095] Spatially relative terms, such as “under,” “below,” “lower,” “over,” “upper,” and the like, may be used herein for ease of description to describe one element or feature's relationship to another element(s) or feature(s) as illustrated in the figures. It will be understood that the spatially relative terms are intended to encompass different orientations of the device in use or operation in addition to the orientation depicted in the figures. For example, if a device in the figures is inverted, elements described as “under” or “beneath” other elements or features would then be oriented “over” the other elements or features. Thus, the term “under” may encompassboth an orientation of over and under. The device may be otherwise oriented (rotated 90 degrees or at other orientations) and the spatially relative descriptors used herein interpreted accordingly. Similarly, the terms “upwardly,” “downwardly,” “vertical,” “horizontal,” and the like are used herein for the purpose of explanation only unless specifically indicated otherwise. In addition, terms such as “outer” and “inner” are used herein for purposes of description and are not intended to indicate or imply relative importance or significance.

[0096] When a feature or element is herein referred to as being “on” or “over” another feature or element, it may be directly on or over the other feature or element; or intervening features and / or elements may also be present. In other words, when a feature or element is herein referred to as being “on” or “over” another feature or element, it may be indirectly on or over the other feature or element. In contrast, when a feature or element is referred to as being “directly on” or “directly over” another feature or element, there are no intervening features or elements present.

[0097] When a feature or element is referred to as being “mounted,” “connected,” “supported,” “attached,” or “coupled” to another feature or element, it may be directly mounted, connected, supported, attached, or coupled to the other feature or element or intervening features or elements may be present. In contrast, when a feature or element is referred to as being “directly mounted,” “directly connected,” “directly supported,” “directly attached,” or “directly coupled” to another feature or element, there are no intervening features or elements present. Although described or shown with respect to one embodiment, the features and elements so described or shown may apply to other embodiments. It will also be appreciated by those skilled in the art that references to a structure or feature that is disposed “adjacent” another feature may have portions that overlap or underlie the adjacent feature.

[0098] Whenever the term “at least,” “greater than,” or “greater than or equal to” precedes the first numerical value in a series of two or more numerical values, the term “at least,” “greater than” or “greater than or equal to” applies to each of the numerical values in that series of numerical values. For example, greater than or equal to 1, 2, or 3 is equivalent to greater than or equal to 1 , greater than or equal to 2, or greater than or equal to 3.

[0099] Whenever the term “no more than,” “less than,” or “less than or equal to” precedes the first numerical value in a series of two or more numerical values, the term “no more than,” “less than,” or “less than or equal to” applies to each of the numerical values in that series of numerical values. For example, less than or equal to 3, 2, or 1 is equivalent to less than or equal to 3, less than or equal to 2, or less than or equal to 1 .

[0100] The term “about” or “approximately” means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on howthe value is measured or determined, i. e., the limitations of the measurement system. For example, “about” can mean within 1 or more than 1 standard deviation, per the practice in the art. In one example, “about” can mean a range of up to ±20% - e.g., up to ±10%, up to ±5%, or up to ±1%, or smaller, of a given value. In one example, “about” includes no deviation, thereby referring to the value itself. In one example, particularly with respect to biological systems or processes, the term can mean within an order of magnitude, e.g., within 5-fold, within 2-fold, or smaller, of a value. Where particular values are described in the application and claims, unless otherwise stated, the term “about” meaning within an acceptable error range for the particular value should be assumed.

[0101] The term “substantially” as used herein in reference to a given parameter, property, or condition means and includes to a degree that one of ordinary skill in the art would understand that the given parameter, property, or condition is met with a degree of variance, such as within acceptable manufacturing tolerances. By way of example, depending on the particular parameter, property, or condition that is substantially met, the parameter, property, or condition may be at least 90.0% met - e.g., at least 95.0% met, at least 99.0% met, at least 99.9% met, or higher. In one example, “substantially” includes no deviation, thereby referring to the value itself. The range implied by the term “substantially” should also be read to include the perfect result that is within thatrange. Thus, the term “substantially complete” shall be read as including “perfectly complete” while also including a range of completeness that is functionally equivalent to perfectly complete. As another example, terms such as “substantially straight” and “substantially flat” shall be read as including “perfectly straight” and “perfectly flat,” respectively; while also including a range of straightness or flatness that is functionally equivalent to perfectly straight or flat, respectively. As with the terms “approximately” and “about,” the term “substantially” may indicate a suitable dimensional tolerance, or otherform of reasonable expected range, that allows a part or collection of components to function for its intended purpose as described herein.

[0102] The term “perpendicular” shall be understood to include arrangements where one element (e.g., surface, feature, component, axis, etc.) defines an angle of 90 degrees with another element (e.g., surface, feature, component, axis, etc.). The term “perpendicular” shall also be understood to include arrangements where one element (e.g., surface, feature, component, axis, etc.) defines an angle of approximately 90 degrees with another element (e.g., surface, feature, component, axis, etc.).

[0103] Although the terms “first” and “second” may be used herein to describe various features / elements (including steps), these features / elements should not be limited by these terms, unless the context indicates otherwise. These terms are used to distinguish one feature / elementfrom another feature / element, and unless specifically pointed out, do not denote a certain order. Thus, a first feature / element discussed below could be termed a second feature / element, and similarly, a second feature / element discussed below could be termed a first feature / element without departing from the teachings of the present invention. The terms “first,” “second,” and “third,” etc. are thus used merely as labels, and are notintended to impose numerical requirements on their objects.

[0104] As used herein, the terms “system,” “apparatus,” and “device” may be read as being interchangeable with each other. A system, apparatus, and device may each include a plurality of components having various kinds of structural and / or functional relationships with each other.

[0105] The term “fluid” shall be understood to include liquids and gases, including pneumatic pressure. Similarly, “fluidic communication” shall be understood to include the communication of liquids and the communication of gases, including pneumatic pressure.

[0106] The term “morphology” or “morphological characteristic” of a cell as used herein generally refers to the form, structure, and / or configuration of the cell. The morphology of a cell can comprise one or more aspects of a cell’s appearance, such as, for example, shape, size, arrangement, form, structure, pattem(s)of one or more internal and / or external parts of the cell, or shade (e.g., color, greyscale, etc.). Non-limiting examples of a shape of a cell can include, but are not limited to, circular, elliptic, shmoo-like, dumbbell, star-like, flat, scale-like, columnar, invaginated, having one or more concavely formed walls, having one or more convexly formed walls, prolongated, having appendices, having cilia, having angle(s), having corner(s), etc. A morphological feature of a cell may be visible with treatment of a cell (e.g., small molecule or antibody staining). Alternatively, the morphological feature of the cell may not and need not require any treatment to be visualized in an image or video.

[0107] The terms “unstructured” or “unsorted, ” asused interchangeably herein, generally refers to a mixture of cells(e.g., an initial mixture of cells)thatis not substantially sorted (or rearranged) into separate partitions. An unstructured population of cells can comprise at least two types of cells that can be distinguished by exhibiting different properties (e.g., one or more physical properties, such as one or more different morphological characteristics as disclosed herein). The unstructured population of cells can be a random (or randomized) mixture of the at least two types of cells. The cells as disclosed herein can be viable cells. A viable cell, as disclosed herein, can be a cell that is not undergoing necrosis or a cell that is not in an early or late apoptotic state. Assays for determining cell viability can include, e.g., as using propidium iodide (PI) staining which may be detected by flow cytometry, Alternatively, the cells may not and need not be viable (e.g., fixed cells).

[0108] A “viable cell” as disclosed herein can be characterized by exhibiting one or more characteristics (e.g., morphology, one or more gene expression profiles, etc.) that is substantially unaltered (or that is not substantially impacted by) by any step or process of the methods disclosed herein (e.g., partitioning). In some cases, a characteristic of a viable cell can be a gene transcript accumulation rate, which can be characterized by a change in transcript levels of a same gene (e.g., a same endogenous gene) between mother and daughter cells over the time between cell divisions, as ascertained by single cell sequencing, polymerase chain reaction (PCR), etc.

[0109] The term “heterologous marker” as used herein generally refers to a heterologous composition detectable by one or more analytical or sensing techniques, such as, for example, fluorescence detection, spectroscopic detection, photochemical detection, biochemical detection, immunochemical detection, electrical detection, optical detection, chemical detection, imaging (e.g., via one or more cameras), or omics (e.g., genomics, transcriptomics, or proteomics, etc.).

[0110] The heterologous marker can be a tag that can be coupled to (e.g., covalently or non- covalently) a particle (e.g., at least a portion of a cell, such as a cellular component). The heterologous marker can exhibit specific binding affinity to the at least the portion of the cell. The heterologous marker can be a label or an identifier that can convey information about the at least the portion of the cell (e.g., an analyte derived from the cell, or the cell in its entirety). The heterologous marker can be, for example, a polypeptide (e.g., an antibody or a fragment thereof), a nucleic acid molecule (e.g., a deoxyribonucleic acid (DNA) molecule, a ribonucleic acid (RNA) molecule, etc.) exhibiting at least a partial complementarity to a target nucleic acid sequence of the cell, or a small molecule configured to bind to a target epitope (e.g., a polypeptide sequence, a polynucleotide sequence, one or more polysaccharide moieties) of the cell.

[0111] The heterologous marker can comprise an optically detectable moiety, such as a dye. In some implementations, the heterologous marker can comprise or can be functionalized with (e.g, covalently or non-covalently) one or more optically detectable moieties, such as, a dye (e.g., a fluorescent dye), biotin-streptavidin conjugates, magnetic beads, radiolabels, enzymes (e.g., horse radish peroxidase, alkaline phosphatase, etc.), and calorimetric labels such as colloidal gold or colored glass or plastic (e.g., polystyrene) beads.

[0112] Alternatively or in addition to, the heterologous maker can comprise an object in the shape of a sphere, cuboid, or disc, or any partial shape or combination of shapes thereof. The object may have a cross-section that is circular, triangular, square, rectangular, pentagonal, hexagonal, or any partial shape or combination of shapes thereof.

[0113] The heterologous marker may not and need not be coupled to the cell. The heterologous marker can be a reference object used for analyzing (e.g., indirectly analyzing) particles (e.g.,cells). The heterologous marker can have one or more known characteristics (e.g., size, morphology or shape, weight, density, colorimetric properties, magnetic properties, omics as disclosed herein, etc.), such that when one or more particles are co -flowing or sorted with the heterologous marker, detection of the heterologous marker can be used to determine presence of the one or more particles.

[0114] The term “cellular component” as used herein generally refers to matter derived from a cell, such as matter contained inside a cell (i.e., intracellular) or presented outside of the cell (i.e., extracellular). A cellular component can include matter naturally derived from the cell (e.g., from the membrane of the cell, from the interior of the cell, components secretable or secreted by the cell, etc.) as well as originally foreign agents (e.g., microorganisms, viruses, asbestos, or compounds or extracellular origin) that exist inside the cell. Non -limiting examples of a cellular component can include an amino acid, a polypeptide (e.g., a peptide fragment, a protein, etc.), ion (e.g., Na+, Mg2+, Cu+, Cu2+, Zn2+, Mn2+, Fe2+, and Co2+), polysaccharides, lipid (e.g., fats, waxes, sterols, fat-soluble vitamins such as vitamins A, D, E, and K, monoglycerides, diglycerides, triglycerides, or phospholipids), a nucleotide, a polynucleotide (e.g., DNA or RNA), particle (e.g., nanoparticle), fibers (e.g., asbestos fibers), cytoplasm, organelle (e.g., mitochondria, peroxisome, plastid, endoplasmic reticulum, flagellum, Golgi apparatus, etc.), cellular compartment (e.g., chromatin), microorganism (e.g., bacterium, virus, or fungus), virus, and vesicle (e.g., lysosome, peroxisome), small molecule, protein complex, protein aggregate, or a macromolecule). In implementations, the cellular component is a biomolecule.

[0115] The term “partition” as used herein generally refers to a space or volume that may be suitable to contain one or more species or conduct one or more reactions. A partition may be a physical compartment, suchas a droplet(e.g., a dropletin an emulsion), ahead, a well, a container, a tube, a plate (e.g., a 96 well plate or a 384 well plate), a channel, etc. A partition may isolate space or volume from another space or volume. In some cases, a partition may be a single compartment partition. In some cases, a partition may comprise one or more other (inner) partitions. In some cases, a partition may be a virtual compartment that can be defined and identified by an index (e.g., indexed libraries) across multiple and / or remote physical compartments. For example, a physical compartment may comprise a plurality of virtual compartments. In another example, a partition can be a repository (e.g., that is downstream of the flow channel) that is configured to receive one or more particles (e.g., cell(s)) from the flow channel, in which the one or more particles can be in a fluid or in a droplet.

[0116] The term “emulsion” as used herein generally refers to a stable suspension of two incompatible fluid materials, where one fluid (e.g., an aqueous liquid, such as water or buffer) issuspended or dispersed as minute particles or globules in another fluid (e.g. , a non -aqueous liquid, such as oil). The suspended fluid can be a carrier for, e.g., one or more cells of interest. An emulsion can be, for example, oil-in-water (o / w), water-in-oil (w / o), water-in-oil-in-water (w / o / w), or oil-in-water-in-oil (o / w / o) dispersions or particles. A water-in-oil emulsion may be referred to as an aqueous droplet. Non-limiting examples of an emulsion can include various lipid structures, such as unilamellar, paucilamellar, and multilamellar lipid vesicles, micelles, and lamellar phases. An emulsion can be a microemulsion. An emulsion can be a nanoemulsion. An emulsion can comprise a single droplet. An emulsion can comprise a plurality of droplets (e.g, at least about 2 droplets - e.g., at least about 5 droplets, at least about 10 droplets, at least about 15 droplets, at least about 20 droplets, at least about 30 droplets, at least about 40 droplets, at least about 50 droplets, at least about 60 droplets, at least about 70 droplets, at least about 80 droplets, at least about 90 droplets, at least about 100 droplets, or more).

[0117] I. General

[0118] Sample analysis devices (e.g., flow cytometric devices) can operate by receiving a sample comprising a plurality of particles, such as cells, and directing the plurality of particles towards a detector (e.g., an optical detector) for detecting and / or analyzing the plurality of particles. Even if the sample is homogenized (e.g., mixed orvortexed) before being provided to such devices, the sample may remain stationary during operation of the devices. As a result, the sample can become heterogenous (e.g., uneven concentration or distribution of the plurality of particles within a medium in the sample) before it can be analyzed by the detector. Thus, there remains an unmet need for sample analysis devices that can maintain or enhance homogeneous dispersion of particles (e.g., cells) in a sample, thereby to analyze a substantially homogenous dispersion of particles. There also remains an unmet need for sample analysis devices to achieve such maintenance or enhancement of the homogeneous dispersion of particles without or with minimal perturbations (e.g., vibrations from moving or shaking the sample) to other components of the sample analysis devices (e.g., a detector such as a camera), thereby to enhance quality of data and / or analysis generated by the sample analysis devices.

[0119] Various aspects of the present disclosure provide systems and methods for receiving and analyzing a sample comprising a plurality of particles, such as cells (e.g., live cells). For example, the systems can comprise an ecosystem comprising a portion for receiving and storing such sample, and an additional portion for analyzing (e.g., detecting or imaging) at least a portion of the sample. The systems and methods can receive and store the sample, while maintaining and / or enhancing homogeneous dispersion of the plurality of particles in the sample, thereby to analyzea substantially homogenous dispersion of particles. The systems and methods can achieve such maintenance and / or enhancement of the homogeneous dispersion of the plurality of particles without or with minimal perturbations (e.g., vibrations) to other components of the system (e.g, optical source, optical detector, microfluidic devices, etc.), thereby to enhance quality of data and / or analysis generated by the sample analysis devices.

[0120] The ecosystem provided herein provides an added benefit of forming a homogeneous suspension of particles for an experiment analyzing each of the individual particles. As used herein, a “homogeneous” suspension is substantially uniform throughout. Homogenizing samples using the apparatuses herein can be decoupled from the analysis process, providing the added technical advantage of providing (e.g., supplying) a homogeneous sample to an analysis unit for an experiment without introducing perturbations (e.g., vibrational) to the analysis unit. For instance, the particles (e.g., cells) in the sample may be suspended, such as homogeneously suspended, within the sample, which can lead to inconsistent or inaccurate data measurements. Specifically, groups of particles may be withdrawn from the source, and artificially skewing the data (e.g., cell size distributions may be larger from groups of cells), thereby defeatingthe purpose of being able to analyze each of the individual particles.

[0121] In some instances, a system (e.g., an ecosystem) for analyzing a cell according to implementations of this disclosure can comprise a cell storage module configured to couple to a container holding the cell. The cell storage module can also be configured to direct the container to move within the cell storage module. In some instances, an imaging module can be configured to capture an image of the cell. In some instances, a flow cell module that can be in optical communication with the imaging module. The flow cell can comprise a flow channel can be configured to retrieve the cell from the container that is coupled to the cell storage module . In some cases, the flow channel can be further configured to direct flow of the cell towards the imaging module to permit the imaging module to capture the image of the cell. In some instances, the flow channel can be configured to retrieve the cell from the container within the cell storage module.

[0122] An example ecosystem for analyzing a sample comprising a plurality of particles (e.g, a plurality of cells) is illustrated in FIG. 1. The ecosystem 100 can comprise a sample management system 110. The sample management system 110 can comprise a cell storage module 112 for holding the sample. The sample management system 110 can comprise a flow cell module 114 that is in fluid communication with the cell storage module 112. The flow cell module 114 can comprise a flow channel (e.g., a microfluidic channel) that can receive one or more particles from the sample that is in the cell storage module 112. While the one or more particles are flowingthrough the flow channel of the flow cell module 114, an imaging module 116 comprising one or more sensors (e.g., a camera) can generate one or more sensing data (e.g., image(s), video(s), etc.) of the one or more particles. The flow cell module 114 can further comprise a particle sorting module, such that the one or more particles can be sorted using at least the one or more sensing data or analysis thereof. In some cases, the flow cell module 114 can be a chip (or a cartridge as used interchangeably herein) that can be inserted into and removed from the sample management system 110. In some cases, the sample management system 110 canbe referred to as a cell sorting system. In some cases, the system comprises a housing disposed adjacent to the cell storage module, the imaging module, and the flow cell module.

[0123] Referring to FIG. 1, the ecosystem 100 can further comprise a control module 120 that is operatively coupledto the sample management system 110. The control module 120 can control operations of one or more components of the sample management system 110, such as the cell storage module 112, the flow cell module 114, and the imaging module 116. The control module 120 can comprise a cell analysis module 125 to analyze the one or more sensing data (e.g., generated by the imaging module 116), and send a resulting analysis back to the sample management system 110 for particle sorting by the flow cell module 114.

[0124] Referring to FIG. 1, the ecosystem 100 can further comprises a user device 130 that comprises a graphical user interface (GUI) 135. A user can utilize the user device 130, e.g., via the GUI 135, to directthe control module 120 to control the operations of the sample management system 110. For example, the user can open and close the cell storage module 112 via the GUI 135 of the user device 130. In addition, the control module can provide any analysis of the cell analysis module 125 to the user via the GUI 135, for the user to obtain particle analysis and / or sorting information in situ.

[0125] Ref erring to FIG. 1 , the ecosystem 100 can further comprise one or more databases 140. In some cases, the database(s) 140 can comprise a plurality of databases that are in digital communication with one another. For example, each of the sample management system 110, the control module 120, and the user device 130 can comprise a database, such that the databases of the ecosystem are in digital communication with one another. Alternatively, or in addition to, the database(s) 140 can comprise a common database (e.g., a cloud database) that is in digital communication with one or more components of the ecosystem 100.

[0126] In some implementations, a system is disclosed. The system may comprise a platform to support a container comprising a sample, which sample comprises a plurality of particles in a solution. In some implementations, the system comprises a top portion disposed above the platform. In some implementations, the system comprises a vertical actuator coupled to at leastone of the platf orm or the top portion, wherein the vertical actuator is to direct a relative m ovement between the platform and the top portion, to bring the platform and the top portion into contact with one another to enclose the container on the platform. In some implementations, the system comprises a motor unit coupled to the platform, wherein the motorunit comprises a rotatable shaft to impart a rotational motion to the container, to thereby generate a substantially uniform suspension of particles in the container. In some instances, the generated suspension has a relatively more uniform distribution of particles throughout a volume of the sample as compared to a sample that has not been manipulated by the system. In some implementations, the system comprises a joint that partially couples the top portion and the vertical actuator to each other, wherein the joint is to permit a relative movement between the top portion and the vertical actuator, to thereby de-couple the rotational motion of the container from the vertical actuator. In some instances, the vertical actuator is coupled to the top portion.

[0127] In some implementations, a system is disclosed. The system may comprise a sample unit comprising a bottom portion. In some cases, the bottom portion is disposed within an inner volume of the receptable and to hold a container comprising a sample, which sample comprises a plurality of particles in a solution. In some instances, the plurality of particles comprises a plurality of cells. In some instances, a motor unit coupled to the platform and disposed within the inner volume of the sample unit. In some cases, the motor unit comprises a rotatable shaft configured impart a rotational motion to the container when the container is disposed over the platform, thereby to generate a substantially uniform suspension of particles in the container. In some instances, a pressurizer line to extend through an opening of the sample unit, wherein the pressurizer line is to direct a pressurizing fluid into the sample unit, thereby to pressurize the inner volume of the sample unit.

[0128] In some instances, the system comprises a controller coupled to the motor unit, wherein the controller is to direct the motor unitto impart the rotational motion to the container, to generate a substantially uniform suspension of particles in the container, wherein the rotational motion comprises: a first rotation along a direction at a first speed; and a second rotation along a different direction at a second speed, wherein the first speed or the second speed is between about 200 rotations per minute (RPM) and about 1,000 RPM.

[0129] A. Cell storage module

[0130] The cell storage module can establish a connection between the cell storage unit and the imaging module or the flow cell module. The cell storage module can establish the connection via the sample unit. The cell storage module can comprise a sample unit, an actuator unit, and a base unit. The cell storage module can comprise a sample unit, an actuator unit, and a base unit. Thesample unit can be configuredto hold a sample via a top portion and a bottom portion. The actuator unit can be configured to manipulate the top portion of the sample unit. The base unit can be configured to provide a platform for the sample unit and the actuator unit. In some instances, the base unit can be configured to stabilize the sample unit and the actuator unit. In some instances, the system further comprises a microfluidic cartridge. The microfluidic cartridge can comprise a sorting junction to sort the plurality of particles using at least particle types.

[0131] B. Sample Unit

[0132] The sample management system (e.g., sample management system 110) can comprise a cell storage module (e.g., cell storage module 112, cell storage module 2000), wherein the cell storage module can be coupled to a container, such as a sample unit. The sample unit can form an enclosure that is configured to hold a sample, which can comprise a plurality of particles (e.g., cells). The cell storage module can rotate the sample to form a homogeneous mixture (e.g., a homogeneous suspension). In some instances, the sample unit of the cell storage module can form the enclosure and rotate the sample to form a homogeneous mixture. The sample unit can be configured to move in a plurality of directions. For example, the sample unit can movein a circular path about an axis. In some instances, when the sample unit moves about a circular path, the sample unit can move in a clockwise direction, counter-clockwise direction, or both. The movement of the sample unit may be continuous. The movement of the sample unit may be intermittent.

[0133] In some implementations, the cell storage module may be a system comprising a sample unit. In some cases, the sample unit may receive (e.g., configured to receive) and hold (e.g., configured to hold) a container comprising a sample . The sample unit can comprise a first opening a second opening, or a third opening. The sample can comprise a plurality of particles (e.g., cells) in a solution. The cell storage module can comprise a tube (e.g., a needle) that extends (e.g., configured to extend) and travels (configured to travel) through the first opening of the sample unit and into the container. In some cases, a washing fluid line can extend (e.g., configured to extend) through the second opening of the sample unit. In some cases, the washing fluid line is to direct (e.g., configured to direct) a washing solution to clean the tube within the sample unit in between two or more sample processing runs. In some instances, the system further comprises a pressurizer line that extends (e.g., configured to extend) through the third opening of the sample unit. The pressurizer is as substantially described below. In some instances, the system further comprises a microfluidic cartridge. The microfluidic cartridge can comprise a sorting junction to sort the plurality of particles using at least particle types. In some instances, the microfluidic cartridge and the cell storage module are operably coupled.

[0134] The cell storage module can be configured from an enclosure in various configurations. In some instances, the cell storage module can comprise a sample unit. In some cases, the sample unit can comprise a vortexer. The sample unit can facilitate formation of the enclosure via two portions: a top portion and a bottom portion. The top portion and the bottom portion may be coupled together to form the enclosure. The bottom portion can include a holder configured to hold a sample container (e.g., a tube). The bottom holder may be fixed relative to the top holder with respect to the axis. The top holder may be moved along the axis into an “open” or “closed” configuration. In the “open” configuration, the top portion does not engage with the bottom portion. In the “closed” configuration, the top portion may be engaged with the bottom portion such that the enclosure is formed. In some implementations, the cell storage module may be in an open configuration, as illustrated in FIG. 20, or in a closed configuration, as illustrated in FIG. 21

[0135] In some aspects, the sample unit is configured to move passively relative to the actuator unit. The sample unit can be configured to move along a plurality of degrees of freedom. The plurality of degrees of freedom can comprise x, y, z, pitch, yaw, and roll.

[0136] The sample unit can be configured to receive a sample holder. In some cases, the sample unit 210 can receive a sample, such as via a sample holder 214 or delivering a sample to a sample holder 214 that is preloaded into the sample unit 210. In some instances, a sample unit can comprise a top portion (e.g., a top portion) and a bottom portion as described herein and is generally illustrated in FIGs. 2-4 and 20-21. The sample unit can be ergonomically designed to receive the sample holder. The sample holder can be a vial, tube, cup, flask, or the like.

[0137] The sample unit can be operably coupled to the actuator unit to enable movement of the sample unit. As generally illustrated in FIG. 2, the sample unit 210 can be operably coupled to the actuator unit 220. In some instances, the sample unit 210 is operably coupled to the actuator unit 220 via the top portion of the sample unit. In some cases, the sample unit 2012 can be operably coupled to an actuator unit 2020, as illustrated in FIG. 20. The actuator unit can comprise a coupling unit that facilitates communication between the actuator unit and the sample unit. In some cases, the coupling unit is in operable communication with the top portion of the sample unit. In yet other cases, the couplingunitis in operable communication with the actuator extension of the actuatorunit. In some cases, the couplingunitis in communicationwith both the top portion of the sample unit and the actuator extension of the actuator unit.

[0138] The top portion can comprise a cylindrical shape with an inner portion. The inner portion of the top portion can be hollow. In some instances, the inner portion of the top portion has a cylindrical shape. The top portion can comprisea space that can hold a sample holder, e.g., sampleholder 214. In some cases, the space can further hold a tube, e.g., a sipper tube 1910. The inner portion may have a dimension such that a sample holder, e.g., sample holder 214, can be positioned within the inner portion without contacting with the inner portion.

[0139] The bottom portion can be configured to interact with a motion apparatus. In some instances, the motion apparatus can comprise a motor. The motion apparatus may be housed within the base. In some instances, the bottom portion is in operable communication with the motion apparatus housed within the base, as is generally illustrated in FIGs. 3, 4, 10, 11, and 20. The bottom portion can further comprise a top bearing (e.g., top bearing 710) that is configured to move with an eccentric cam (e.g., eccentric cam 1010). The eccentric cam can be coupled to a motor, wherein the motor is configured to generate motion. The motion from the motor is propagated to the bottom portion via the eccentric cam, thus enabling motion of the sample unit. In some instances, the motor may be operably coupled to a drive shaft, as illustrated in FIG. 10. The drive shaft can comprise a first end and a second end. The first end can comprise a split bore. The first end can be configured to engage with the motor. The second end can be a free end. The second end may be configured to interact with the bottom bearing.

[0140] In some instances, a plurality of radial bearings may be mounted over the drive shaft. The drive shaft may be coupled to a top bearing, which is in communication with a bottom holder of the bottom portion. The bottom holder can hold the sample holder. As the motor generates motion, the drive shaft, plurality of radial bearings, top bearing, bottom holder, and sample holder move. In some cases, the motion is circular (i.e., rotation). The bottom portion can rotate along a linear path, a circular path, or a combination thereof.

[0141] In one implementation, the bottom portion can comprise a counterweight. As illustrated in FIGs. 4 and 10, a counterweight 818 can be in communication with the bottom housing 810. The counterweight can be configured to offset a weight of the guide unit.

[0142] In one implementation, the bottom portion can comprise a sealing mechanism. In some cases, the sealing mechanism 812 can comprise a floating piston 814 and a sealing agent 816. When the top portion 212 is engaged with the bottom portion 216, the top portion 212 can interact with the sealing mechanism 812 of the bottom portion216, thereby forming a seal (e.g., a hermetic seal). In some cases, the top portion 212 can press downward on the floating piston 814, which can press downward onto the sealing agent 816, thus forminga seal (e.g., a hermetic seal). In some aspects, the sealing agent is an o-ring. In some aspects, the sealing agent comprises Teflon. In some instances, the top portion engages with the bottom portion and the sealing agent. In some cases, as illustrated in FIG. 28, the sample unit may be in an open configuration, where a force is yet to be exerted on the sealing mechanism 2820. In some instances, in order for the sample unitto transition from the open configuration to the closed configuration, the sealing mechanism, such as in FIG. 29, forms a seal between the top portion and the bottom portion of the sample unit to form an enclosure. In some instances, the enclosure of the sample unit comprises a sealed interior volume for enclosing the container. For example, the top portion 2012 may exert a downward force on the sealing agent 2820, as illustrated in FIGs. 28 and 29. As illustrated in FIG. 29, the enclosure may be formed (i.e., the system adopts the closed configuration as in FIG. 21) when the top portion 2012 exerts a force on the sealing agent 2820 of the bottom portion 2016, a seal is formed between thetop portion 2012 and the bottom portion 2016. In some cases, as illustrated in FIG. 29, the enclosure comprises the top portion 2012, the sealing agent 2820, the bottom portion 2016, the container, the tube 2210, and the motor 2410. In some cases, a seal at a contact surface between the plurality of sectionsis formed, such as between the top portion 2012 and the botom portion 2016 as in FIGs. 28 and 29.

[0143] C. Guide Unit

[0144] In some instances, the sample unit can further comprise a guide unit. The guide unit can provide support for the sample unit in various configurations, e.g., the open configuration or the closed configuration. The guide unit can be in operable communication with the top portion (or the top portion) of the sample unit. In some instances, the guide unit can be in operable communication with the bottom portion of the sample unit. The guide unit can comprise a guide block, a guide rail, and a plurality of guide brackets. The plurality of guide brackets can comprise a lower guide bracket and an upper guide bracket. The guide unit can interface with the bottom portion via a lower guide bracket to connect the guide unit to the sample unit. In some instances, the guide unit can interface with the top portion via an upper guide bracket. The guide rail may limit movement of the top portion (e.g., the top portion of the sample unit) along an axis that is different from a vertical axis of the vertical guide rail. The guide rail may provide an alignment between the top portion and the platform (e.g., platform 246 of the sample unit 210) during their relative movement. In some instances, the vertical guide rail is coupled to the top portion. In some cases, the vertical guide rail is to limit movement of the top portion along an axis that is different from a vertical axis of the vertical guide rail, to provide an alignment between the top portion and the platform during their relative movement. In some cases, the vertical guide rail (i) limits movement of the top portion along an axisthatis differentfrom a vertical axis of the vertical guide rail and (ii) provides an alignment between the top portion and the platform during their relative movement.

[0145] The guide brackets (e.g., the upper guide bracket and the lower guide bracket) and the guide rail can be configured to couple the top portion and the bottom portion. An example guideunit is illustrated in FIGs. 4, 8, and 10. In some aspects, the guide unit 410 can couple the top portion 212 and the bottom portion 216 to provide a continuous connection between the top portion and the bottom portion. The guide unit 410 can move in unison with the sample unit 210. In some aspects, the guide unit 410 can move in unison with the sample unit 210 but move independently of the actuator unit 220. In some aspects, the guide unit 410 can move independently of the actuatorunit220 via the couplingunit 228 of the actuatorunit220. The guide unit 410 can move in the same direction as the actuator unit 220. The motion from the motor 910 can enable movement of the guide unit 410 via the lower guide bracket 824.

[0146] For example, the guide unit can allow for the top portion and the bottom portion to form an enclosed space. The top portion can be coupled with the bottom portion by way of the guide unit, thus formingthe “closed” configuration, as illustrated in FIGs. 10 and 13A. As illustrated in FIG. 10, the lower guide bracket 824 can be fixed to a region of the bottom portion 216 (e.g., the bottom holder 822) such that when the bottom portion moves, the lower guide bracket 824 and the guide rail 820 move. The guide brackets (e.g., upper guide bracket 822, lower guide bracket 824) can enable the sample unit 210 to move in unison with the guide unit 410. In some aspects, the lower guide bracket 824 is fixed relative to the upper guide bracket 822 such that the guide rail 820 can enable the top portion 212 to move freely along the guide rail 820 along an axis (e.g, the z-axis). In some instances, the sample unit 210 is configured to move independently from the actuator unit 220, such that the movement of the sampleunit 210 is a passive movement. In some instances, a passive movement includes movement not driven by a motor. In some instances, the movement of the sample unit 210 is an active movement. In some cases, the active movement is driven by a motor (e.g., motor 910). In some aspects, the guide unit 410 and the actuator unit 220 can form a dual-elevator system. For example, when the top portion 212 forms the enclosed space by interacting with the bottom portion 216, the upper guide bracket 822 moves along the guide rail 820, while the lower guide bracket 824 and the actuator unit 220 remains relatively fixed. Thus, the dual-elevator mechanism can enable relative movement of one component (e.g., the sample unit 210) of the cell storage module 112 without moving another component (e.g., the actuator unit 220). In some implementations, the dual-elevator mechanism of the cell storage module can comprise a pair of mechanisms.

[0147] The guide bracket (e.g., upper guide bracket 822, lower guide bracket 824) can interface with the guide rail 820 via a lower guide carriage 840. In some aspects, the upper guide bracket 822 can interface with the guide rail 820 via an upper guide carriage 845. For example, when formingthe closed configuration of the sample unit 210, the upper guide bracket 822 moves the top portion 212 downward by moving along the guide rail 820.

[0148] In some cases, the guide rail can further comprise a stop pin. In some instances, the guide rail can further comprise a lift tab to limit the vertical position of the top portion of the sample unit. For example, as illustrated in FIG. 8, the stop pin 830 can be positioned adjacent to the lower guide block 1320 and below the upper guide block 1325. In some cases, the stop pin can limit a movement of the upper guide bracket along the guide rail. In some cases, the stop pin can prevent the upper guide bracket from contacting the lower guide bracket, as illustrated in FIG. 13. For instance, the stop pin can control a vertical position of the top portion by limiting the position of the upper guide block, and thus limit the position of the top portion of the sample unit (FIG. 13A). In some configurations, the lift tab (e.g., lift tab 1310) can limit the position of the upper guide block (e.g., upper guide block 1325), and thus the position of the top portion (e.g, top portion 212), as in FIG. 13B. In some implementations, the stop pin 830 may be positioned to control (e.g., shorten) a distance traveled by the upper block, as in FIG. 13C.

[0149] The guide unit can interface with the bottom portion. A bottom segment of an example guide unit that can be configured to interface with a bottom portion of the sample unit is illustrated in FIG. 10. The lower guide bracket 824 may be in communication with the bottom portion 216. The lower guide bracket 824 may be fixedto the bottom portion216. In some instances, the bottom portion 216 is mounted to the lower guide bracket 824. The lower guide bracket 824 can be mounted to a guide block 826 that is in communication with a guide rail 820. The upper guide bracket 822 can be in communication with the guide rail 820. In some instances, as in FIG. 10, the guide rail 820 enables each of the upper guide bracket 822 and the lower guide bracket 824 to move relative to each other. In some instances, the lower guide bracket 824 and the guide block 826 remain relatively fixed while in communication with the guide rail 820 as the upper guide bracket 822 moves along the guide rail. When the upper guide bracket 822 moves along the guide rail 820, the upper guide bracket 822 can also move the top portion 212 of the sample unit 210 with the guide rail 820. In some cases, the guide rail 820 is oriented along an axis, such as a z- axis, which runs perpendicular to the plane as defined by a largest surface of the base unit 240.

[0150] The actuator extension interfaces with the top portion. In some aspects, the actuator extension (e.g., actuator extension A 224 and actuator extension B 226) interfaces with the top portion (e.g., top portion 212) via a coupling unit (e.g., coupling unit 228). The coupling unit can be configured to permit a relative movement between the actuator unit (e.g., actuator unit 220) and the sample unit (e.g., sample unit 210). In some aspects, the coupling unit 228 has three degrees of freedom. In some aspects, the coupling unit 228 has two degrees of freedom. In some aspects, the coupling unit 228 has one degree of freedom. For example, the three degrees of freedom can be pitch, yaw, and roll. The two degrees of freedom can be any two of pitch, yaw,and roll. The one degree of freedom can be any one of pitch, yaw, and roll. In some aspects, the couplingunit228 can be configured to hold the top portion212 in a substantially constant position. For example, as the bottom portion 216 rotates, the top portion 212 can be held in a substantially constant position via the coupling unit 228. In some aspects, the coupling unit 228 enables the sample unit 210 to rotate in a substantially conical manner. In some aspects, when the sample unit 210 rotates in a conical manner, the coupling unit 228 acts as a vertex. In some aspects, the coupling unit enables the sample unit 210 to rotate along an orbit. The orbit can comprise a radius of orbit, and the radius of orbit can be constant or variable.

[0151] In some implementations, the coupling unit decouples the guide unit from the actuator unit. In some instances, the guide unit may move with the sample unit, but the guide unit may move independently from the actuator unit. The coupling unit enables the independent movement of the sample unit and guide units. An advantageous result of decoupling the movement between the guide unit and the actuator unit (i.e., that the systems may move independently from each other) enables motions and perturbations resulting from motions of the sample unit from propagating to other elements within the ecosystem, such as an imaging module.

[0152] A coupling unit is illustrated in FIG. 11. The coupling unit may comprise a ball bearing secured to a portion of the actuator extension, such as either actuator extension A 224 or actuator extension B, as illustrated in FIG. 12. The ball bearing may be secured via a pin. In some instances, the ball bearing may be secured via a pair of pins to the actuator extension. The ball bearing may be in communication with the top portion 212 of the coupling unit 228 via the trunnion shaft 714, which is in communication with the top portion 212 of the sample unit 210.

[0153] The cell storage module can comprise a plurality of bearings that can be configured to stabilize the cell storage module. In some implementations the cell storage module comprises at least one bearing. The at least one bearing can comprise a top bearing or a bottom bearing. In some cases, the cell storage module comprises a plurality of bearings, such that the plurality of bearings can comprise a dual bearing system. In some aspects, the top portion can comprise a top bearing. A top portion 212 comprising a top bearing 710 is illustrated in FIG. 7. The top bearing 710 can restrict movement of the sample unit 210 as it moves. In some aspects, the top bearing 710 and the bottom bearing 820 are coupled to restrict motion of the sample unit 210 during motion of the sample unit 210. In some aspects, the top bearing 710 and the bottom bearing 820 decouple motion of the sample unit 210 from the rest of the ecosystem 100. In some aspects, the top bearing 710 need not be present. In some aspects, when the top bearing 710 is present, the top bearing 710 and the bottom bearing 820 are oriented along an axis that runs through and is perpendicular to the base unit 240. In some aspects, the axis that run s through and is perpendicularto the base unit 240 is a z axis.

[0154] In some implementations, the top portion comprises a plurality of openings. The top portion may comprise a first opening and a second opening. For example, as illustrated in FIG. 20, the cell storage module 2000 may include a top portion 2012, wherein the top portion 2012 comprises a first opening 2060, a second opening 2062. In some instances, the top portion further comprises a third opening 2064. The first opening 2060 may receive (e.g., configured to receive) a tube (e.g., a tube, such as tube 2210 in FIG. 22). The tube may travel and extend through the first opening of the sample unit and into the container. The tube may direct (e.g., configured to direct) the plurality of cells in the sample to flow out of the container for processing by the microfluidic cartridge. In some cases, the second openingmay receive (e.g., configuredto receive) a washing fluid line. The washing fluid line may direct a washing solution to clean the tube within the sample unit (e.g., between two or more processingruns). In some cases, the tube extends along a first longitudinal axis. In some cases, the washing fluid line extends along a second longitudinal axis. In some cases, the first longitudinal axis and the second longitudinal axis are different. In some cases, the first longitudinal axis and the second longitudinal axis are substantially perpendicular to one another. In some instances, the first longitudinal axis and the second longitudinal axis may be oriented (e.g., configured to be oriented) about 90 degrees relative to each other. In some cases, the first longitudinal axis and the second longitudinal axis may be oriented about 80 degrees, about 82 degrees, about 84 degrees, about 84 degrees, about 86 degrees, about 88 degrees, about 90 degrees, about 92 degrees, about 94 degrees, about 96 degrees, about 98 degrees, or about 100 degrees relative to each other. For example, as illustrated in FIG. 10, the cleansing port 620 is oriented about 90 degrees relative to the tube, which extends in a direction from the top portion to the bottom portion. In some cases, the first opening is located at a distal end portion of the sample unit. In some cases, the second opening is located at a side portion of the sample unit.

[0155] In some instances, the system further comprises a washing solution source comprising the washing solution. The washing solution source may direct the washing solution through the washing fluid line towards the tube within the sample unit. In some cases, the sample unit comprises a housing having a plurality of sections that are to move relative to one another along a vertical axis of the sample unit, wherein the first opening and the second opening are disposed over a same section, as in FIG. 22.

[0156] The top portion can comprise atop bearing. The top bearing can be configuredto enable the top portion to pivot independently from the actuator unit. As illustrated in FIG. 7, the top portion can comprise a top bearing disposed around a trunnion shaft 714 of a trunnion 712. Thetop bearingmay be in contact with the trunnion 712 and the actuator extension B 226. In some instances, the top bearing may be in further contact with a coupling unit 228. The coupling unit can comprise an arm 720 and a joint 722. The joint may be configured to permit a relative movementbetweenthe top portion andthe vertical actuator, thereby de-coupling rotational motion of the container from the vertical actuator. The arm 720 can be configured to resist a motion of the top portion of the sample unit. Thejointcan comprise aballjoint(e.g., a ball-and-socket joint). The trunnion 712 may comprise a hollowed region configured to form a space for a tube (e.g., a cannula or a sipper tube) to pass through the top portion of the sample unit. In some instances, the tube may be a tube. The top bearing may comprise a spherical bearing. The trunnion shaft may be in communication with the actuator extension B 226. In some instances, the top portion canfurther comprise a bearing retainer 726. In some cases, the top portion can further comprise a seal (e.g., an o-ring) positioned between a top housing and the trunnion. In some instances, the relative movementbetween the top portion and the vertical actuator has at least two degrees of freedom. In some instances, the relative movement between the top portion and the vertical actuator has at least three degrees of freedom.

[0157] The top bearing and the bottom bearing can comprise a mechanism that restricts movement along at least one axis. In some aspects, the top bearing 710 and the bottom bearing 820 can restrict movement along the same axis. In some aspects, the top bearing 710 and the bottom bearing 820 are each independently a plain bearing, a fluid bearing, a rolling-element bearing (e.g., a ball bearing, a roller bearing), a jewel bearing, a fluid bearing, a magnetic bearing a flexure bearing, or a combination thereof. The combination of the top bearing of the top portion and the bottom bearing of the bottom portion provided an advantage of isolating movement of the sample unit to the sample unit.

[0158] The bottom portion can be in communication with a movement unit that enables movement of the sample unit. For example, the bottom portion 216 may comprise a b ottom holder 822, as illustrated in FIG. 8. The bottom holder 822 may be in communication with the movement unit, e.g., movementunit900.Themovementunit900 may comprise a motor 910, a motor bracket 912, a drive shaft 914, a plurality of radial bearings 920, a bottom bearing 820, an additional bearing 925. In some instances, the movement unit 900 can further comprise a snap ring 916. The movement unit 900 may be enclosed within a housing, e.g., housing 248. The bottom holder 822 of the bottom portion 216 may be in communication with a drive shaft 914. The drive shaft may be coupled to a plurality of radial bearings 920. In some instances, the plurality of radial bearings 920 may be disposed around the drive shaft 914. In some cases, a motor bracket 912 may be disposed around the drive shaft 914. In some cases, the bottom portion 216 can comprise a snapring 916 adjacent to the bottom bearing 820 and the bottom holder 822. The drive shaft 914 may be in communication with a motor, e.g., motor 910, as illustrated in FIG. 9. As the motor generates motion, e.g., circular motion, the drive shaft 914 propagates the circular motion from the motor to the bottom holder 822, andthus to the sample holder 214 of the sampleunit210. In some instances, the drive shaft 914 is in communication with an eccentric cam 1010.

[0159] In some instances, the bottom holder 822 interfaces with a sealing mechanism 812. The sealing mechanism 812 can comprise a floating piston 814 and a sealing agent 816. The top portion 212 may exert a force on the floating piston 814, which forms a seal with the sealing agent 816. In some instances, the sealing agent 816 can contact the floating piston 814 and can contact the bottom holder 822. In some instances, the bottom holder 822 is adjacent to a bottom housing 810. In some instances, a gap may be interposed between the bottom holder 822 and the bottom housing 810. The gap may allow for rotation of the bottom holder 822 without contacting or moving the bottom housing 810.

[0160] In some instances, the bottom holder 822 is in communication with a lower guide bracket 824. The lower guide bracket 824 can establish a connection with the guide unit 410.

[0161] In some aspects, the sample unit 210 can rotate in an orbit. In some cases, the bottom holder 822 can rotate in an orbit. The orbit can comprise a radius of orbit of about 1 millimeter (mm), about 2 mm, about 3 mm, about 4 mm, about 5 mm, about 6 mm, about 7 mm, about 8 mm, about 9 mm, or about 10 mm. In some aspects, the radius of orbit can range from about 0.5 mm to about 10 mm, from about 1 mm to about 9 mm, from about 2 mm to about 8 mm, from about 3 mm to about 6 mm, or from about 4 mm to about 5 mm. In some aspects, the radius of orbit is no more than about 5 mm. In some aspects, the radius of orbit is at least about 0.5 mm. In some aspects, the radius of orbit is from about 0.5 mm to about 5 mm, or any value therebetween. In some aspects, the radius of orbit can be varied for the duration of an experiment.

[0162] D. Methods

[0163] In some aspects of the disclosure, a method for providing a suspension of particles is provided. The method can comprise obtaining a sample and moving the sample. Methods for moving the sample can comprise rotating the sample by a first rotation and a second rotation. The first rotation can comprise a first direction and a first speed, and the second rotation can comprise a second direction and a second speed. In some aspects, the first direction and the second direction are the same. In some aspects, the first direction and the second direction are different. In some aspects, the first speed and the second speed are the same. In some aspects, the first speed and the second speed are different. In some aspects, the first rotation can comprise a first direction at a first speed, and the second rotation can comprise a second direction at a second speed, whereinthe first direction and the second direction are the same, and the first speed and the second speed are different. In some aspects, the first rotation can comprise a first direction at a first speed, and the second rotation can comprise a second direction at a second speed, wherein the first direction and the second direction are the same, and the first speed and the second speed are the same. In some aspects, the first rotation can comprise a first direction at a first speed, and the second rotation can comprise a second direction at a second speed, wherein the first direction and the second direction are different, and the first speed and the second speed are different.

[0164] The method can further comprise rotating the sample at a particular speed for a particular amount of time. For example, the method can comprise rotating the sample in a first direction at a first speed for a first period of time. The method can also comprise rotating the sample in a second direction at a second speed for a second period of time. In some cases, each of the first period of time and the second period of time can independently range from about 1 second (s) to about 1 hour (hr). In some cases, each of the first period of time and the second period of time can independently range from about 1 s to about 10 s. In some cases, each of the first period of time and the second period of time can independently range from about 1 s to about 5 s. In some instances, each of the first period of time and the second period of time can independently range from about 10 s to about 30 minutes (min), from about 30 s to about 15 min, orfrom about 1 min to about 10 min. In some instances, the first period of time and the second period of time can be the same amount of time. In some instances, the first period of time and the second period of time are different. In some instances, the method can comprise rotating the sample in a first direction at a first speed for a first period of time and rotating the sample in a second direction at a second speed for a second period of time, wherein the first direction and the second direction are the same, the first speed and the second speed are different, and the first period of time and the second period of time are different. In some instances, the method can comprise rotating the sample in a first direction at a first speed for a first period of time and rotating the sample in a second direction at a second speed for a second period of time, wherein the first direction and the second direction are different, the first speed and the second speed are the same, and the first period of time and the second period of time are different. In some instances, the method can comprise rotating the sample in a first direction at a first speed for a first period of time and rotating the sample in a second direction at a second speed for a second period of time, wherein the first direction and the second direction are different, the first speed and the second speed are different, and the first period of time and the second period of time are the same. In some aspects, the first speed is substantially constantforthe duration ofthefirstperiod of time. In some aspects, the second speed is substantially constant for the duration of the second period of time.

[0165] In other aspects, provided herein is a method for analyzing a cell. The method can comprise (a) directing a container (e.g., sample unit 210) that is holding the cell to move within a cell storage module, wherein the container is coupled to the cell storage module (e.g., cell storage module 112); (b) retrieving, via a flow cell module (e.g., flow cell module 114), the cell from the container that is coupled to the cell storage module; (c) subsequent to (b), directing flow of the cell towards an imaging unit that is in optical communication with the flow cell module, to permit the imaging unit to capture the image of the cell. In some instances, the directing can comprise rotating the container (e.g., sample unit) relative to the actuator of the cell storage module. In some cases, the rotating can comprise rotating the container in a first direction at a first speed. In some instances, the method can further comprise rotating the container in a second direction at a second speed. In some cases, the first direction and the second direction are not the same. For example, in some cases, if the first direction is clockwise, then the second direction is counterclockwise. In some cases, the first speed is at least about 200 RPMs. In some instances, the second speed is at most about 700 RPMs. In some instances, rotating the container relative to an actuator of the cell storage module can comprise rotating the container along an orbit. In some cases, the orbit has a radius of orbit of about 1 mm.

[0166] In some aspects, the first speed or the second speed can rotate at a rate of about 100 RPMs to about 650 RPMs. In some cases, the first speed or the second speed may increase over a range, such as ranging from about 0 RPM to about 100 RPMs, from 0 RPM to about 200 RPMs, from 0 RPM to about 300 RPMs, from 0 RPM to about 400 RPMs, from 0 RPM to about 500 RPMs, from 0 RPM to about 600 RPMs, or from 0 RPM to about 700 RPMs. In some cases, the second speed may decelerate over a range. The speed may decelerate from about 700 RPMs to 0 RPMs, from about 600 RPMs to 0 RPM, from about 500 RPMs to 0 RPM, from about 400 RPMs to 0 RPM, from about 300 RPMs to 0 RPM, from about 200 RPMs to 0 RPM, or from about 100 RPMs to 0 RPM. In some aspects, the first speed or the second speed can rotate at a rate of about 100 RPMs to about 150 RPMs, about 100 RPMs to about 200 RPMs, about 100 RPMs to about 250 RPMs, about 100 RPMs to about 300 RPMs, about 100 RPMs to about 350 RPMs, about 100 RPMs to about400 RPMs, about 100 RPMs to about 450 RPMs, about lOO RPMs to about 500 RPMs, about 100 RPMs to about 550 RPMs, about 100 RPMs to about 600 RPMs, about 100 RPMs to about 650 RPMs, about 150 RPMs to about 200 RPMs, about 150 RPMs to about 250 RPMs, about 150 RPMs to about 300 RPMs, about 150 RPMs to about 350 RPMs, about 150 RPMs to about 400 RPMs, about 150 RPMs to about 450 RPMs, about 150 RPMs to about 500 RPMs, about 150 RPMs to about 550 RPMs, about 150 RPMs to about 600 RPMs, about 150 RPMs to about 650 RPMs, about 200 RPMs to about 250 RPMs, about 200 RPMs to about 300RPMs, about 200 RPMs to about 350 RPMs, about200 RPMs to about 400 RPMs, about 200 RPMs to about 450 RPMs, about 200 RPMs to about 500 RPMs, about 200 RPMs to about 550 RPMs, about 200 RPMs to about 600 RPMs, about 200 RPMs to about 650 RPMs, about 250 RPMs to about 300 RPMs, about 250 RPMs to about 350 RPMs, about 250 RPMs to about 400 RPMs, about 250 RPMs to about 450 RPMs, about 250 RPMs to about 500 RPMs, ab out 250 RPMs to about 550 RPMs, about 250 RPMs to about 600 RPMs, about 250 RPMs to about 650 RPMs, about 300 RPMs to about 350 RPMs, about 300 RPMs to about 400 RPMs, about 300 RPMs to about 450 RPMs, about 300 RPMs to about 500 RPMs, about 300 RPMs to ab out 550 RPMs, about 300 RPMs to about 600 RPMs, about 300 RPMs to about 650 RPMs, about 350 RPMs to about400 RPMs, about 350 RPMs to about 450 RPMs, about 350 RPMs to about 500 RPMs, about 350 RPMs to about 550 RPMs, about 350 RPMs to about 600 RPMs, about 350 RPMs to about 650 RPMs, about 400 RPMs to about 450 RPMs, about 400 RPMs to about 500 RPMs, about 400 RPMs to about 550 RPMs, about 400 RPMs to about 600 RPMs, about 400 RPMs to about 650 RPMs, about 450 RPMs to about 500 RPMs, about 450 RPMs to about 550 RPMs, about 450 RPMs to about 600 RPMs, about450 RPMs to about 650 RPMs, about 500 RPMs to about 550 RPMs, about 500 RPMs to about 600 RPMs, about 500 RPMs to about 650 RPMs, about 550 RPMs to about 600 RPMs, about 550 RPMs to about 650 RPMs, or about 600 RPMs to about 650 RPMs. In some aspects, the first speed or the second speed can rotate at a rate of about 100 RPMs, about 150 RPMs, about200RPMs, about 250 RPMs, about 300 RPMs, about 350 RPMs, about 400 RPMs, about 450 RPMs, about 500 RPMs, about 550 RPMs, about 600 RPMs, or about 650 RPMs. In some aspects, the first speed or the second speed can rotate at a rate of at least about 100 RPMs, about 150 RPMs, about 200 RPMs, about 250 RPMs, about 300 RPMs, about 350 RPMs, about 400 RPMs, about450 RPMs, about 500 RPMs, about 550RPMs, or about 600 RPMs. In some aspects, the first speed or the second speed can rotate at a rate of at most about 150 RPMs, about200 RPMs, about250 RPMs, about 300 RPMs, about 350 RPMs, about400RPMs, about450RPMs, about500RPMs, about550RPMs, about600 RPMs, or about 650 RPMs.

[0167] In some implementations, the method comprisesobtaininga sample, rotatingthe sample in a first orientation, and rotating the sample in a second orientation. The first orientation can comprise rotatingthe sample clockwise at about 600 RPM. The second orientation can comprise rotating the sample counterclockwise at about 650 RPM. In some implementations, the method comprises obtaining a sample, rotating the sample in a first orientation, and rotating the sample in a second orientation. The first orientation can comprise rotatingthe sample clockwise at 500 RPM The second orientation can comprise rotating the sample counterclockwise at about 700 RPM.The first orientation can comprise rotating the sample clockwise at about 750 RPM. The second orientation can comprise rotating the sample counterclockwise at about 800 RPM. The first orientation can comprise rotatingthe sample clockwise atabout650 RPM. The second orientation can comprise rotating the sample counterclockwise at about 650 RPM.

[0168] In some aspects, the method can comprise applying a routine, wherein the routine comprises at least one interval, wherein the interval comprises rotating the sample. In some instances, the routine can comprise a plurality of periods, such as a first period, a second period, a third period, and so forth. The first period may include moving the sample unit at a predetermined rate (e.g., about 300 RPMs, about 400 RPMs, about 500 RPMs, about 600 RPMs, about 800 RPMs) in a predetermined direction, such as clockwise or counter-clockwise. For instance, the routine can comprise rotatingthe sample at 300 RPMs clockwise during a first period, and the routine can further comprise rotating the sample at 600 RPMs counterclockwise during a second period. In some instances, the first period may comprise a range of speeds in a first direction. Forexample, the firstperiod may include a speed from 0 RPM to about500RPM, about 550 RPM, about 600 RPM, 650 RPM, or about 700 RPM in a first direction. In some instances, a subsequent period (e.g., a last period) may include a speed from about 700 RPM, about 650 RPM, about 600 RPM, about 550 RPM, or about 500 RPM down to 0 RPM.

[0169] VI. Pressurizer

[0170] In some aspects, the sample unit can comprise a pressurizer. The pressurizer introduces (e.g., is configured to introduce) a positive pressure (e.g., pressure greater than atmospheric pressure) in the sample unit. In some cases, the sample unit and the base unit are pressurized, as illustrated by the dashed box in FIG. 27. The pressurizer may be connected to the sample unit via the top portion. In some cases, the pressurizer is operably coupled to a third opening of a sample unit (e.g., a sample unit), such as operably coupledto a third openingin a top portion of the sample unit. In some instances, the system comprises a pressurizer line to extend through a third opening of the sample unit, wherein the pressurizer line is to direct a pressurizing fluid into the sample unit to thereby pressurize the sample unit. In some cases, an example sample unit is illustrated in FIG. 6 A and 6C, where the sample unit 210 is equipped with a pressurizer 610. The pressurizer can be manipulated to introduce a positive pressure. In some cases, the positive pressure can control a flow rate of the sample to a downstream instrument, e.g., an imaging module. The pressurizer 610 can be coupled to the top portion 212. In some aspects, the pressurizer 610 can be coupled to a transport system, as described below. The pressurizer 610 can comprise a valve, and the valve can be configured to regulate the flow rate and pressure of a gas entering the sample unit 210. The pressure can comprise a tubing to enable fluid (e.g., gas) transport into the top portion 212. Thefluid may be a pressurizing fluid. The pressurizing fluid is to create pressure within the sample unit so as to direct flow of the plurality of particles from the container and through the tube. The pressurizing fluid may be a compressed gas. In some instances, positive pressure can be applied when the sample unit is in the “closed” configuration, as illustrated in FIGS. 5B and 21. The system can be in communication with a pressurizing fluid source. In some cases, the system can be configured to be in communication (e.g., fluidic communication) with a pressurizing fluid source. The pressurizing fluid source may comprise the pressurizing fluid. In some cases, the pressurizing fluid introduces a positive pressure throughout the sample unit (e.g., sample unit 2010), as illustrated in FIG. 27. The portion of the system under positive pressure is denoted by the region 2710, as illustrated in FIG. 27. In some instances, the portion of the system under positive pressure includes the sample unit (e.g., sample unit 2010), comprising the top portion 2012, the sample holder 2014, and the bottom portion 2016. In some cases, a pressure exerted by the pressurizing fluid is sufficient to pressurize the sample unit and direct flow of the plurality of particles from the container and through the tube.

[0171] In some aspects, the fluid introduced by the pressurizer can comprise a distribution of gases and at a predesignated pressure. In some implementations, the fluid is introduced by a pressurizing fluid source. In some instances, the fluid comprises air. For example, the pressurizer can pass air comprising about 5%, about 10%, about 15% or about 20% carbon dioxide. The pressurizer 610 can pass air comprising about 25%, about 30%, or about40% dioxygen gas. The pressurizer 610 can pass air comprising about 50%, about 60%, about 70%, about 80%, about 90%, or about 100% dinitrogen gas. The pressurizer 610 can apply a positive pressure in the sample unit (e.g., sample unit 210 or sample unit 2010) of about 15 psi, about 20 psi, or about 25 psi. The pressurizer can apply a positive pressure in the sample of from about 15 psi to about 30 psi or from about 20 psi to about 25 psi. The pressurizer can apply a pressure of at least 10 psi. The pressurizer can apply a pressure of atmost30 psi. The pressurizer can apply varying pressures during an experiment. For example, a program or a workflow can allow for a predefined pressure regime to be administered during the experiment. The predefined pressure regime can comprise a first period, during which 0 psi is applied. The predefined pressure regime can comprise a second period, during which a positive pressure is applied. The predefined pressure regime can be cycled to control the amount and timing of sample transport from the sample unit to the downstream component, e.g., a flow cell or an imaging module.

[0172] Provided herein is a method of transferring samples from the sample unit to a downstream component. For example, the method of transferring samples can include using the sample unit as described above and herein. An example of the sample unit 210 that allows forsample transfer is illustrated in FIGs. 16 and 17. The sample unit 210 can comprise a tube (e.g., a sipper tube) that fluidically couples the sample unit 210 to a downstream component, such as an imaging module 116. The method can include applying a positive pressure into the sample unit 210 via a pressurizer 610. The positive atmosphere can push the sample in the sample holder 214 into a sipper tube 1910, where the sipper tube 1910 can direct the sample to a downstream component.

[0173] E. Actuator Unit

[0174] The actuator unit can manipulate the sample unit to move, e.g., to rotate. The actuator unit may also raise (e.g., lift) or lower the top portion of the sample unit to form the enclosure. The actuator unit may comprise a rod, an actuator rail, a mechanism, and a coupling unit. The coupling unit may interface directly with the top portion of the sample unit, wherein the coupling unit is in communication with the rod and the actuator rail. In some instances, the actuator rail, the rod, and the mechanism are relatively stationary relative to the coupling unit. The actuator unit enables opening and closing of the system, as illustrated in FIGs. 5A, 5B, 25A, and 25B. Some examples of actuator units are illustrated in FIGs. 12, 13, 14, 23, 25A, 25B, and 26.

[0175] The actuator unit 220 can comprise an elevator mechanism. The elevator mechanism can comprise an actuator rail 222, an actuator extension 224 and a mechanism 1420. The actuator rail 222 can be connected to the actuator extension 224, which can be coupled to the top portion 212 of the sample unit 210. The mechanism 1420 can control a height ofthe actuator unit 220 via raising or lowering the actuator bracket 1430. The sample unit 210 and actuator unit 220 can be disposed over the base unit 240. For example, the base unit 240 can counteract the motion generated by the sample unit 210, such as, via a plurality of dampers 242. In some implementations, the mixing apparatus 210 can comprise a transport system 250, which is in communication with the sample holder 214 via an orifice.

[0176] In some implementations, the actuator unit can comprise a mechanism, an actuator rod, an actuatorrail, an actuatorbracket, and a couplingunit. The couplingunit and the actuator bracket are coupled (e.g., physically coupled). The couplingunitis coupled to the top portion of the sample unit. The coupling unit may move vertically (e.g., along an axis perpendicular to a largest face of the base unit) by way of the actuator rod and mechanism. For example, and as illustrated in FIGs. 25A and 25B, the coupling unit (e.g., coupling unit 2050) via the actuator bracket (e.g., actuator bracket 2026) is coupled to the actuator rod (e.g., actuator rod 2022) via a nut (e.g., nut 2028). The mechanism (e.g., mechanism 2420) may be a motor (e.g., a stepper motor) that enables the nut (e.g., nut 2028) to travel vertically, and thus allow for the coupling unit (e.g., coupling unit 2050) and top portion to travel vertically. In some cases, the actuator rod (e.g., actuator rod 2024)is in communication with the actuator bracket (e.g., actuator bracket 2026) via the nut (e.g., nut 2028), as illustrated in FIG. 25A. In some instances, the actuator bracket comprises a top bracket piece and a bottom bracket piece that may be physically coupled (e.g., via screws, glue, and the like). In some implementations, the mechanism 2420 controls the open and closed configurations of the sample unit 2010 by allowing for a relative movement of the nut, actuator bracket, and coupling unit, wherein the relative movement is independent of the actuator rod and the mechanism. In some cases, the actuator rod and the mechanism are substantially stationary, while the nut, actuator bracket, and coupling unit can travel vertically along the actuator rod, as illustrated in FIGS. 25A, 25B, and 26. In some cases, the coupling unit may comprise a plurality of holes to receive a plurality of aligners (e.g. , aligners 2250 as illustrated in FIG. 22). The aligners may comprise screws having at least two degrees of freedom. In some cases, the screws may have degrees of freedom along the x-axis and the y-axis, wherein thex- and y-axes define an xy -plane, which corresponds to the largest plane ofthe base unit. In some cases, the aligners may be screws that couple the couplingunit to the top portion of the sample unit (e.g., sample unit2010). The aligners may interface with a plurality of threads that span the coupling unit (e.g., coupling unit 2050) and the top portion (e.g., top portion 2012) of the sample unit (e.g., sample unit 2010).

[0177] The actuator unit can comprise a mechanism, an actuator, an actuator guide, and an actuator extension. An example actuator unit 220 is illustrated in FIG. 3. Referring to FIG. 3, the actuator guide 1445 is coupled to an actuator bracket 1430, which is coupled to the actuator rail 222. In some aspects, the actuatorguide 1445, the actuator bracket 1430, andthe actuator rail 222 form one continuous piece. In some aspects, when the actuator extension 224 is coupled to the top portion 212, the mechanism 1420 can raise or lower the actuator unit 220 andthe top portion212. In some aspects, the mechanism 1420 can raise or lower the actuator unit 220 and the top portion 212 independently from the bottom portion 216.

[0178] The actuator unit 220 can move independently ofthe sample unit 210. In some aspects, the actuator extension 224 can comprise a coupling unit, e.g., the coupling unit 228 in FIG. 4. In some aspects, the couplingunit can compriseafree-floatingballbearingoraball-and-socketjoint. In some instances, the coupling unit comprises a joint. In some instances, the joint comprises a ball-and-socket joint.

[0179] In some instances, the system further comprises a computer processor operatively coupled to the actuator unit. The computer processor can be configuredto control the actuator unit to direct the top portion of the sample unit to move relative to the bottom portion of the sample unit to form the space for holding the sample. The computer processor may be in electronic communication with the mechanism. The computer processor can be configured to control themechanism, and thus control the actuator.

[0180] The actuator unit can comprise an actuator rail and a rod to allow movement of the actuator unit. For example, as illustrated in FIG. 14, the actuator unit 220 can comprise an actuator rail 222 and a rod 1435. The actuator rail can comprise an actuator rail 222 and a slider 1460. A mounting surface 724 may extend over the slider 1460. The actuator rail 222 may be in communication with a carriage 1410. In some instances, the carriage is a linear bearing carriage 1410. In some instances, the linear bearing carriage 1410 may be fixed to an actuator bracket 1430. In some instances, the actuator rail 222 and the rod 1435 are in communication via an outrigger bearing mount 1450. At an interface between the outrigger bearing mount 1450 and the rod 1435 may be a radial bearing 1440. In some instances, the rod 1435 can be coupled to a nut 1425. In some cases, the nut 1425 is in communication with the actuator rail 222 via the actuator bracket 1430. The actuator bracket 1430 can be in communication with the actuator rail 222. In some instances, the rod 1435 may be a threaded screw. In some instances, the rod 1435 may be integrated into the mechanism (e.g., mechanism 1420). The mechanism 1420 may be a motor, e.g., a stepper motor. The mechanism 1420 may be in communication with a housing (e.g., housing 248) via an actuator bracket. In some instances, the nut may be fixed to the actuator bracket 1430. In some instances, the actuator bracket 1430 may be fixed to the actuator rail 222 such that the mechanism can move the nut, actuator bracket, actuator rail, actuator extension A, and actuator extension B. In some instances, the actuator unit 220 comprises a limit switch 1490 that can be configured to limit a position of the actuator unit 220.

[0181] F. Base Unit

[0182] The base unit can support the sample unit and the actuator unit. The base unit can comprise a plurality of dampers, a platform, and a cover. An example base unit is illustrated in FIGs. 4, 15, 16, 20, and 24. The plurality of dampers (e.g., dampers 242 or dampers 2042) can be configured to absorb or decrease an amplitude of motion generated from the sample unit (e.g., sample unit 210 or sample unit 2010). The plurality of dampers are in communication with the cover (e.g., cover 244 or cover 2044). In some aspects, the plurality of dampers are in communication with the platform (e.g., platform 246 or platform 2046) via the cover, which is disposed over the platform 246. In some aspects, the plurality of dampers comprises a plurality of springs. The plurality of dampers 242 is in communication with a motor unit (e.g., motor units 910 or 2410) of the sample unit (e.g., sampleunit 210 or 2010). In some instances, the motor unit comprises a motor shaft coupled to the motor and the bottom portion. In some cases, the motor can be disposed over the cover and can be configured to generate a motion when moving. In some cases, the motor (e.g. , motor 2410, as illustrated in FIG.24), may be directly coupledto the bottomportion (e.g., bottom portion 2016) through the rotatable shaft. The rotatable shaft may impart a rotational motion to the container (e.g., the bottom portion of the container) when the container is held within the sample unit or sample unit, thereby generating a substantially uniform suspension of particles in the container. In some cases, the motor 2410 moves (e.g., rotates) the bottom portion 2016 and the container about a central axis that is coaxial (e.g., parallel) with the first longitudinal axis of the tube. The motion generated by the motor can be neutralized (e.g., absorbed). In some instances, the motion generated by the motor may be neutralized by the dampers (e.g., dampers 242 or 2042). In some cases, the motor unit is disposed within the sample unit. In some cases, the motor unit is disposed outside of the sample unit.

[0183] In some instances, the system comprises a base unit, the base unit comprising a motor unit and a controller coupled to the motor unit. In some cases, the controller is to direct the motor unitto impart the rotational motion to the container, to generate a substantially uniform suspension of particles in the container. In some cases, the rotational motion comprises: a first rotation along a direction at a first speed, and a second rotation along a different direction at a second speed, wherein the first speed or the second speed is between about 200 rotations per minute (RPM) and about 1,000 RPM. In some cases, the direction and the different direction are opposite to one another. In some cases, each of the first speed and the second speed is b etween about 200 RPM and about 1,000 RPM. In some cases, the first speed or the second speed is greater than or equal to about 400 RPM. In some cases, the first speed or the second speed is greater than or equal to about 500 RPM.

[0184] In some instances, the rotational motion further comprises a third rotation along the direction at a third speed, wherein the first speed and the third speed are different, or a fourth rotation along the additional direction at a fourth speed, wherein the second speed and the fourth speed are different. In some cases, the rotational motion comprises the third rotation and the fourth rotation. In some cases, the rotational motion comprises, in a sequential order, the first rotation, the third rotation, the second rotation, and the fourth rotation. In some cases, each of the third speed and the fourth speed is between about 200 RPM and about 1 ,000 RPM. In some cases, each of the third speed and the fourth speed is greater than or equal to about 400 RPM. In some cases, each of the third speed and the fourth speed is greater than or equal to about 500 RPM.

[0185] In some instances, the system comprises a base for holding at least the motor unit the base comprises atleast one damperto de-couple rotational motion of the motorunitfrom the base. In some instances, the motorunitis coupled to abottom surface of the platform. In some instances, the at least one damper comprises a plurality of dampers. In some cases, the at least one damper comprises a spring damper.

[0186] In some instances, the dampers comprise springs, foam, rubber pieces, or any other material configured to absorb vibrational motion generated by the motor. In some instances, the base unit comprises at least 3 dampers. In some instances, the base unit comprises at least 4, 5, 6, 7, or 8 dampers.

[0187] In some aspects, the motor unit enables movement of the actuator unit 220. In some cases, the motor unit comprises a motor, e.g., motor 910 or motor 2410. For example, the motor can comprise a stepper motor. In some aspects, the motor can be coupled to the actuator guide 1445, and the actuator guide 1445 is coupled to the actuator rail 222 via an actuator bracket 1430. The plurality of dampers may be disposed near comers of the base unit, as illustrated in FIGs. 4 and 15. In some instances, as in FIG. 15A, a plurality of dampers may be disposed near comers of the base unit 240. The dampers may be in communication with the cover 244, wherein the cover 244 can be in communication with the sample unit 210, guide unit 410, and actuator unit 220. In some cases, the dampers 242 can interact with (e.g., dampen, absorb) motion generated from the sample unit 210 via the cover 244. The plurality of dampers 242 may be in communication with the platform 246 of the base unit 240 to provide support for the dampers.

[0188] The dampers can be a spring system, as illustrated in FIG. 15B. In some cases, the damper 242 can comprise a spring 1510, and a plurality of spring pins. The spring 1510 may comprise afirstend and a second end. A first pin of the plurality of pins may be in communication with the first end of the spring 1510. A second pin of the plurality of pins may be in communication with the second end of the spring 1510. In some cases, the first pin can comprise an anchoring spring pin 1512. In some cases, the second pin can comprise a floating spring pin 1512. In some cases, the spring 1510 and plurality of spring pins may be disposed over a post 1516. The post 1516 may be in communication with the platform 246 of the base unit 240.

[0189] In some aspects, a positional monitor may be integrated into the sample unit. For example, as illustrated in FIGS. 16, 17A and 17B, a positional monitor 260 may be mounted at a distance from the sample unit 210. The positional sensor can be configured to determine the presence or absence of a sample holder, e.g., sample holder 214. The positional monitor 260 may be positioned adjacent to the actuator rail 222 of the actuator unit 220. The positional monitor 260 may be configured to record a position of the sample unit during a movement of the sample unit.

[0190] In some implementations, a computer processor is in electronic communication with the motor. The computer processor can be configured to control a speed and a direction of the motor. The computer processor may implement a workflow to the motor, such that the motor can generate motion of the sample unit. In some instances, the computer processor is in electronic communication with the motor and the mechanism of the actuator unit.

[0191] II. Transport System

[0192] In some aspects, the sample unit can comprise a transport system. The transport system can be in communication with a flow cell module. The flow cell module can comprise a flow channel that is configured to retrieve the cell from the container (e.g., sample unit) that is coupled to the cell storage module (e.g., cell storage module 112). In some cases, the flow channel can be configured to direct flow of the cell towards the imaging module to permit the imaging module to capture the image of the cell, by way of the transport system of the cell storage module. In some cases, the flow channel receives (e.g., is configured to retrieve) the cell from the container (i.e., the sample unit 210) within the cell storage module (e.g., cell storage module 112). In some cases, the flow channel receives the cell from the container via a tube.

[0193] The transport system may be coupled to the sample unit via a tube. The tube may be in operable communication with the sample unit (e.g., the sample unit) via the first opening. In some cases, the tube (e.g., the tube) travels and extends through the first opening or the orifice of the sample unit (e.g., the top portion) into the container. The tube may direct (e.g., configured to direct) a plurality of cells out of the container. The tube may be a tube. The tube may direct a plurality of particles to flow out of the container for processing by a microfluidic cartridge. In some instances, the tube is a tube. In some instances, the tube is configured to travel and extend to an inner volume of the container. In some instances, when the tube is disposed within the inner volume of the container, a distance between (i) a distal end of the tube and (ii) a bottom surface of the container ranges between about 0.2 millimeters (mm) and about 1 mm.

[0194] As illustrated in FIGs. 18A, 18B, and 19, the transport system 250 can comprise a tube (e.g., tube 1810, tube 1910) configured to transfer (e.g., extract) a sample from the sample unit to a component of the sample management system 110 (e.g., the flow cell module 114 or imaging module 116). The transport system 250 can further comprise an orifice 1920. The tube 1910 can be a sipper tube that establishes fluid communication between the sample unit (e.g., sample unit 210 or sample unit 2010) of the sample management system 110 to a downstream component, such as an imaging module 116. In some instances, the tube 1910 may be a needle. The tube 1910 can be configured to thread through an orifice 1920 of the transport system 250, as illustrated in FIGS. 6 and 19. In some cases, the orifice 1920 may be fitted to a compression fitting 630 and a tube fitting 635. In some cases, the compression fitting 630 and the tube fitting 635 secure the tube 1910 in the sample unit 210. When the sample unit undergoes motion, the tube 1910 may transport cells out of the sample unit 210 when it is secured via the compression fitting 630 and tube fitting 635. In some instances, the tube can be in fluidic communication with a transport tube.The transport tube can be configured to transport cells from the cell storage unit to the imaging module or the flow cell module via the tube.

[0195] In some implementations, the tube comprises a plurality of dimensions. In some instances, the tube comprises an inner diameter. In some cases, the inner diameter of the tube ranges from about 1 / 500 inches (in) to about 1 / 100 in. In some instances, the inner diameter is about 0.05 millimeters (mm) to about 0.25 mm, about 0.06 mm to 0.2 mm, about 0.07 mm to about 0.15 mm, or about 0.08 mm to about 0.1 mm. In some instances, the inner diameter is at least about 0.02 mm, about 0.03 mm, about 0.04 mm, about 0.05 mm, about 0.06 mm, about 0.07 mm, about 0.08 mm, about 0.09 mm, or about 0.1 mm. In some instances, the tube comprises an outer diameter. In some cases, the outer diameter is about 1 / 100 in to about 1 / 10 in. In some cases, the outer diameter is about 0.2 mm to about 3.0 mm, about 0.3 mm to about 2.9 mm, about 0.4 mm to about 2.8 mm, about 0.5 mm to about 2.7 mm, about 0.6 mm to about 2.6 mm, about 0.7 mm to about 2.5 mm, about 0.8 mm to about2.4 mm, about 0.9 mm, to about 2.3 mm, or about 1.0 mm to about 2.2 mm. In some cases, the outer diameter is at least about 0.5 mm, about 0.6 mm, about 0.7 mm, about 0.8 mm, about 0.9 mm, about 1.0 mm, about 1.1 mm, about 1.2 mm, about 1.3 mm, about 1.4 mm, about 1.5 mm, or about 2.0 mm. In some instances, the tube comprises a length. In some cases, the length corresponds to the distance of the tube extending from a top of the first opening to a distal end of the tube. The distal end of the tube may be oriented (e.g., configured to be oriented) at a distance from a bottom of the container when present. In some instances, the length of the tube is about 1 inch to about 6 inches, about 2 inches to about 5 inches, or about 3 inches to 4 inches. In some instances, the length is about 1 inch to about 4 inches, about 2 inches to about 5 inches, or about 3 inches to about 6 inches. In some instances, the length of the tube is about 25 mm to about 200 mm, about 50 mm to about 150 mm, about 75 mm to about 125 mm. In some instances, the length ofthe tubeis at least about 25 mm, about 50 mm, about 75 mm, or about 100 mm. The distal end of the tube may be about 0.2 mm to about 2 mm from the bottom of the container. In some instances, the distal end of the tube may be about 0.3 mm to 1.9 mm, about 0.4 mm to about 1.8 mm, about 0.5 mm to about 1.7 mm, about 0.6 mm to about 1.6 mm, about 0.7 mm to about 1.5 mm, about 0.8 mm to about 1.4 mm, about 0.9 mm to about 1.3 mm, or about 1.0 mm to about 1 .2 mm from the bottom of the container.

[0196] Additionally, spatial resolution of each of the individual particles for subsequent analysis is crucial for good sample resolution (i.e., confidence that each sample corresponds to a particle). Because sample reservoirs and the analysis platforms are usually spatially separated, mechanisms are used to transport the samples containing the particle from the source to the analysis platform. However, current transport mechanisms suffer from sedimentation of thesample during transport. Current transport mechanisms utilize tubing that is vertically positioned to transport samples from the source to the analysis platform. Sedimentation may be caused, in part, by gravity pulling the sample in a particular direction without compensation by a force from an opposite direction (e.g., a compensating normal force).

[0197] In some implementations, the sample comprising particles may be agitated by the vortexer, such as rotating the sample, as described herein. The sample may be transported to a flow cell (e.g., flow cell 9105) by a pressurizing fluid source (e.g., a pump, a pressurizing fluid source 9104), as illustrated in FIG. 30A. The pressurizing fluid source may provide a non-contact method to push the sample through the system. In another implementation, the pressurizing fluid source may provide a contact method (e.g., pump) to push the sample through the system. In some aspects, the sample comprising particles may be manipulated by pressurizing fluid source 9104 and flowed into flow cell 9105. In some aspects, the sample comprising the particles may be directed toward a flow cell 9105 via the sample unit.

[0198] Provided herein is a method for sample processing. In some implementations, the method comprises (a) moving a container and a sample unit relative to each other thereby causing the container to be secured in the sample unit. In some cases, the container comprises a sample, which sample comprises a plurality of particles in a solution. In some implementations, the method comprises (b) directing the plurality of particles to flowthrough a tube and out of the container for processingby a microfluidic cartridge. In some cases, the tube extends through a first opening of the sample unit and is disposed in the container. In some implementations, prior to or subsequent to directing the plurality of particles (e.g., cells), the method comprises directing a washing solution to flow through a washing fluid line to clean the tube within the sample unit, wherein the washing fluid line extends through a second opening of the sample unit.

[0199] In some instances, the method comprises replacing the container with a different container comprising a different plurality of particles for processing of the different plurality of particles by the microfluidic cartridge. In some instances, (b) is performed when the container is enclosed within a sealed interior volume of the sample unit. In some instances, in (b) the tube extends through the first opening along a first longitudinal axis, and in (c) the washing fluid line extends along a second longitudinal axis different from the first longitudinal axis. In some cases, the first longitudinal axis and the second longitudinal axis are substantially perpendicular to one another. In some cases, the first opening is located at a distal end portion of the sample unit, and wherein the second opening is located at a side portion of the sample unit.

[0200] In some instances, (c) comprises directingthe washing solution from a washing solution source, through the washing fluid line, and towards the tube disposed within the sample unit. Insome instances, the method further comprises, subsequent to (b), sorting the plurality of particles using at least particle types using a sorting junction of the microfluidic cartridge. In some instances, the sample unit comprises a housing comprising a plurality of sections, wherein the first opening and the second opening are disposed over a same section. In some cases, the method further comprises moving the plurality of sections relative to one another along a vertical axis of the sample unit to close or seal the sample unit. In some cases, the housing comprises a seal at a contact surface between the plurality of sections.

[0201] In some implementations, the method further comprises directing a pressurizing fluid into the sample unit through a pressurizer line to pressurize the sample unit, wherein the pressurizerline extends through a third opening of the sample unit. In some cases, the pressurizing fluid is a pressurized gas. In some cases, the pressurizing fluid is directed from a pressurizing fluid source in fluidic communication with the pressurizer line. In some instances, the method further comprises using a pressure exerted by the pressurizing fluid to create pressure within the sample unit to direct flow of the plurality of particles from the container and through the tube. In some instances, the method further comprises using a motor unit coupled to the sample unit to impart a rotational motion to the container when the container is held within the sample unit, to generate a substantially uniform suspension of particles in the container. In some cases, the motor unit is disposed within the sample unit. In some cases, the motor unit is disposed outside of the sample unit. In some instances, the method further comprises, prior to (b), extending the tube to an inner volume of the container.

[0202] Provided herein is a method of transferring a sample in a plurality of paths prior to introducing the sample to a downstream component, e.g., a processor, a flow cell module, or an imaging module. As generally illustrated in FIGs. 18A and 18B, a tubing from the sample unit can establish a connection between the sample unit and other components within the sample management system, such as a flow cell module. The tubing may form a first circular path and a second circular path, as illustrated in FIG. 18A. In some instances, the tubing may form a first loop, as illustrated in FIG. 18B. Each of the first circular path and the second circular path may have a radius of curvature. For the first circular path, the first circular path can include a first radius of curvature (RCi). For the second circular path, the second circular path can include a second radius of curvature (RC2). In some instances, RCi is smaller than RC2. In some instances, RCi is greater than RC2. In some instances, RCi is about equal to RC2. Each of RCi and RC2can comprise a radius of curvature of about 0.5 cm, about 1.0 cm, about 1.5 cm, about 2.0 cm, about 2.5 cm, or about 5.0 cm. In some instances, RCi is at least about 0.5 cm, about 1.0 cm, about 1.5 cm, about 2.0 cm, about 2.5 cm, about 5.0 cm, or about 10 cm. In some instances, RCi is at mostabout20 cm, about 15 cm, or about 10 cm. In some instances, RC2is at least about 0.5 cm, about 1 .0 cm, about 1.5 cm, about2.0 cm, about2.5 cm, about 5.0 cm, or about 10 cm. In some instances, RC2is at most about 20 cm, about 15 cm, or about 10 cm.

[0203] Provided herein is a method of transferring a sample to a target location. In some instances, the method of transferring a sample comprises receiving a medium comprising a cell to flow from a source comprising the medium. The method can comprise directing the medium from the source and towards a target location via a flow channel. In some cases, the flow channel comprises a plurality of regions comprising a first region and a second region. In some cases, the medium is directed to flow through the first region along a first non-horizontal direction. In some cases, the medium is directed to flow through the second region along a second non-horizontal direction that is different from the first non-horizontal direction.

[0204] In some instances, the method comprises transferring a sample at an angle. Transferring the sample at an angle can reduce, and in some instances even prevent, sedimentation of the particles in the sample. The method can comprise transferring a sample at an angle, such as transferring the sample from a source to an analysis module. In some aspects, the method can comprise transferring the sample at a plurality of angles, as illustrated in FIG. 19. The plurality of angles can comprise a first angle 0ba second angle 02, a third angle 03, and so forth. The magnitude of each of the plurality of angles is determined with reference to a normal axis that runs perpendicular to the base of the system. For example, an actuator (e.g., an actuator system) runs perpendicular to the base unit240 of the cell storage module 112 in FIG. 12. In some aspects, the method can comprise transferring a sample in a first orientation comprising a first angle 0 In some aspects, the method can further comprise transferring the sample at a second orientation comprising a second angle 02. In some aspects, the method can yet further comprise transferring the sample at a third orientation comprising a third angle 03.

[0205] In some aspects, 0i is substantially vertical. In some aspects, 0i is substantially 0 degrees.

[0206] In some aspects, 02is at least orup to about 15 degrees, atleast orup to about20 degrees, at least or up to about 30 degrees, at least or up to about 40 degrees, at least or up to about 50 degrees, atleast orup to about 60 degrees, atleast orup to about 70 degrees, atleast or up to about 80 degrees, or at least or up to about 90 degrees. 02can be substantially vertical. In some aspects, 02is from about 5 degrees to about 85 degrees, from about 10 degrees to about 80 degrees, from about 15 degrees to about 75 degrees, from about20 degrees to about 70 degrees, from about 25 degrees to about 65 degrees, from about 30 degreesto about 60 degrees, from about 35 degrees to about 55 degrees, or from about 40 degrees to about 50 degrees. In some aspects, 02is from about 15 degrees to about 60 degrees. In some aspects, 02is at most 45 degrees, at most 50 degrees, atmost 55 degrees, or at most 60 degrees. In some instances, the first non -horizontal direction corresponds to 02.

[0207] In some aspects, 03is at least or up to about 5 degrees, at least or up to about 10 degrees, at least or up to about 15 degrees, at least or up to about 20 degrees, at least or up to about 30 degrees, at least or up to about 40 degrees, at least or up to about 50 degrees, at least or up to about 60 degrees, at least or up to about 70 degrees, or at least or up to about 80 degrees relative to a horizontal axis (e.g., horizontal axis in FIG. 19). In some aspects, 03is from about 5 degrees to about 85 degrees, from about 10 degrees to about 80 degrees, from about 15 degrees to about 75 degrees, from about 20 degrees to about 70 degrees, from about 25 degrees to about 65 degrees, from about 30 degrees to about 60 degrees, from about 35 degrees to about 55 degrees, or from about 40 degrees to about 50 degrees relative to a horizontal axis (e.g., horizontal axis in FIG. 19). In some aspects, 03is from about 10 degrees to about 45 degrees relative to a horizontal axis (e.g., horizontal axis in FIG. 19). In some aspects, 03is at most 45 degrees, at most 50 degrees, at most 55 degrees, or at most 60 degrees relative to a horizontal axis (e.g., horizontal axis in FIG. 19). In some aspects, 03is from about 15 degrees to about 60 degrees relative to a horizontal axis (e.g., horizontal axis in FIG. 19). In some instances, the second non -horizontal direction corresponds to 03.

[0208] In some instances, the tube may comprise two regions external to the cell storage module. For example, as illustrated in FIG. 18, the tube 1810 may comprise a first tube region 1812 and a second tube region 1814. In some instances, the tube 1810 may further comprise a third tube region 1816. In some instances, the firsttube region 1812may be shorterthanthe second tube region 1814. In some instances, the firsttube region 1812 and the second tube region 1814 may have the same length. In some instances, the first tube region 1812 can be longer than the second tube region 1814. In some instances, the third tube region 1816 can be longer than the second tube region 1814, which can be longer than the first tube region 1812. In some instances, the third tube region 1816 is shorterthan the second tube region, which is shorterthan the first tube region 1812. In some instances, the firsttube region 1812 and the second tube region 1814 are the same, and the third tube region 1816 is longer than each of the firsttube region 1812 and the second tube region 1814. In some instances, the first tube region 1812 and the second tube region 1814 are the same, and the third tube region 1816 is shorter than each of the first tube region 1812 and the second tube region 1814. In some instances, the second tube region 1814 is longer than each of the firsttube region 1812 and the third tube region 1816. In some instances, the second tube region 1814 is longer than the first tube region 1812 and the third tube region 1816 combined.

[0209] In some instances, the tube may comprise two regions external to the sample unit. For example, the tube may comprise a first region and a second region. For example, as illustrated in FIG. 19, the tube 1910 may comprise a first region (e.g., first tube region 1912) and a second region (e.g., second tube region 1914). In some instances, the tube 1910 may further comprise a third tube region 1916. In some instances, the first tube region 1912may be shorterthanthe second tube region 1914. In some instances, the first tube region 1912 and the second tube region 1914 may have the same length. In some instances, the first tube region 1912 can b e longer than the second tube region 1914. In some instances, the third tube region 1916 can be longer than the second tube region 1914, which can be longer than the first tube region 1912. In some instances, the third tube region 1916 is shorter than the second tube region, which is shorter than the first tube region 1912. In some instances, the first tube region 1912 and the second tube region 1914 are the same, and the third tube region 1916 is longer than each of the first tube region 1912 and the second tube region 1914. In some instances, the first tube region 1912 and the second tube region 1914 are the same, and the third tube region 1916 is shorter than each of the first tube region 1912 and the second tube region 1914. In some instances, the second tube region 1914 is longer than each of the first tube region 1912 and the third tube region 1916. In some instances, the second tube region 1914 is longer than the first tube region 1912 and the third tube region 1916 combined.

[0210] In some instances, a spacer region may be interspaced between the second region and the third region. The spacer region may intersectthe secondregion and the third region. The spacer region may be designed to avoid a substantially horizontal configuration of the tube (e.g., tube 1910). The spacerregion may be curved. The spacerregion may be substantially linear. The spacer region may comprise a radius of curvature, wherein the radius of curvature may range from about 1 mm to about 25 cm. In some instances, the radius of curvature may range from about 1 cm to about 25 cm. The radius of curvature can be at least about 1 cm, about 5 cm, about 10 cm, about 15 cm, about 20 cm, or about 25 cm. In some cases, the radius of curvature may be at least 1 cm. In some cases, the radius of curvature may be up to about 1 cm, about 2 cm, about 5 cm, about 10 cm, about 15 cm, about 20 cm, about 25 cm, about 30 cm, about 35 cm, or about 40 cm. In some instances, the radius of curvature may be at least about 90 cm, at least about 95 cm, or at least about 100 cm. In some instances, the radius of curvature can be up to about 100 cm, up to about 95 cm, or up to about 90 cm. In some instances, the spacer region may form a loop. In some cases, the spacer region may form part of a loop. In some instances, the spacer region may resemble a fraction of a loop (e.g., a portion of a circular loop or an elliptical loop). In some instances, the spacer region may resemble a fraction of a loop (e.g., a portion of a circular or elliptical loop).

[0211] The method can further comprise transferring the sample in the sipper tube in a third orientation, wherein the sample is transferred at a third angle. The third orientation can comprise transferring the sample upward or downward at the angle. Transferring the sample in the third orientation can comprise transferring the sample to the imaging module 116. In some aspects, the third orientation is at least 15 degrees. In some aspects, the third orientation is from about 10 degrees to about 45 degrees. In some aspects, the third orientation is at most 45 degrees. In some aspects, each of the first orientation, second orientation, and third orientation are different. In some aspects, the second orientation and the third orientation are the same. In some aspects, the first orientation is different from the second orientation, which is the same as the third orientation.

[0212] In some aspects, transferringthe sample can comprise transferringthe sample in a sipper tube 1910 that can be oriented at the plurality of angles. In some aspects, the tube 1910 can adopt the first orientation, the second orientation, the third orientation, and so forth. In some aspects, the sipper tube is oriented in the first orientation when the sipper tube extends a length (£) of the sample unit210 and through the orifice 1920. In some aspects, the sippertube is oriented in the second orientation for a first distance from the orifice 1920 to the imaging module 116. In some aspects, the sippertube adopts the second orientation for a second length of the sipper tube 1910 and adopts a third orientation for a third length of the tube 1910.

[0213] A. Methods

[0214] Provided herein is a method of sanitizing the sample unit (e.g., sample unit 210 or sample unit 2010). The method can comprise administering a sterilizing solution to the sample unit, such as sample unit 210 or 2010. In some instances, the sterilizing solution may be administered via a cleaning port, such as cleaning port 612 in FIG. 6B or the third opening in FIG. 20. The method can further comprise moving (e.g., rotating) the sterilizing solution. The method can further comprise applying a positive pressure via a pressurizer into the sample unit 210 or 2010. The method can further comprise creating a positive atmosphere within the sample unit 210 or 2010 to allow the sterilizing solution to move (e.g., flow) into a sipper tube that fluidically couples the sample unit 210 or 2010 with a waste container. In some instances, the method can comprise creating a positive atmosphere within the sample unit 210 to allow the sterilizing solution to move (e.g., flow) externally to a sipper tube, thus cleaning an exterior of the sippertube. The sterilizing solution can comprise alcohol, antibiotic, buffer, an acidic solution, a basic solution, bleach, or any solution configured to kill undesirable biological species, such as bacteria or yeast. Provided herein are methods for sample processing. The method comprises (a) moving a container or a sample unit relative to each other thereby causing the container to be secured in the sample unit, wherein the container comprises a sample, which sample comprises aplurality of particles in a solution. In some instances, the method further comprises (b) directing the plurality of particles to flow through a tube and out of the container for processing by a microfluidic cartridge, wherein the tube extends through a first opening of the sample unit and is disposed in the container. In some instances, the method further comprises (c) prior to or sub sequent to (b), directing a washing solution to flow through a washing fluid line to clean the tube within the sample unit, wherein the washing fluid line extends through a second opening of the sample unit. In some cases, the method further comprises, subsequent to (c), replacing the container with a different container comprising a different plurality of particles for processing of the different plurality of particles by the microfluidic cartridge. In some cases, (b) is performed when the container is enclosed within a sealed interior volume of the sample unit. In some cases, (b) the tube extends through the first opening along a first longitudinal axis, and in (c) the washing fluid line extends along a second longitudinal axis different from the first longitudinal axis. In some cases, the first longitudinal axis and the second longitudinal axis are substantially perpendicular to one another. In some instances, the first opening is located at a distal end portion of the sample unit, and wherein the second opening is located at a side portion of the sample unit.

[0215] In some implementations, (c) comprises directing the washing solution from a washing solution source, through the washing fluid line, and towards the tube disposed within the sample unit. In some instances, subsequent to (b), sorting the plurality of particles using at least particle types using a sorting junction of the microfluidic cartridge. In some instances, the sample unit comprises a housing comprising a plurality of sections, wherein the first opening and the second opening are disposed over a same section, and wherein the method further comprises moving the plurality of sections relative to one another along a vertical axis of the sample unit to close or seal the sample unit. In some cases, the housing comprises a seal at a contact surface between the plurality of sections.

[0216] Provided herein are methods for sample processing, the method comprising (a) holding a container on a platform. In some instances, the container comprises a sample, which sample comprises a plurality of particles in a solution. In some implementations, the method comprises (b) imparting, using a motor unit coupled to the platform, a rotational motion to the container when the container is disposed over the platform, to generate a substantially uniform suspension of particles in the container. In some cases, the rotational motion comprises: a first rotation along a direction at a first speed; and a second rotation along a different direction at a second speed, wherein the first speed or the second speed is between about 200 rotations per minute (RPM) and about 1,000 RPM.

[0217] In some instances, the direction and the different direction are opposite to one another.In some instances, each of the first speed and the second speed is between about 200 RPM and about 1,000 RPM. In some instances, the first speed orthe second speed is greater than or equal to about 400 RPM. In some instances, the first speed orthe second speed is greater than or equal to about 500 RPM. In some cases, the rotational motion further comprises: a third rotation along the direction at a third speed, wherein the first speed and the third speed are different. In some cases, the method further comprises a fourth rotation along the additional direction at a fourth speed, wherein the second speed and the fourth speed are different. The rotational motion can comprise the third rotation and the fourth rotation. In some cases, the rotational motion comprises, in a sequential order, the first rotation, the third rotation, the second rotation, and the fourth rotation. In some cases, each of the third speed and the fourth speed is between about 200 RPM and about 1,000 RPM. In some cases, each of the third speed and the fourth speed is greater than or equal to about 400 RPM. In some cases, each of the third speed and the fourth speed is greater than or equal to about 500 RPM.

[0218] In some implementations, one or more components of the device can include or can be fabricated from materials such as polyvinyl chloride, polyvinylidene chloride, low density polyethylene, linear low density polyethylene, polyisobutene, polyfethylene-vinylacetate] copolymer, lightweight aluminum foil, stainless steel alloys, commercially puretitanium, titanium alloys, silver alloys, copper alloys, Grade 5 titanium, super-elastic titanium alloys, cobalt-chrome alloys, stainless steel alloys, superelastic metallic alloys (e.g., Nitinol, super elasto -plastic metals, such as GUM METAL® manufactured by Toyota Material Incorporated of Japan), ceramics and composites thereof such as calcium phosphate (e.g., SKELITETM manufactured by Biologix Inc.), thermoplastics such as polyaryletherketone (PAEK) including polyetheretherketone (PEEK), polyetherketoneketone (PEKK) and poly etherketone (PEK), carbon -PEEK composites, PEEK-BaSO4polymeric rubbers, polyethylene terephthalate (PET), fabric, silicone, p olyurethane, silicone-polyurethane copolymers, polymeric rubbers, polyolefin rubbers, hydrogels, semi-rigid and rigid materials, elastomers, rubbers, thermoplastic elastomers, thermoset elastomers, elastomeric composites, rigid polymers including polyphenylene, polyamide, polyimide, polyetherimide, polyethylene, epoxy, partially resorbable materials, such as, for example, composites of metals and calcium -housing based ceramics, composites of PEEK and calcium housing based ceramics, composites of PEEK with resorbable polymers, totally resorbable materials, such as, for example, calcium housing based ceramics such as calcium phosphate, tricalcium phosphate (TCP), hydroxyapatite (HA)-TCP, calcium sulfate, or other resorbable polymers such as polyaetide, polyglycolide, polytyrosine carbonate, polycaroplaetohe or combinations thereof.

[0219] In some cases, the tube can include or can be fabricated with a hydrophilic material. The tube may be coated with a hydrophilic material. In some instances, the tube maybe partially coated with the hydrophilic material. The hydrophilic material may coat a face, such as an interior face or an exterior face, of the tube. The hydrophilic material may coat an entire surface of the tube. The hydrophilic material may enable an even coatingto form whena fluid (e.g., the cleaning fluid) passes through the tube.

[0220] B. Systems and Methods for Particle Analysis

[0221] One or more properties (e.g., morphological properties) of a cell can be used to, for example, study cell type and cell state, or to diagnose diseases. Morphological properties of a cell, for example, can include cell shape. Cell shape can be one of the markers of cell cycle. For example, eukaryotic cells can show physical changes in shape which can be cell-cycle dependent, such as a yeast cell undergoing budding or fission. Cell shape can be an indicator of cell state and, thus, can be an indicator used for clinical diagnostics. For example, shape of a blood cell may change due to many clinical conditions, diseases, and medications (e.g., changes in red blood cells’ morphologies resulting from parasitic infections). Additional examples of the morphological properties of the cell that can be used to analyze the cell can include, but are not limited to, features of cell membrane, nuclear -to-cytoplasm ratio, nuclear envelope morphology, and chromatin structure. Systems, methods, compositions, and information (e.g., data) thereof provided herein can be used to analyze cells (e.g., previously uncharacterized or unknown cells) based at least in part on such morphological properties of the cells.

[0222] Cellular analysis can be performed solely based on the morphological properties. Analyzing a cell based on one or more images of the cell and one or more morphological features of the cells extracted therefrom - without the need to rely on other types of data (e.g., omics data, such as analysis or genomics, RNA analysis or transcriptomics, protein analysis or proteomics, metabolite analysis or metabolomics, etc.) - can enhance speed and / or scalability of cell analysis systems and methods while maintaining or even enhancing accuracy of the analysis. In some cases, analysis of a population of cells based on their morphological features can uncover unique or new parameters to define a cell or a collection of cells (e.g., clusters of cells) that would otherwise not be identified in other methods.

[0223] Alternatively or in addition to, the analysis of the cells can be performed based the morphological properties and an additional information about the cells, such as omics data as provided herein. For example, the additional information can be used to verify the morphologybased analysis, or generate a new type of analysis in combination with the morphological data.

[0224] Accordingly, some aspects of the present disclosure provide systems and methods foranalyzing particles, such as cells (e.g., mammalian cells from a biological sample). Cells can be directed to flow through a flow channel, e.g., to enhanceimagingoranalysisofthe cells. A sample of cells (e.g., unstructured cells, such as a mixture of cells) flowing through a flow channel can be split up (e.g., sorted based on cellular analysis performed while the cells are flowing through the flow channel) into a plurality of subpopulations, each subpopulation of the plurality having different characteristics (e.g., different average physical characteristics).

[0225] In some aspects, the present disclosure provides a tool comprising a graphical user interface (GUI) for visualization of information (e.g., data) generatedatleastinpartby the systems and methods provided herein. The GUI can be used for visualization of patterns or profiles associated with the one or more morphological features of particles (e.g., cells) analyzed as provided herein. In some aspects, the present disclosure provides an optical system operatively coupled to the flow channel, e.g., to generate optical data comprising one or more morphological properties of the particles (e.g., cells). The optical system can comprise at least an optical source (e.g., a light source) to direct at least one light towards the flow channel, and at least one optical receiver to detect one or more optical characteristics of the at least one light subsequent to coming in contact with the flow channel (e.g., with a cell flowing through the flow channel), such as light emission, transmission, reflectance, absorbance, fluorescence, luminescence, etc. In some aspects, the present disclosure provides systems and methods for providing the particles (e.g., cells) to the flow channel, e.g., to enhance analysis of the particles.

[0226] C. Additional Aspects

[0227] The systems and methods provided herein can be utilized to analyze a cell and / or sort (or partition) the cell from a population of cells. A cell may be directed through a flow channel, and one or more imaging devices (e.g., sensor(s), camera(s)) can be configured to capture one or more images / videos of the cell passing through. Subsequently, the image(s) and / or video(s) of the cell can be analyzed as disclosed herein . For example, the image(s) and / or video(s) may be plotted as a datapoint in a cell morphology map, to determine a most likely cluster to which the cell(s) belong. The image(s) and / or video(s) may allow for a determination of a final classification of the cell based on the selected cluster in real-time. A decision can be made in real-time (e.g., automatically by the machine learning algorithm) to determine (i) whether to sort the cell or not and / or (ii) which sub-channel of a plurality of sub-channels into which to sort the cell.

[0228] The cell sorting system as disclosed herein can comprise a flow channel configured to transport a cell through the channel. The cell sorting system can comprise an imaging device configured to capture an image of the cell from a plurality of different angles as the cell is transported through the flow channel. The cell sorting system can comprise a processor configuredto analyze the image using a deep learning algorithm to enable sorting of the cell. The cell sorting system can be a cell classification system. In some cases, the flow channel can be configured to transport a solvent (e.g., liquid, water, media, alcohol, etc.) without any cell. The cell sorting system can have one or more mechanisms (e.g., a motor) for moving the imaging device relative to the channel. Such movement can be relative movement, and thus the moving piece can be the imaging device, the channel, or both. The processor can be further configured to control such relative movement.

[0229] FIGs. 30A and 30B show schematic illustrations of the cell sorting system, such as system 9000, with a flow cell design (e.g., a microfluidic design). The cell sorting system 9000 can be operatively coupled to a machine learning or artificial intelligence controller. Such ML / AI controller can be configured to perform any of the methods disclosed herein. Such ML / AI controller can be operatively coupled to any of the platforms disclosed herein.

[0230] In operation, a sample 9102 is prepared and injected by a pressurizing fluid source 9104 into a flow cell 9105, or flow-through device. In some aspects, the sample 9102 may be directed toward a flow cell 9105 via the sample unit. In some implementations, the flow cell 9105 is a microfluidic device. Although FIG. 30A illustrates a classification and / or sorting system utilizing a pump or any of a number of perfusion systems can be used such as (but not limited to) gravity feeds, peristalsis, or any of a number of pressure systems. In some implementations, the sample is prepared by fixation and staining. In some examples, the sample comprises live cells. As can readily be appreciated, the specific manner in which the sample is prepared is largely dependent upon the requirements of a specific application.

[0231] Examples of the flow unit may be, but are not limited to, a syringe pump, a vacuum pump, an actuator (e.g., linear, pneumatic, hydraulic, etc.), a compressor, or any other suitable device to exert pressure (positive, negative, alternating thereof, etc.) to a fluid that may or may not comprise one or more particles (e.g., one or more cells to be classified, sorted, and / or analyzed). The flow unit may be configured to raise, compress, move, and / or transfer fluid into or away from the microfluidic channel. In some examples, the flowunitmay be configured to deliver positive pressure, alternating positive pressure and vacuum pressure, negative pressure, alternating negative pressure and vacuum pressure, and / or only vacuum pressure. The flow cell of the present disclosure may comprise at least 1 - e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, or more, flow units. The flow cell may comprise at most 10 - e.g., 9, 8, 7, 6, 5, 4, 3, 2, or 1 , flow unit.

[0232] Each flow unit may be in fluid communication with at least 1 - e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, or more, sources of fluid. Each flow unit may be in fluid communication with at most 10 - e.g., 9, 8, 7, 6, 5, 4, 3, 2, or 1 , fluid. The fluid may contain the particles (e.g., cells). Alternatively,the fluid may be particle-free. The flow unit may be configured to maintain, increase, and / or decrease a flow velocity of the fluid within the microfluidic channel of the flow unit. Thus, the flow unit may be configured to maintain, increase, and / or decrease a flow velocity (e.g., downstream of the microfluidic channel) of the particles. The flow unit may be configured to accelerate or decelerate a flow velocity of the fluid within the microfluidic channel of the flow unit, thereby accelerating or decelerating a flow velocity of the particles.

[0233] The fluid may be liquid or gas (e.g., air, argon, nitrogen, etc.). The liquid may be an aqueous solution (e.g., water, buffer, saline, etc.). Alternatively, the liquid may be oil. In some cases, only one or more aqueous solutions may be directed through the microfluidic channels. Alternatively, only one ormore oilsmay be directed through the microfluidic channels. In another alternative, both aqueous solution(s) and oil(s) may be directed through the microfluidic channels. In some examples, (i) the aqueous solution may form droplets (e.g., emulsions containing the particles) that are suspended in the oil, or (ii) the oil may form droplets (e.g., emulsions containing the particles) that are suspended in the aqueous solution.

[0234] As can readily be appreciated, any perfusion system, including but not limited to peristalsis systems and gravity feeds, appropriate to a given classification and / or sorting system can be utilized.

[0235] As noted above, the flow cell 9105 can be implemented as a fluidic device that focuses cells from the sample into a single streamline that is imaged continuously. In the illustrated implementation, the cell line is illuminated by a light source 9106 (e.g., a lamp, such as an arc lamp or an LED lamp) and an optical system 9110 that directs light onto an imaging region 9138 of the flow cell 9105. The light source 9106 may be any source of electromagnetic radiation. An objective lens system 9112 magnifies the cells by directing light toward the sensor of a high -speed camera system 9114.

[0236] As schematically illustrated in FIG. 30B, at least a portion of the objects (e.g., cells) flowing through the flow channel as disclosed herein can be sorted and collected into a receptacle that is in fluid communication with the flow channel via split junction (e.g., a fork, such as a bifurcation that is disposed at an end of the flow channel). Alternatively, the flow channel may not have split junction. Instead, a side of the flow channel may be in fluid communication with a suction device (e.g., aflowunitas disclosedherein, such as a syringe), suchthatthe suction device can suck out and collect one or more cells of interest that are flowing through the flow channel. In an example, the one or more cells collected by the suction device may be cells partitioned within the flow channel. The suction device can retain the collected one or more cells. Alternatively, the suction device can be in fluid communication with a sample unit, to direct flow of the collectedcells into a sample unit as disclosed herein.

[0237] In some implementations, a 10*, 20*, 40*, 60*, 80*, 100*, or 200 x objective is used to magnify the cells. In some implementations, a 10x, objective is used to magnify the cells. In some implementations, a 20 objective is used to magnify the cells. In some implementations, a 40x objective is used to magnify the cells. In some implementations, a 60 objective is used to magnify the cells. In some implementations, a 63 x objective is used to magnify the cells. In some implementations, an 80x objective is used to magnify the cells. In some implementations, a 100x objective is used to magnify the cells. In some implementations, a 200x objective is used to magnify the cells. In some implementations, a 1 Ox to a 200 x objective is used to magnify the cells, for example a 10x-20x, a 10x-40x, a 10x-60x, a 10x-80x, or al0x-100x objective is used to magnify the cells.

[0238] As can readily be appreciated by a person having ordinary skill in the art, the specific magnification utilized can vary greatly and is largely dependent upon the requirements of a given imaging system and cell types of interest.

[0239] In some implementations, one or more imaging devices may be used to capture images of the cell. In some aspects, the imaging device is a high-speed camera. In some aspects, the imaging device is a high-speed camera with a micro-second exposure time. In some instances, the exposure time is about 1 millisecond. In some instances, the exposure time is between about 1 millisecond (ms) and about 0.75 millisecond. In some instances, the exposure time is between about 1 ms and about 0.50 ms. In some instances, the exposure time is between about 1 ms and about 0.25 ms. In some instances, the exposure time is between about 0.75 ms and about 0.50 ms. In some instances, the exposure time is between about 0.75 ms and about 0.25 ms. In some instances, the exposure time is between about 0.50 ms and about 0.25 ms. In some instances, the exposure time is between about 0.25 ms and about 0. 1 ms. In some instances, the exposure time is between about 0.1 ms and about 0.01 ms. In some instances, the exposure time is between about 0.1 ms and about 0.001 ms. In some instances, the exposure time is between about 0.1 ms and about 1 microsecond (ps). In some aspects, the exposure time is between about 2 ps and about 0.5 ps. In some aspects, the exposure time is between about 1 ps and about 0.1 ps. In some aspects, the exposure time is between about 1 ps and about 0.01 ps. In some aspects, the exposure time is between about 0.1 ps and about 0.01 ps. In some aspects, the exposure time is between about 1 ps and aboutO.OOl ps. In some aspects, the exposure time is between aboutO. l psand aboutO.OOl ps. In some aspects, the exposure time is between about 0.01 ps and about 0.001 ps.

[0240] In some cases, the flow cell 9105 may comprise atleast 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more imaging devices (e.g., the high-speed camera system 9114) on or adjacent to the imagingregion 9138. In some cases, the flow cell may comprise at most 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 imaging device on or adjacent to the imaging region 9138. In some cases, the flow cell 9105 may comprise a plurality of imaging devices. Each of the plurality of imaging devices may use light from a same light source. Alternatively, each of the plurality of imaging devices may use light from different light sources. The plurality of imaging devices may be configured in parallel and / or in series with respect to one another. The plurality of imaging devices may be configured on one or more sides (e.g., two adjacent sides or two opposite sides) of the flow cell 9105. The plurality of imaging devices may be configured to view the imaging region 9138 along a same axis or different axes with respect to (i) a length of the flow cell 9105 (e.g., a length of a straight channel of the flow cell 9105) or (ii) a direction of migration of one or more particles (e.g., one or more cells) in the flow cell 9105.

[0241] One or more imaging devices of the present disclosure may be stationary while imaging one or more cells, e.g., at the imaging region 9138. Alternatively, one or more imaging devices may move with respect to the flow channel (e.g., along the length of the flow channel, towards and / or away from the flow channel, tangentially about the circumference of the flow channel, etc.) while imaging the one or more cells. In some examples, the one or more imaging devices may be operatively coupled to one or more actuators, such as, for example, a stepper actuator, linear actuator, hydraulic actuator, pneumatic actuator, electric actuator, magnetic actuator, and mechanical actuator (e.g., rack and pinion, chains, etc.). In some cases, the one or more imaging devices is stationary relative to the flow cell (e.g., a micro fluidic). In some cases, the one or more imaging devices may not be stationary relative to the flow cell, e.g., may be configured to move relative to the flow cell during alignment or imaging.

[0242] In some cases, the flow cell 9105 may comprise atleast 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more imaging regions (e.g., the imaging region 9138). In some cases, the flow cell 9105 may comprise at most 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 imaging region. In some examples, the flow cell 1115 may comprise a plurality of imaging regions, and the plurality of imaging regions may be configured in parallel and / or in series with respect to each another. The plurality of imaging regions may or may not be in fluid communication with each other. In an example, a first imaging region and a second imaging region may be configured in parallel, such that a first fluid that passes through the first imaging region does not pass through a second imaging region. In another example, a first imaging region and a second imaging region may be configured in series, such that a first fluid that passes through the first imaging region also passes through the second imaging region.

[0243] The imaging device(s) (e.g., the high-speed camera) ofthe imaging system can comprisean electromagnetic radiation sensor (e.g., IR sensor, color sensor, etc.) that detects at least a portion of the electromagnetic radiation that is reflected by and / or transmitted from the flow cell or any content (e.g., the cell) in the flow cell. The imaging device can be in operative communication with one or more sources(e.g., atleast 1, 2, 3, 4, 5, or more) of the electromagnetic radiation. The electromagnetic radiation can comprise one or more wavelengths from the electromagnetic spectrum including, but not limited to x-rays (aboutO. 1 nanometers (nm)to about 10.0 nm ; or ab out 1018Hertz (Hz) to ab out 1016Hz), ultraviolet (U V) ray s (ab out 10.0 nm to ab out 380 nm; or about 8* 1016Hz to about 1015Hz), visible light (about 380 nm to about 750 nm; or about 8* 1014Hz to about 4*1014Hz), infrared (IR) light (about 750 nm to about 0.1 centimeters (cm); or about 4* 1014Hz to about 5 * 1011Hz), and microwaves (about 0.1 cm to about 100 cm; or about 108Hz to about 5 * 1011Hz). In some cases, the source(s) of the electromagnetic radiation can be ambient light, and thus the cell sorting system may not have an additional source of the electromagnetic radiation.

[0244] The imaging device(s) can be configured to take a two-dimensional image (e.g., one or more pixels) of the cell and / or a three-dimensional image (e.g., one or more voxels) of the cell.

[0245] As can readily be appreciated, the exposure times can diff er across different systems and can largely be dependent upon the requirements of a given application or the limitations of a given system such as but not limited to flow rates. Images are acquired and can be analyzed using an image analysis algorithm.

[0246] In some implementations, the images are acquired and analyzed post-capture. In some aspects, the images are acquired and analyzed in real-time continuously. Using object tracking software, single cells can be detected and tracked while in the field of view of the camera. Background subtraction can then be performed. In a number of implementations, the flow cell 9106 causes the cells to rotate as they are imaged, and multiple images of each cell are provided to a computing system 9116 for analysis. In some implementations, the multiple images comprise images from a plurality of cell angles. In some implementations, cells that are partitioned into a planar current may be rotating, such that when these cells in the planar current are imaged, each cell can be imaged from multiple angles to generate a plurality of imaging data from different angles for each cell. Alternatively, the cells that are partitioned into the planar current may not and need not be rotated, e.g., for imaging and / or analysis as disclosed herein.

[0247] The flow rate and channel dimensions can be determined to obtain multiple images of the same cell from a plurality of different angles (i.e., a plurality of cell angles). A degree of rotation between an angle to the next angle may be uniform or non-uniform. In some examples, a full 360° view of the cell is captured. In some implementations, 4 images are provided in whichthe cell rotates 90° between successive frames. In some implementations, 8 images are provided in which the cell rotates 45° between successive frames. In some implementations, 24 images are provided in which the cell rotates 15° between successive frames. In some implementations, at least three or more images are provided in which the cell rotates at a first angle between a first frame and a second frame, and the cell rotates at a second angle between the second frame and a third frame, wherein the first and second angles are different. In some examples, less than the full 360° view of the cell may be captured, and a resulting plurality of images of the same cell maybe sufficient to classify the cell (e.g., determine a specific type of the cell).

[0248] The cell can have a plurality of sides. The plurality of sides of the cell can be defined with respect to a direction of the transport (flow) of the cell through the channel. In some cases, the cell can comprise a top side, a bottom side that is opposite the top side, a front side (e.g., the side towards the direction of the flow of the cell), a rear side opposite the front side, a left side, and / or a right side opposite the left side. In some cases, the image of the cell can comprise a plurality of images captured from the plurality of angles, whereinthe plurality of images comprise: (1) an image captured from the top side of the cell, (2) an image captured from the bottom side of the cell, (3) an image captured from the front side of the cell, (4) an image captured from the rear side of the cell, (5) an image captured from the left side of the cell, and / or (6) an image captured from the right side of the cell.

[0249] In some implementations, a two-dimensional “hologram” of a cell can be generated by superimposing the multiple images of the individual cell. The “hologram” can be analyzed to automatically classify characteristics of the cell based upon features including but not limited to the morphological features of the cell.

[0250] In some implementations, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 images are captured for each cell. In some implementations, 5 or more images are captured for each cell. In some implementations, from 5 to 10 images are captured for each cell. In some implementations, 10 or more images are captured for each cell. In some implementations, from 10 to 20 images are captured for each cell. In some implementations, 20 or more images are captured for each cell. In some implementations, from 20 to 50 images are captured for each cell. In some implementations, 50 or more images are captured for each cell. In some implementations, from 50 to 100 images are captured for each cell. In some implementations, 100 or more images are captured for each cell. In some cases, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, or more images may be captured for each cell at a plurality of different angles. In some cases, atmost 50, 40, 30, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, or 2 images may be captured for each cell at a plurality of different angles.

[0251] In some implementations, the imaging device is moved so as to capture multiple imagesof the cell from a plurality of angles. In some aspects, the images are captured at an angle between 0 and 90 degrees to the horizontal axis. In some aspects, the images are captured at an angle between 90 and 180 degrees to the horizontal axis. In some aspects, the images are captured at an angle between 180 and 270 degreesto the horizontal axis. In some aspects, the images are captured at an angle between 270 and 360 degrees to the horizontal axis.

[0252] In some implementations, multiple imaging devices (for e.g. multiple cameras) are used wherein each device captures an image of the cell from a specific cell angle. In some aspects, 2, 3, 4, 5, 6, 7, 8, 9, or 10 cameras are used. In some aspects, more than 10 cameras are used, wherein each camera images the cell from a specific cell angle,

[0253] As can readily be appreciated, the number of images that are captured is dependent upon the requirements of a given application or the limitations of a given system. In several implementations, the flow cell has different regions to focus, order, and / or rotate cells. Although the flow cell has regions for focusing, ordering, and / or rotating cells are discussed as affecting the sample in a specific sequence, a person having ordinary skill in the art would appreciate that the various regions can be arranged differently, where the focusing, ordering, and / or rotating of the cells in the sample can be performed in any order. Regions within a microfluidic device implemented in accordance with an implementation of the disclosure are illustrated in FIG. 30B. Flow cell 9105 may include filtration 9130 to prevent channel clogging by aggregates / debris or dust particles. Cells pass through a region that focuses 9132 the cells into a single streamline of cells that are then spaced by an order 9134. In some implementations, the focusing region utilizes “inertial focusing” to form the single streamline of cells. In some implementations, the focusing region utilizes ‘hydrodynamic focusing” to focus the cells into the single streamline of cells. In some instances, the focusing region utilizes “inertial focusing” and “hydrodynamic focusing” In one implementation, prior to imaging, rotation 9136 can be imparted upon the cells. The spinning cells can then pass through an imaging region 9138 in which the cells are illuminated for imaging prior to exiting the flow cell. These various regions are described and discussed in further detail below. In some cases, the rotation 9136 may precede the imaging region 9138. In some cases, the rotation 9136 may occur within any part (e.g., a beginning portion, a middle portion, and / or an end portion with respect to a migration of a cell within the flow cell) of the imaging region 9138. In some cases, filtration 9130, focusing 9132, ordering 9134, and rotation 9136 may occur within a same region. In some cases at least two of filtration 9130, focusing 9132, ordering 9134, and rotation 9136 may occur within a same region.

[0254] In some cases, the flow system as disclosed herein may not and need not comprise a separate focusing channel 9132 and / or a separate channel 9134 that are shown in FIG. 30B.Instead, by ways of manipulating flow of the cells as described throughout herein and illustrated, focusing and ordering cells of a common physical characteristic class into at least one common equilibrium file / plane can be sufficient for analysis and / or classification of such cells.

[0255] In some cases, only a single cell may be allowed to be transported across a cross-section of the flow channel perpendicular to the axis of the flow channel. In some cases, a plurality of cells (e.g., at least 2, 3, 4, 5, or more cells; at most 5, 4, 3, 2, or 1 cell) may be allowed to be transported simultaneously across the cross-section of the flow channel perpendicular to the axis of the flow channel. In such a case, the imaging device (or the processor operatively linked to the imaging device) may be configured to track each of the plurality of cells as they are transported along the flow channel.

[0256] The imaging system can include, among other things, a camera, an objective lens system and a light source. In a number of implementations, flow cells similar to those described above can be fabricated using standard 2D microfluidic fabrication techniques, requiring minimal fabrication time and cost.

[0257] Although specific classification and / or sorting systems, flow cells, and microfluidic devices are described above with respect to FIGs. 30A and 30B, classification and / or sorting systems can be implemented in any of a variety of ways appropriate to the requirements of specific applications in accordance with various implementations of the disclosure. Specific elements of microfluidic devices that can be utilized in classification and / or sorting systems in accordance with some implementations of the disclosure are discussed further below.

[0258] In some cases, implementations, the microfluidic system can comprise a microfluidic chip (e.g., comprising one or more microfluidic channels for flowing cells) operatively coupled to an imaging device (e.g., one or more cameras). A microfluidic device can comprise the imaging device, and the chip can be inserted into the device, to align the imaging device to an imaging region of a channel of the chip. To align the chip to the precise location for the imaging, the chip can comprise one or more positioning identifiers (e.g., pattem(s), such as numbers, letters, symbols, or other drawings) that can be imaged to determine the positioning of the chip (and thus the imaging region of the channel of the chip) relative to the device as a whole or relative to the imaging device. For image-based alignment (e.g., auto-alignment) of the chip within the device, one or more images of the chip can be capture upon its coupling to the device, and the image(s) can be analyzed by any of the methods disclosed herein (e.g., using any model or classifier disclosed herein) to determine a degree or score of chip alignment. The positioning identifiers) can be a “guide” to navigate the stage holdingthe chip within the device to move within the device towards a correct position relative to the imaging unit.

[0259] In some cases, rule-based image processing can be used to navigate the stage to a precise range of location or a precise location relative to the image unit.

[0260] In some cases, machine learning / artificial intelligence methods as disclosed herein can be modified or trained to identify the pattern on the chip and navigate the stage to the precise imaging location for the image unit, to increase resilience.

[0261] In some cases, machine learning / artificial intelligence methods as disclosed herein can be modified or trained to implement reinforcement learning based alignment and focusing. The alignment process for the chip to the instrument or the image unit can involve movingthe stage holding the chip in, e.g., either X or Y axis and / or movingthe imaging plane on the Z axis. In the training process, (i) the chip can start at a X, Y, and Z position (e.g., randomly selected), (ii) based on one or more image(s) of the chip and / or the stage holding the chip, a model can determine a movement vector for the stage and a movement for the imaging plane, (iii) depending on whether such movement vector may take the chip closer to the optimum X, Y, and Z position relative to the image unit, an error term can be determined as a loss for the model, and (iv) the magnitude of the error can be either constant or be proportional to how far the current X, Y, and Z position is from an optimal X, Y, and Z position (e.g., may be predetermined). The trained model can be used to determine, for example, the movementvector and / or movement of the imagingplane to enhance relative alignment between the chip and the image unit (e.g., one or more sensors).

[0262] The alignment can occur subsequent to capturing of the image(s). Alternatively or in addition to, the alignment can occur real-time while capturing images / videos of the positioning identifier(s) of the chip.

[0263] One or more flow channels of the flow cell of the present disclosure may have various shapes and sizes. For example, referring to FIGs. 30A and 30B, at least a portion of the flow channel (e.g., the focusing region 9132, the region 9134, the rotation region 9136, the imaging region 9138, and / or connecting region therebetween) may have a cross-section that is circular, triangular, square, rectangular, pentagonal, hexagonal, or any partial shape or combination of shapes thereof.

[0264] D. Cell Rotating Regions and Imaging Regions

[0265] Architecture of the microfluidic channel of the flow cell of the present disclosure may be controlled (e.g., modified, optimized, etc.) to modulate cell flow along the microfluidic channels. Examples of the cell flow may include (i) cell focusing (e.g., into a single streamline) and (ii) rotation of the at least one cell (or the one or more cells) as the cell(s) are migrating (e.g., within the single streamline) down the length of the microfluidic channels. In some implementations, microfluidic channels can be configured to impart rotation on ordered cells inaccordance with a number of implementations of the disclosure. One or more cell rotation regions (e.g., the cell rotation region 9136) of microfluidic channels in accordance with some implementations of the disclosure use co-flow of a particle-free buffer to induce cell rotation by using the co-flow to apply differential velocity gradients across the cells. In some cases, a cell rotation region may introduce co-flow of atleast 1, 2, 3, 4, 5, or more buffers (e.g., particle -free, or containing one or more particles, such as polymeric or magnetic particles) to impart rotation on one or more cells within the channel. In some cases, a cell rotation region may introduce co-flow of at most 5, 4, 3, 2, or 1 buffer to impart the rotation of one or more cells within the channel. In some examples, the plurality of buffers may be co-flown at a same position along the length of the cell rotation region, or sequentially at different positions along the length of the cell rotation region. In some examples, the plurality of buffers may be the same or different. In several implementations, the cell rotation region of the microfluidic channel is fabricated using a two- layer fabrication process so thatthe axis of rotation is perpendicularto the axis of cell downstream migration and parallel to cell lateral migration.

[0266] Cells may be imaged in at least a portion of the cell rotating region, while the cells are tumbling and / or rotating as they migrate downstream. Alternatively, or in addition to, the cells may be imaged in an imaging region that is adjacent to or downstream of the cell rotating region. In some examples, the cells may be flowing in a single streamline within a flow channel, and the cells may be imaged as the cells are rotating within the single streamline. A rotational speed of the cells may be constant or varied along the length of the imaging region. This may allow for the imaging of a cell at different angles (e.g., from a plurality of images of the cell taken from a plurality of angles due to rotation of the cell), which may provide more accurate information concerning cellular features than can be captured in a single image or a sequence of images of a cell that is not rotating to any significant extent. This also allow a 3D reconstruction of the cell using available software since the angles of rotation across the images are known. Alternatively, every single image of the sequence of images may be analyzed individually to analyze (e.g., classify) the cell from each image. In some cases, results of the individual analysis of the sequence of images may be aggregated to determine a final decision (e.g., classification of the cell).

[0267] E. Flow Cells

[0268] In some implementations, the system and methods of the present disclosure focuses the cells in microfluidic channels. The term focusing as used herein broadly means controlling the trajectory of cell / cells movement and comprises controlling the position and / or speed at which the cells travel within the microfluidic channels. In some implementations controlling the lateral position and / or the speed at which the particles travel inside the microfluidic channels, allows toaccurately predict the time of arrival of the cell at a bifurcation. The cells may then be accurately sorted. The parameters critical to the focusing of cells within the microfluidic channels include, but are not limited to channel geometry, particle size, overall system throughput, sample concentration, imaging throughput, size of field of view, and method of sorting.

[0269] In some implementations the focusing is achieved using inertial forces. In some implementations, the system and methods of the present disclosure focus cells to a certain height from the bottom of the channel using inertial focusing. In these implementations, the distance of the cells from the objective is equal and images of all the cells will be clear. As such, cellular details, such as nuclear shape, structure, and size appear clearly in the outputted images with minimal blur. In some aspects, the system disclosed herein has an imaging focusing plane that is adjustable. In some aspects, the focusing plane is adjusted by moving the objective or the stage. In some aspects, the best focusing plane is found by recording videos at different planes and the plane wherein the imaged cells have the highestFourier magnitude, thus, the highest level of detail and highest resolution, is the best plane.

[0270] In some implementations, the system and methods of the present disclosure utilize a hydrodynamic-based z focusing system to obtain a consistentz height for the cells of interests that are to be imaged. In some aspects, the design comprises hydrodynamic focusing using multiple inlets for main flow and side flow. In some aspects, the hydrodynamic-based z focusing system is a triple-punch design. In some aspects, the design comprises hydrodynamic focusing with three inlets, wherein the two side flows pinch cells at the center. For certain channel designs, dual z focus points may be created, wherein a double-punch design similar to the triple-punch design may be used to send objects to one of the two focus points to get consistent focused images. In some aspects, the design comprises hydrodynamic focusing with 2 inlets, wherein only one side flow channel is used and cells are focused near channel wall. In some aspects, the hydrodynamic focusing comprises side flows that do not contain any cells and a middle inlet that contains cells. The ratio of the flow rate on the side channel to the flow rate on the main channel determines the width of cell focusing region. In some aspects, the design is a combination of the above. In all aspects, the design is integrable with the bifurcation and sorting mechanisms disclosed herein. In some aspects, the hydrodynamic-based z focusing system is used in conjunction with inertia-based z focusing.

[0271] F. Imaging and Classification

[0272] A variety of techniques can be utilized to classify images of cells captured by classification and / or sorting systems in accordance with various implementations of the disclosure. In some implementations, the image captures are saved for futureanaly sis / classification either manually orby image analysis software. Any suitable image analysis software can be used for image analysis. In some implementations, image analysis is performed using OpenCV. In some implementations, analysis and classification is performed in real time.

[0273] In some implementations, the system and methods of the present disclosure comprise collecting a plurality of images of objects in the flow. In some aspects, the plurality of images comprises at least 20 images of cells. In some aspects, the plurality of images comprises at least 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, or 2 images of cells. In some implementations, the plurality of images comprises images from multiple cell angles. In some aspects, the plurality of images, comprising images from multiple cell angles, help derive extra features from the particle which would typically be hidden if the particle is imaged from a single point-of-view. In some aspects, without wishing to be bound by theory, the plurality of images, comprising images from multiple cell angles, help derive extra features from the particle which would typically be hidden if a plurality of images is combined into a multi-dimensional reconstruction (e.g., a two-dimensional hologram or a three-dimensional reconstruction).

[0274] In some implementations, the systems and methods of present disclosure allow for a tracking ability, wherein the system and methods track a particle (e.g., cell) under the camera and maintain the knowledge of which frames belong to the same particle. In some implementations, the particle is tracked until it has been classified and / or sorted. In some cases, the particle may be tracked by one or more morphological (e.g., shape, size, area, volume, texture, thickness, roundness, etc.) and / or optical (e.g., light emission, transmission, reflectance, absorbance, fluorescence, luminescence, etc.) characteristics of the particle. In some examples, each particle may be assigned a score (e.g., a characteristic score) based on the one or more morphological and / or optical characteristics, thereby to track and confirm the particle as the particle travels through the microfluidic channel.

[0275] In some implementations, the systems and methods of the disclosure comprise imaging a single particle in a particular field of view of the camera. In some aspects, the system and methods of the present disclosure image multiple particles in the same field of view of camera. Imaging multiple particles in the same field of view of the camera can provide additional advantages, for example it will increase the throughput of the system by batching the data collection and transmission of multiple particles. In some instances, at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, or more particles are imaged in the same field of view of the camera. In some instances, 100 to 200 particles are imaged in the same field of view of the camera. In some instances, atmost about 100, 90, 80, 70, 60, 50, 40, 30, 20, 10, 9, 8, 7, 6, 5, 4, 3, or 2 particles are imaged in the same field of view of the camera. In some cases, the number ofthe particles (e.g., cells) that are imaged in the same field of viewmay notbe changed throughout the operation of the flow cell. Alternatively, the number of the particles (e.g., cells)thatare imaged in the same field of view may be changed in real-time throughout the operation of the flow cell, e.g., to increase speed of the classification and / or sorting process without negatively affecting quality or accuracy of the classification and / or sorting process.

[0276] The imaging region may be downstream of the focusing region and the ordering region. Thus, the imaging region may not be part of the focusing region and the ordering region. In an example, the focusing region may not comprise or be operatively coupled to any imaging device that is configured to capture one or more images to be used for particle analysis (e.g., cell classification).

[0277] G. Cell Clustering Map

[0278] In some implementations, cell imaging data can be analyzed to plot (e.g., in silico) a plurality of cells into a cell clustering map. Image data (or imaging data, as used interchangeably herein) of a plurality of cells can be obtained. The image data can comprise tag-free images of single cells. Alternatively, the image data can comprise images of single cells that are tagged (e.g., with a heterologous marker as disclosed herein). The image data can be processed to generate a cell morphology map (e.g., one or more cell morphology maps). The cell morphology map can comprise a plurality of morphologically distinct clusters corresponding to different types or states of the cells. In some cases, a classifier (e.g., a cell clustering machine learning algorithm or deep learning algorithm) can be trained by using the cell morphology map. In some cases, the classifier can be configured to classify (e.g., automatically classify) a cellular image sample based on its proximity, correlation, or commonality with one or more of the morphologically distinct clusters. Thus, in some cases, the classifier can be used to classify (e.g., automatically classify) the cellular image sample accordingly.

[0279] The term “cluster” as used herein generally refers to a group of datapoints, such that datapoints in one group (e.g., a first cluster) are more similar to each other than datapoints of another group (e.g., a second cluster). A cluster can be a group of like datapoints (e.g., each datapointrepresentingacell oran image of a cell) that are grouped togetherbased on the proximity of the datapoints, to a measure of central tendency of the cluster. For example, a population of cells can be analyzed based on one or more morphological properties of each cell (e.g., by analyzing one or more images of each cell), and each cell can be plotted as a datapoint on a map base on the one or more morphological properties of each cell. Following, one or more clusters comprising a plurality of datapoints b ased on the proximity of the datapoints. The central tendency of each cluster can be measured by one or more algorithms (e.g., hierarchical clustering models,K-means algorithm, statistical distribution models, etc.). For instance, the measure of central tendency may be the arithmetic mean of the cluster, in which case the datapoints are joined together based on their proximity to the average value in the cluster (e.g., K-means clustering), their correlation, or their commonality.

[0280] The term “cell type” as used herein generally refers to a kind, identity, or classification of cells according to one or more criteria, such as a tissue and species of origin, a differentiation state, whether or not they are healthy / normal or diseased, cell cycle stage, viability, etc. In nonlimiting examples, the term “cell type” can refer specifically to any specific kind of cell, such as an embryonic stem cell, a neural precursor cell, a myoblast, a mesodermal cell, etc.

[0281] The term “cell state” as used herein generally refers to a specific state of the cell, such as but not limited to an activated cell, such as activated neuron or immune cell, resting cell, such as a resting neuron or immune cell, a dividing cell, quiescent cell, or a cell during any stages of the cell cycle.

[0282] The term “cell cycle” as used herein generally refers to the physiological and / or morphological progression of changes that cells undergo when dividing (e.g., proliferating). Examples of different phases of the cell cycle can include “interphase,” “prophase,” “metaphase,” “anaphase,” and “telophase”. Additionally, parts of the cell cycle can be “M (mitosis),” “S (synthesis),” “GO,” “G1 (gap 1 )” and “G2 (gap2)” . Furthermore, the cell cycle can include periods of progression that are intermediate to the above named phases.

[0283] FIG. 31 schematically illustrates an example method for classifying a cell. The method can comprise processing image data 9210 comprising images / videos of single cells (e.g., image data 9210 consisting of tag-free images / videos of single cells). Various clustering analysis models 9220 as disclosed herein can be used to process the image data 9210 to extract one or more morphological properties of the cells from the image data 9210 and generate a cell morphology map 9230A based on the extracted one or more morphological properties. For example, the cell morphology map 9230A can be generated based on two morphological properties as dimension 1 and dimension 2. The cell morphology map 9230A can comprise one or more clusters (e.g., clusters A, B, and C) of datapoints, each datapoint representing an individual cell from the image data 9210. The cell morphology map 9230A and the clusters A-C therein can be used to train classifier(s) 9250. Subsequently, a new image 9240 of a new cell can be obtained and processed by the trained classifier(s) 9250 to automatically extract and analyze one or more morphological features fromthe cellular image 9240 andplotit as a datapoint on the cell morphology map 9230A. Based on its proximity, correlation, or commonality with one or more of the morphologically- distinct clusters A-C on the cell morphology map 9230A, the classifier(s) 9250 can automaticallyclassify the new cell. The classifier(s) 9250 can determine a probability that the cell in the new image data 9240 belongs to cluster C (e.g., the likelihood for the cell in the new image data 9240 to share one or more commonalities and / or characteristics with cluster C more than with other clusters A / B). For example, the classifier(s) 9250 can determine and report that the cell in the new image data 9240 has a 95% probability of belonging to cluster C, 1% probability of belonging to cluster B, and 4% probability of belong to cluster A, solely based on analysis of the image (e.g., a tag-free image) 9240 and one or more morphological features of the cell extracted therefrom.

[0284] An image and / or video (e.g., a plurality of images and / or videos) of one or more cells as disclosed herein (e.g., that of image data 9210 in FIG. 31) can be captured while the cell(s) is suspended in a fluid (e.g., an aqueous liquid, such as a buffer) and / or while the cell(s) is moving (e.g., transported across a microfluidic channel). For example, the cell may not and need not be suspended in a gel-like or solid-like medium. The fluid can comprise a liquid that is heterologous to the cell(s)’s natural environment. For example, cells from a subject’ s blood can be suspended in a fluid that comprises (i) at least a portion of the blood and (ii) a buffer that is heterologous to the blood. The cell(s) may not be immobilized (e.g., embedded in a solid tissue or affixed to a microscope slide, such as a glass slide, for histology) or adhered to a substrate. The cell(s) may be isolated from its natural environment or niche (e.g., a part of the tissue the cell(s) would b e in if not retrieved from a subject by human intervention) when the image and / or video of the cell(s) is captured. For example, the image and / or video may not and need not be from a histological imaging. The cell(s) may not and need not be sliced or sectioned prior to obtaining the image and / or video of the cell, and, as such, the cell(s) may remain substantially intact as a whole during capturing of the image and / or video.

[0285] When the image data is processed, e.g., to extract one or more morphological features of a cell, each cell image may be annotated with the extracted one or more morphological features and / or with information that the cell image belongs to a particular cluster (e.g., a probability).

[0286] The cell morphology map can be a visual (e.g., graphical) representation of one or more clusters of datapoints. The cell morphology map can be a 1 -dimensional (ID) representation (e.g, based on one morphological property as one parameter or dimension) or a multi-dimensional representation, such as a 2-dimensional (2D) representation (e.g., based on two morphological properties as two parameters or dimensions), a 3 -dimensional (3D) representation (e.g., based on three morphological properties as three parameters or dimensions), a 4 -dimensional (4D) representation, etc. In some cases, one morphological properties of a plurality of morphological properties used for blotting the cell morphology map can be represented as a non-axial parameter (e.g., non-x, y, or z axis), such as, distinguishable colors (e.g., heatmap), numbers, letters (e.g.,texts of one or more languages), and / or symbols (e.g., a square, oval, triangle, square, etc.). For example, a heatmap can be used as colorimetric scale to represent the classifier prediction percentages for each cell against a cell class, cell type, or cell state.

[0287] The cell morphology map can be generated based on one or more morphological features (e.g., characteristics, profiles, fingerprints ,etc.) from the processed image data. Nonlimiting examples of one or more morphological properties of a cell, as disclosed herein, that can be extracted from one or more images of the cell can include, but are not limited to (i) shape, curvature, size (e.g., diameter, length, width, circumference), area, volume, texture, thickness, roundness, etc. of the cell or one or more components of the cell (e.g., cell membrane, nucleus, mitochondria, etc.), (ii) number or positioning of one or more contents (e.g., nucleus, mitochondria, etc.) of the cell within the cell (e.g., center, off-centered, etc.), and (iii) optical characteristics of a region of the image(s) (e.g., unique groups of pixels within the image(s)) that correspond to the cell or a portion thereof (e.g., light emission, transmission, reflectance, absorbance, fluorescence, luminescence, etc.).

[0288] Non-limiting examples of clustering as disclosed herein can be hard clustering (e.g., determining whether a cell belongs to a cluster or not), soft clustering (e.g., determining a likelihood that a cell belongs to each clusterto a certain degree), strict partitioning clustering (e.g., determining whether each cell belongs to exactly one cluster), strict partitioning clustering with outliers (e.g., determining whether a cell can also belong to no cluster), overlapping clustering (e.g., determining whether a cell canbelongto more than one cluster), hierarchical clustering (e.g, determining whether cells that belong to a child cluster can also belong to a parent cluster), and subspace clustering (e.g., determining whether clusters are not expected to overlap).

[0289] Cell clustering and / or generation of the cell morphology map, as disclosed herein, can be based on a single morphological property of the cells. Alternatively, cell clustering and / or generation the cell morphology map can be based on a plurality of different morphological properties of the cells. In some cases, the plurality of different morphological properties of the cells can have the same weight or different weights. A weight can be a value indicative of the importance or influence of each morphological property relative to one another in training the classifier or using the classifier to (i) generate one or more cell clusters, (ii) generate the cell morphology map, or (iii) analyze a new cellular image to classify the cellular image as disclosed herein. For example, cell clustering can be performedby having 50% weight on cell shape, 40% weight on cell area, and 10% weight on texture (e.g., roughness) of the cell membrane. In some cases, the classifier as disclosed herein can be configured to adjust the weights of the plurality of different morphological properties of the cells during analysis of new cellular image data, therebyto yield a most optimal cell clustering and cell morphology map. The plurality of different morphological properties with different weights can be utilized during the same analysis step for cell clustering and / or generation of the cell morphology map.

[0290] The plurality of different morphological properties can be analyzed hierarchically. In some cases, a first morphological property can be used as a parameter to analyze image data of a plurality of cells to generate an initial set of clusters. Subsequently, a second and different morphological property can be used as a second parameter to (i) modify the initial set of clusters (e.g., optimize arrangement among the initial set of clusters, re-group some clusters of the initial set of clusters, etc.) and / or (ii) generate a plurality of sub -clusters within a cluster of the initial set of clusters. In some cases, a first morphological property can be used as a parameter to analyze image data of a plurality of cells to generate an initial set of clusters, to generate a ID cell morphology map. Subsequently, a second morphological property can be used as a parameter to further analyze the clusters of the ID cell morphology map, to modify the clusters and generate a 2D cell morphology map (e.g., a first axis parameter based on the first morphological property and a second axis parameter based on the second morphological property).

[0291] One or more dimension of the cell morphology map can be represented by various approaches (e.g., dimensionality reduction approaches), such as, for example, principal component analysis (PCA), multidimensional scaling (MDS), t-distributed stochastic neighbor embedding (t-SNE), and uniform manifold approximation and projection (UMAP). For example, UMAP can be a machine learning technique for dimension reduction. UMAP can be constructed from a theoretical framework based in Riemannian geometry and algebraic topology. UMAP can be utilized for a practical scalable algorithm that applies to real world data, such as morphological properties of one or more cells.

[0292] The cell morphology map as disclosed herein can comprise an ontology of the one or more morphological features. The ontology can be an alternative medium to represent a relationship amongvarious datapoints (e.g., each representing a cell) analyzed from an image data. For example, an ontology can be a data structure of information, in which nodes can be linked by edges. An edge can be used to define a relationship between two nodes. For example, a cell morphology map can comprise a cluster comprising sub -clusters, and the relationship between the cluster and the sub -clusters can be represented in a node(s) / edge(s) ontology (e.g., an edge can be used to describe the relationship as a subclass of, genus of, part of, stem cell of, differentiated from, progeny of, diseased state of, targets, recruits, interacts with, same tissue, different tissue, etc.).

[0293] In some cases, one-to-one morphology to genomics mapping can be utilized. An imageof a single cell or images of multiple “similar looking” cells can be mapped to its / their molecular profile(s) (e.g., genomics, proteomics, transcriptomics, etc.). In some examples, classifier-based barcoding can be performed. Each sorting event (e.g., positive classifier) can push the sorted cell(s) into an individual well or droplet with a unique barcode (e.g., nucleic acid or small molecule barcode). The exact barcode(s) used for that individual classifier positive event can be recorded and tracked. Following, the cells can be lysed and molecularly analyzed together with the barcode(s). The result of the molecular analysis can then be mapped (e.g., one-to-one) to the image(s) of the individual (or ensemble of) sorted cell(s) captured while the cell(s) was / were flowing in the flow channel. In some examples, class-based sorting can be utilized. Cells that are classified in the same class based at least on their morphological features can be sorted into a single well or droplet with a pre-determined barcoded material, and the cells can be lysed, molecularly analyzed, then any molecular information can be used for the one-to-one mapping as disclosed herein.

[0294] H. Samples

[0295] In some implementations, the particles ( e.g., cells) analyzed by the systems and methods disclosed herein are comprised in a sample. The sample may be a biological sample obtained from a subject. In some implementations, the biological sample comprises a biopsy sample from a subject. In some implementations, the biological sample comprises a tissue sample from a subject. In some implementations, the biological sample comprises liquid biopsy from a subject. In some implementations, the biological sample can be a solid biological sample, e.g., a tumor sample.

[0296] In some implementations, the sample can be a liquid biological sample. In some implementations, the liquid biological sample can be a blood sample (e.g., whole blood, plasma, or serum). A whole blood sample can be subjected to separation of cellular components (e.g, plasma, serum) and cellular components by use of a Ficoll reagent. In some implementations, the liquid biological sample can be a urine sample. In some implementations, the liquid biological sample can be a perilymph sample. In some implementations, the liquid biological sample can be a fecal sample. In some implementations, the liquid biological sample can be saliva. In some implementations, the liquid biological sample can be semen. In some implementations, the liquid biological sample can be amniotic fluid. In some implementations, the liquid biological sample can be cerebrospinal fluid. In some implementations, the liquid biological sample can be bile. In some implementations, the liquid biological sample can be sweat. In some implementations, the liquid biological sample can be tears. In some implementations, the liquid biological sample can be sputum. In some implementations, the liquid biological sample can be synovial fluid. In someimplementations, the liquid biological sample can be vomit.

[0297] In some implementations, samples can be collected over a period of time and the samples may be compared to each other or with a standard sample using the systems and methods disclosed herein. In some implementations the standard sample is a comparable sample obtained from a different subject, for example a different subject that is known to be healthy or a different subject that is known to be unhealthy. Samples can be collected over regular time intervals, or can be collected intermittently over irregular time intervals.

[0298] J. Sample Preparation

[0299] In some implementations, the sample comprising particles may be agitated prior to injection by a pressurizing fluid source (e.g., pressurizing fluid source 9104) or by the sample unit (e.g., sample unit 210) into a flow cell (e.g., flow cell 9105). In some aspects, the sample comprising particles may be agitated by pressurizing fluid source 9104 and flowed into flow cell 9105.

[0300] K. Point-of-Care Diagnostics

[0301] Any one of the systems and methods disclosed herein (e.g., cell morphology -based classification, such as for sorting or enrichment) can be utilized for point-of-care diagnostics. A point-of-care diagnostics or point-of-care diagnostics can encompass analysis of one or more samples (e.g., biopsy samples, such as blood samples) of a subject (e.g., a patient) in a point-of- care environment, such as, for example, hospitals, emergency departments, intensive care units, primary care setting, medical centers, patient homes, a physician's office, a pharmacy or a site of an emergency. The point-of-care diagnostics as disclosed herein can be utilized to identify a pathogen (e.g., any infectious agents, gems, bacteria, virus, etc.), identify immune response in the subject (e.g., via classifying and / or sorting specific immune cell types), generate a count of cells of interest (e.g., diseased cells, healthy cells, etc.), etc.

[0302] L. Others

[0303] An image of the image data can be processed in various image processing methods, such as horizontal or vertical image flips, orthogonal rotation, gaussian noise, contrast variation, or noise introduction to mimic microscopic particles or pixel-level aberrations. One or more of the processing methods can be used to generate replicas of the image or analyze the image. In some cases, the image can be processed into a lower-resolution image or a lower-dimension image (e.g, by using one or more deconvolution algorithm).

[0304] In some cases, one or more reference images or videos of the flow channel (e.g., with or without any cell) can be stored in a database and used as a frame of reference to help identify, account for, and / or exclude any artifact. The reference image(s) / video(s) can be obtained beforeuse of the microfluidic system. The reference image(s) / video(s) can be obtained during the use of the microfluidic system. The reference image(s) / video(s) can be obtained periodically during the use of the microfluidic system.

[0305] M. Machine Learning and Artificial Intelligence

[0306] In some implementations, analysis of imaging data as disclosed herein (e.g., particle imaging data, such as cell imaging data) can be performed using artificial intelligence, such as one or more machine learning algorithms. In some cases, one or more classifiers can be used to automatically sort or categorize particles (e.g., cells) in the imaging data into one or more classes (e.g., one or more physical characteristics or morphological features, as used interchangeably herein). In some examples, cell imaging data can be analyzed via the machine learning algorithm(s) to classify (e.g., sort) a cell (e.g., a single cell) in a cell image or video. In some examples, cell imaging data can be analyzed via the machine learning algorithm(s) to determine a focus score of a cell (e.g., a single cell) in a cell image or video. In some examples, cell imaging data can be analyzed via the machine learning algorithm(s) to determine a relative distance between (i) a first plane of cells exhibiting first similar physical characteristic(s) and (ii) a second plane of cells exhibiting second similar physical characteristic(s), which first and second planes denote fluid streams flowing substantially parallel to each other in a channel. In some examples, one or more cell morphology maps as disclosed herein can be used to train one or more classifiers (e.g., at least or up to about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more classifiers) as disclosed herein. Each classifier can be trained to analyze one or more images of a cell (e.g., to extract one or more morphological features of the cell) and categorize (or classify) the cell into one or more determined class or categories of a cell (e.g., based on a type of state of the cell). Alternatively, the classifier can be trained to create a new category to categorize (or classify) the cell into the new category, e.g., when determining that the cell is morphologically distinct than any pre-existing categories of other cells.

[0307] In some implementations, the entire process of cell focusing as disclosed herein (e.g., partitioning of cells into one or more planar currents flowing through the channel) may be accomplished based on de novo Al-mediated analysis of each cell (e.g., via analysis of one or more images of each cell using machine learning algorithm). This may be a complete Al or a full Al approach for cell sorting and analysis. Alternatively, a hybrid approachcan be utilized, wherein Al-mediated analysis can analyze cells and one or more heterologous markers that are co- partitioned with the cells (e.g., into the same planar current flowing through the channel), confirm or determine the co-partitioning, afterwhichamore conventional approach (e.g., imagingto detect presence of the heterologous markers, such as fluorescent imaging) can be utilized to sort asub sequent population of cells and the heterologous markers that are co -partitioned into the same planar current.

[0308] The term “classifier” as used herein generally refers to an analysis model (e.g., a metamodel) that can be trained by using a learning model and applying learning algorithms (e.g, machine learning algorithms) on a training dataset (e.g., a dataset comprising examples of specific classes). In some cases, given a set of training examples / cases, each marked for belonging to a specific class (e.g., specific cell type or class), a training algorithm can build a classifier model capable of assigning new examples / cases (e.g., new datapoints of a cell or a group of cells) into one category orthe other, e.g., to makethe model a non -probabilistic classifier. In some cases, the classifier model can be capable of creating a new category to assign new examples / cases into the new category. In some cases, a classifier model can be the actual trained classifier that is generated based on the training model.

[0309] The machine learning algorithm as disclosed herein can be configured to extract one or more morphological feature of a cell from the image data of the cell. The machine learning algorithm can form a new data set based on the extracted morphological features, and the new data set may not and need not contain the original image data of the cell. In some examples, replicas of the original images in the image data can be stored in a database disclosed herein, e.g, prior to using any of the new images fortraining, e.g., to keep the integrity of the images of the image data. In some examples, processed images of the original images in the image data can be stored in a database disclosed herein during or sub sequent to the classifier training. In some cases, any of the newly extracted morphological features as disclosed herein can be utilized as new molecular markers for a cell or population of cells of interest to the user. As cell analysis platform as disclosed herein can be operatively coupled to one or more databases comprising non- morphological data of cells processed (e.g., genomics data, transcriptomics data, proteomics data, metabolomics data), a selected population of cells exhibitingthe newly extracted morphological feature(s) can be further analyzed by their non-morphological properties to identify proteins or genes of interest that are common in the selected population of cells but not in other cells, thereby determining such proteins or genes of interest to be new molecular markers that can be used to identify such selected population of cells.

[0310] In some cases, a classifier can be trained by applying machine learning algorithms on at least a portion of one or more cell morphology maps as disclosed herein as a training dataset. Nonlimiting examples of machine learning algorithms for training a classifier can include supervised learning, unsupervised learning, semi-supervised learning, reinforcement learning, self -learning feature learning, anomaly detection, association rules, etc. In somecases, a classifier can be trainedby using one or more learning models on such training dataset. Non-limiting examples of learning models can include artificial neural networks (e.g., convolutional neural networks, U-net architecture neural network, etc.), b ackpropagation, boosting, decision trees, support vector machines, regression analysis, Bayesian networks, genetic algorithms, kernel estimators, conditional random field, random forest, ensembles of classifiers, minimum complexity machines (MCM), probably approximately correct learning (PACT), etc.

[0311] The machine learning algorithm as disclosed herein can utilize one or more clustering algorithms to determine that objects in the same cluster can be more similar (in one or more morphological features) to each other than those in other clusters. Non-limiting examples of the clustering algorithms can include, but are not limited to, connectivity models (e.g., hierarchical clustering), centroid models (e.g. K-means algorithm), distribution models (e.g., expectationmaximization algorithm), density models (e.g., density -based spatial clustering of applications with noise (DBSCAN), ordering points to identify the clustering structure (OPTICS)), subspace models (e.g., biclustering), group models, graph-based models (e.g., highly connected subgraphs (HCS) clustering algorithms), single graph models, and neural models (e.g., using unsupervised neural network). The machine learning algorithm can utilize a plurality of models, e.g., in equal weights or in different weights.

[0312] In some cases, unsupervised and self-supervised approaches can be used to expedite labeling of image data of cells. For the case of unsupervised, an embedding for a cell image can be generated. For example, the embedding can be a representation of the image in a space with reduced dimensions than the original image data. Such embeddings can be used to cluster images that are similar to one another. Thus, the labeler can be configured to batch -label the cells and increase the throughput as compared to manually labeling one or more cells.

[0313] In some cases, for the case of self -supervised learning, additional meta information (e.g, additional non-morphological information) about the sample (e.g., what disease is known or associated with the patient who provided the sample) can be used for labeling of image data of cells.

[0314] In some cases, embedding generation can use a neural net trained on predefined cell types. To generate the embeddings described herein, an intermediate layer of the neural net that is trained on predetermined image data (e.g., image data of known cell types and / or states) can be used. By providing enough diversity in image data / sample data to the trained model / classifier, this method can provide an accurate way to cluster future cells.

[0315] In some cases, embedding generation can use neural nets trained for different tasks. To generate the embeddings described herein, an intermediate layer of the neural net that is trainedfor a different task (e.g., a neural net that is trained on a canonical dataset such as ImageNet). Without wishing to be bound by theory, this can allow to focus on features that matter for image classification (e.g., edges and curves) while removing a bias that may otherwise be introduced in labeling the image data.

[0316] In some cases, autoencoders can be used for embedding generation. To generate the embeddings described herein, autoencoders can be used, in which the input and the output can be substantially the same image and the squeeze layer can be used to extract the embeddings. The squeeze layer can force the model to learn a smaller representation of the image, which smaller representation may have sufficient information to recreate the image (e.g., as the output).

[0317] In some cases, for clustering-based labeling of image data or cells, as disclosed herein, an expanding training data set can be used. With the expanding training data set, one or more revisions of labeling (e.g., manual relabeling) may be needed to, e.g., avoid the degradation of model performance due to the accumulated effect of mislabeled images. Such manual relabeling may be intractable on a large scale and ineffective when done on a random subset of the data. Thus, to systematically surface images for potential relabeling, for example, similar embeddingbased clustering can be used to identify labeled images that may cluster with members of other classes. Such examples are likely to be enriched for incorrect or ambiguous labels, which can be removed (e.g., automatically or manually).

[0318] In some cases, adaptive image augmentation can be used. In order to make the models and classifiers disclosed herein more robust to artifacts in the image data, (1) one or more images with artifacts can be identified, and (2) such images identified with artifacts can be added to training pipeline (e.g., for trainingthe model / classifier). Identifyingthe image(s) with artifacts can comprise: (la) while imaging cells, one or more additional sections of the image frame can be cropped, which frame(s) being expected to contain just the background without any cell; (2a) the background image can be checked for any change in one or more characteristics (e.g., optical characteristics, such as brightness); and (3 a) flagging / labeling one or more images that have such change in the characteristic(s). Adding the identified images to training pipeline can comprise: (2a) adding the one or more images that have been flagged / labeled as augmentation by first calculating an average feature of the changed characteristic(s) (e.g., the background median color); (2b) creating a delta image by subtracting the average feature from the image data (e.g., subtractingthe median for each pixel of the image); and (3 c) addingthe delta image to the training pipeline.

[0319] In any of the methods or platforms disclosed herein, the model(s) and / or classifier(s) can be validated (e.g., for the ability to demonstrate accurate cell classification performance).Non-limiting examples of validation metrics that can be utilized can include, but are not limited to, threshold metrics (e.g., accuracy, F-measure, Kappa, Macro-Average Accuracy, Mean-Class- Weighted Accuracy, Optimized Precision, Adjusted Geometric Mean, Balanced Accuracy, etc.), the ranking methods and metrics (e.g., receiver operating characteristics (ROC) analysis or “ROC area under the curve (ROC AUC)”), and the probabilistic metrics (e.g., root -mean-squared error). For example, the model(s) or classifier(s) can be determined to be balanced or accurate when the ROC AUC is greater than 0.5, greater than 0.55, greater than 0.6, greaterthan 0.65, greaterthan 0.7, greaterthan 0.75, greaterthan 0.8, greaterthan 0.85, greaterthan 0.9, greaterthan 0.91, greater than 0.92, greater than 0.93, greater than 0.94, greater than 0.95, greater than 0.96, greater than 0.97, greater than 0.98, greater than 0.99, or more.

[0320] Computer Systems

[0321] The present disclosure provides computer systems that are programmed to implement methods of the disclosure. FIG. 32 shows a computer system 9301 that is programmed or otherwise configured to control one or more components of the cell storage module or flow of the sample into or away from the cell storage module as disclosed herein. The computer system 9301 can regulate various aspects of the microfluidic channel of the present disclosure, such as, for example, introducing particles or cells into the microfluidic channel, imaging cells within the microfluidic channel, and / or partitioning, upon analysis, cells of interest into one or more sample units that are downstream of the channel. The computer system 9301 can be an electronic device of a user or a computer system that is remotely located with respect to the electronic device. The electronic device can be a mobile electronic device.

[0322] The computer system 9301 includes a central processing unit (CPU, also “processof’ and “computer processor” herein) 9305, which can be a single core or multi core processor, or a plurality of processors for parallel processing. The computer system 9301 also includes memory or memory location 9310 (e.g., random-access memory, read-only memory, flash memory), electronic storage unit 9315 (e.g., hard disk), communication interface 9320 (e.g., network adapter) for communicating with one or more other systems, and peripheral devices 9325, such as cache, other memory, data storage and / or electronic display adapters. The memory 9310, storage unit 9315, interface 9320 and peripheral devices 9325 are in communication with the CPU 9305 through a communication bus (solid lines), such as a motherboard. The storage unit 9315 can be a data storage unit (or data repository) for storing data. The computer system 9301 can be operatively coupled to a computer network (“network”) 9330 with the aid of the communication interface 9320. The network 9330 can be the Internet, an internet and / or extranet, or an intranet and / or extranet that is in communication with the Internet. The network 9330 in some cases is atelecommunication and / or data network. The network 9330 can include one or more computer servers, which can enable distributed computing, such as cloud computing. The network 9330, in some cases with the aid of the computer system 9301, can implement a peer-to-peer network, which may enable devices coupled to the computer system 9301 to behave as a client or a server.

[0323] The CPU 9305 can execute a sequence of machine-readable instructions, which can be embodied in a program or software. The instructions may be stored in a memory location, such as the memory 9310. The instructions can be directed to the CPU 9305, which can subsequently program or otherwise configure the CPU 9305 to implement methods of the present disclosure. Examples of operations performed by the CPU 9305 can include fetch, decode, execute, and writeback.

[0324] The CPU 9305 can be part of a circuit, such as an integrated circuit. One or more other components of the system 9301 can be included in the circuit. In some cases, the circuit is an application specific integrated circuit (ASIC).

[0325] The storage unit 9315 can store files, such as drivers, libraries and saved programs. The storage unit 9315 can store user data, e.g., user preferences and user programs. The computer system 9301 in some cases can include one or more additional data storage units that are external to the computer system 9301, such as located on a remote server that is in communication with the computer system 9301 through an intranet or the Internet.

[0326] The computer system 9301 can communicate with one or more remote computer systems through the network 9330. For instance, the computer system 9301 can communicate with a remote computer system of a user. Examples of remote computer systems include personal computers (e.g., portable PC), slate or tablet PC’s (e.g., Apple® iPad, Samsung® Galaxy Tab), telephones, Smart phones (e.g., Apple® iPhone, Android -enabled device, Blackberry®), or personal digital assistants. The user can access the computer system 9301 via the network 9330.

[0327] Methods as described herein can be implemented by way of machine (e.g., computer processor) executable code stored on an electronic storage location of the computer system 9301, such as, f or example, on the memory 9310 or electronic storage unit 9315. The machine executable or machine readable code can be provided in the form of software. During use, the code can be executed by the processor 9305. In some cases, the code can be retrieved from the storage unit 9315 and stored on the memory 9310 for ready access by the processor 9305. In some situations, the electronic storage unit 9315 can be precluded, and machine -executable instructions are stored on memory 9310.

[0328] The code can be pre-compiled and configured for use with a machine having a processor adapted to execute the code or can be compiled during runtime. The code can be supplied in aprogramming language that can be selected to enable the code to execute in a pre -compiled or as- compiled fashion.

[0329] Aspects of the systems and methods provided herein, such as the computer system 9301, can be embodied in programming. Various aspects of the technology may be thought of as “products” or “articles of manufacture” in the form of machine (or processor) executable code and / or associated data that is carried on or embodied in a type of machine readable medium. Machine-executable code can be stored on an electronic storage unit, such as memory (e.g., readonly memory, random-access memory, flash memory) or a hard disk. “ Storage” type media can include any or all of the tangible memory of the computers, processors or the like, or associated modules thereof, such as various semiconductor memories, tape drives, disk drives and the like, which may provide non-transitory storage at any time for the software programming. All or portions of the software may at times be communicated through the Internet or various other telecommunication networks. Such communications, for example, may enable loading of the software from one computer or processor into another, for example, from a management server or host computer into the computer platform of an application server. Thus, another type of media that may bear the software elements includes optical, electrical and electromagnetic waves, such as used across physical interfaces between local devices, through wired and optical landline networks and over various air-links. The physical elements that carry such waves, such as wired or wireless links, optical links or the like, also may be considered as media bearing the software. As used herein, unless restricted to non-transitory, tangible “storage” media, terms such as computer or machine “readable medium” refer to any medium that participates in providing instructions to a processor for execution.

[0330] Hence, a machine readable medium, such as computer-executable code, may take many forms, including but not limited to, a tangible storage medium, a carrier wave medium or physical transmission medium. Non-volatile storage media include, for example, optical ormagnetic disks, such as any of the storage devices in any computer(s) orthe like, such as may be usedto implement the databases, etc. shown in the drawings. Volatile storage media include dynamic memory, such as main memory of such a computer platform. Tangible transmission media include coaxial cables; copper wire and fiber optics, including the wires that comprise a bus within a computer system. Carrier-wave transmission media may take the form of electric or electromagnetic signals, or acoustic or light waves such as those generated during radio frequency (RF) and infrared (IR) data communications. Common forms of computer-readable media therefore include for example: a floppy disk, a flexible disk, hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD or DVD-ROM, any other optical medium, punch cardspapertape, any other physical storagemedium with patterns of holes, a RAM, a ROM, a PROM and EPROM, a FLASH -EPROM, any other memory chip or cartridge, a carrier wave transporting data or instructions, cables or links transporting such a carrier wave, or any other medium from which a computer may read programming code and / or data. Many of these forms of computer readable media maybe involved in carrying one or more sequences of one or more instructions to a processor for execution.

[0331] The computer system 9301 can include or be in communication with an electronic display 9335 that comprises a user interface (UI) 9340 for providing, for example, control various parameters of the flow channel as disclosed herein. Examples of UI’s include, without limitation, a graphical user interface (GUI) and web -based user interface.

[0332] Methods and systems of the present disclosure can be implemented by way of one or more algorithms. An algorithm can be implemented by way of software upon execution by the central processing unit 9305. The algorithm can, for example, analyze one or more cell imaging data, as disclosed herein, to classify cells, determine focusing score of the cells within the cell imaging data, etc.

[0333] Methods, systems, and compositions of the present disclosure may be combined with or modified by other methods, systems, and compositions, such as, for example, those described in Patent Cooperation Treaty Publication No. 2020 / 037070 (“Systems and methods for particle analysis”) and Patent Cooperation Treaty Publication No. 2022 / 178095 (“Methods and systems for cell analysis”), each of which is entirely incorporated herein by reference.

[0334] Implementations

[0335] Implementation 1 . A system for analyzing a plurality of cells, comprising: a cell storage module comprising a container for holding the cell, wherein the cell storage module further comprises a sample unit configured to provide an agitation force to direct movement of the plurality of cells within the container within the cell storage module; an imaging module is in communication with the cell storage module and is configured to capture an image of a cell of the plurality of cells; and a flow cell module in optical communication with the imaging module, wherein the flow cell module comprises a flow channel configured to (i) retrieve the cells from the container that is coupled to the cell storage module and (ii) direct flow of the cells towards the imaging module to permit the imaging module to capture the image of the cell.

[0336] The system of Implementation 1, wherein the sample unit comprises a vortexer.

[0337] The system of Implementation 2, wherein the sample unit is in communication with a guide unit that is configured to move in a same direction as the actuation unit.

[0338] The system of any one of the preceding Implementations, wherein the sample unit comprises a plurality of bearings.

[0339] The system of any one of the preceding Implementations, wherein the cell storage module comprises a damper to isolate movement of the container from the imaging module and the flow cell module.

[0340] The system of any one of the preceding Implementations, wherein the sample unit comprises: (i) a top portion, and (ii) a bottom portion for coupling to a sample holder that comprises the cells, wherein the top portion andthe bottom portion are configuredto move relative to one another to form the container that is substantially sealed.

[0341] The system of any one of the preceding Implementations, wherein the top portion is in communication with an actuation unit configured to direct the relative movement between the top portion and the bottom portion, via a non-rotation mechanism.

[0342] The system of any one of the preceding Implementations, wherein the actuation unit is linked to the top portion via a coupling unit, wherein the coupling unit is configured to permit a relative movementbetween the actuationunit and the top portion one or more degrees of freedom.

[0343] The system of any one of the preceding Implementations, wherein the sample unit is in communication with a guide unit configuredto provide a path for the relative movementbetween the top portion and the bottom portion, wherein the guide unit is configured to move with the sample unit.

[0344] The system of any one of the preceding Implementations, wherein the cell storage module comprises a pressurizer configured to introduce a positive pressure to at least a portion of the sample unit.

[0345] The system of any one of the preceding Implementations, wherein the cell storage module is configured to direct the container to move (i) sequentially along a plurality of directions and / or (ii) sequentially along a plurality of movement speeds.

[0346] The system of Implementation 1, wherein the system further comprising a housing wherein the cell storage module, the imaging module, and the flow cell module are disposed within the housing.

[0347] A method for analyzing a plurality of cells, comprising: (a) moving a container in a sample unit, the container being coupled to a sample unit; (b) retrieving the plurality of cells from the container in the sample unit; (c) sub sequent to (b), directing flow of the plurality of cells towards an imaging module that is in communication with the flow cell module, wherein the container is configured to hold the plurality of cells, wherein the imaging module is configured to capture an image of a cell in the plurality of cells.

[0348] The method of Implementation 13 , whereinthe moving comprises rotatingthe container relative to an actuator of the cell storage module.

[0349] The method of any one of Implementations 13 or 14, wherein the cell storage module comprises a damper to isolate movement of the container from the imaging module and the flow cell module.

[0350] The method of any one of Implementations 13 to 15, wherein the container comprises(i) a top portion for coupling to a sample holder that comprises the plurality of cells and (ii) a bottom portion, wherein the top portion and the bottom portion are configured to move relative to one another to form the container that is substantially sealed.

[0351] The method of any one of Implementations 13 to 16, wherein the bottom portion is linked to an actuation unit configured to direct the relative movement between the top portion and the bottom portion, via a non-rotation mechanism.

[0352] The method of any one of Implementations 13 to 17, wherein the actuation unitis linked to the top portion via a coupling unit, wherein the coupling unit is configured to permit a relative movement between the actuation unit and the bottom portion one or more degrees of freedom.

[0353] The method of any one of Implementations 13 to 18, wherein the container is linked to a guide rail configured to provide a path for the relative movement between the top portion and the bottom portion, wherein the guide rail is configured to move along with the container during the movement of the container.

[0354] The method of any one of Implementations 13 to 19, wherein the cell storage module comprises a pressurizer configured to introduce a positive pressure to at least a portion of the cell storage module.

[0355] The method of any one of Implementations 13 to 20, wherein the cell storage module is configured to direct the container to move (i) sequentially along a plurality of directions and / or(ii) sequentially along a plurality of movement speeds.

[0356] The method of any one of Implementations 13 to 21, wherein the cell storage module, the imaging module, and the flow cell module are disposed within a housing.

[0357] The method of any one of Implementations 13 to 22, wherein the sample unit is a vortexer.

[0358] A method of transferring a sample, the method comprising: (a) receiving a sample comprising cells to flow from a source; and (b) directing the medium from the source and towards a target location via a flow channel, wherein the flow channel comprises a plurality of regions comprising a first region and a second region, wherein: (i) the medium is directed to flow through the first region along a first non -horizontal direction; and (ii) the medium is directed to flow through the second region along a second non -horizontal direction that is different from the first non-horizontal direction.

[0359] The method of Implementation 23 , wherein the first non -horizontal direction may be a direction orthogonal to a largest plane of the source.

[0360] The method of Implementations 23 or 24, wherein the second non -horizontal direction may be a direction orthogonal to a largest plane of the source.

[0361] The method of any one of Implementations 23 to 25, wherein the first non-horizontal direction and the second non-horizontal direction are different.

[0362] The method of any one of Implementations 23 to 26, wherein the first non-horizontal direction is substantially vertical.

[0363] The method of any one of Implementations 23 to 27, wherein the first non-horizontal direction is about 30 degrees relative to a normal axis.

[0364] III. Example of Cell Analysis System

[0365] The systems and methods described herein may be utilized to analyze a cell and / or sort (or partition) the cell from a population of cells. A cell may be directed through a flow channel, and one or more imaging devices (e.g., sensor(s), camera(s)) may capture one or more images / videos of the cell passing through the flow channel. Subsequently, the image(s) / video(s) of the cell may be analyzed in real-time, such that a decision may be made in real-time (e.g., automatically by the machine learning algorithm) to determine (i) whether to sort the cell or not and / or (ii) which sub-channel of a plurality of sub-channels to sort the cell into.

[0366] FIG. 33 shows an example of a cell analysis system 3100, which may be used to capture images of cells, apply machine learning or artificial intelligence to analyze the captured images of the cells, and / or automatically sort the cells based on the analysis. The system 3100 of this example may include a pump 3110 that may be used to drive a sample cell -containing fluid from a reservoir 3112 into a cartridge 3120. The cartridge 3120 may be provided as a modular component, such that the cartridge 3120 may be readily replaced within the system 3100 (e.g., to analyze different batches of sample cells, etc.). The remaining components of the system 3100 that do not get replaced each time the cartridge 3120 is replaced may be collectively referred to as “the instrument.” The instrument of the system 3100 may include a pump 3110. In some cases, the pump 3110 may be considered as a separate component such that a different pump 3110 may be used when a different batch of sample cells is being analyzed. Similarly, the instrument of the system 3100 may include a reservoir 3112. In other cases, the reservoir 3112 may be considered as a separate component such that a different reservoir 3112 may be used when a different batch of sample cells is being analyzed.

[0367] In some cases, the reservoir 3112 comprises a syringe barrel and the pump 3110 comprises a syringe pump. In other cases, the pump 3110 may take any other suitable form,includingbut not limited to a gravity feed, a peristaltic pump, etc. The reservoir 3112 may also take any other suitable form, including but not limited to a vial, tube, etc. The sample in reservoir 3112 may be prepared by fixation and staining and may contain viable cells. The fluid in which the sample cells are contained may include an aqueous solution (e.g., water, buffer, saline, etc.), an oil, or any other suitable fluid.

[0368] The cartridge 3120 may include a flow channel 3122 fluidically coupled with the pump 3110 such that the pump 3110 is operable to drive the sample cell -containing fluid from the reservoir 3112 through the flow channel 3122. The cartridge 3120 may comprise a micro fluidic chip, a flow cell, or any other kind of structure through which fluid may flow and through which cells in the fluid may be imaged. A light source 3130 may generate light for such imaging. In particular, an optical assembly 3132 may direct light from the light source 3130 toward an imaging region of the flow channel 3122. In some examples, the light source 3130 may comprise a source of incoherent white light, such as an arc lamp, etc. In other examples, the light source 3130 may take any other suitable form. An optical assembly 3132 may comprise any suitable number and / or arrangement of lenses and / or other elements as will be apparent to those skilled in the art in view of the teachings herein.

[0369] The light from the light source 3130, as directed by optical assembly 3132, may illuminate cells as the cells pass through the imaging region of the flow channel 3122. An objective lens assembly 3140 may be positioned on the opposite side of the imaging region of flow channel 3122. This objective lens assembly 3140 may magnify the images of cells passing through the imaging region of the flow channel 3122 and direct the magnified images to a camera 3142. The objective lens assembly 3140 and camera 3142 may thus cooperate to capture high resolution images of cells that pass through the imaging region of the flow channel 3122 as illuminated by the light source 3130 and the optical assembly 3132. By way of example only, the objective lens assembly 3140 may provide magnification ranging from approximately 10x to approximately 200 x. In other examples, the objective lens assembly 3140 may provide any other suitable level of magnification. By way of further example only, the camera 3142 may provide an exposuretimerangingfrom approximately 0.001 ps to approximately 1 ms. In other examples, the camera 3142 may provide any other suitable exposure time. In examples described below, the objective lens assembly 3140 and camera 3142 may have an optical axis along the z-dimension.

[0370] In some cases, an image processing module 3144 may receive images from the camera 3142 and processes those received images in real time. The image processing module 3144 may include one or more processors, one or more memories, and various other suitable electrical components. The image processing module 3144 may also include software, firmware and / orhardware. In some cases, the image processing module 3144 may be in communication with a remote server and / or with other components. The one or more processors of image processing module 3144 may comprise one or more of a programmable processor, a programmable controller, a microprocessor, a microcontroller, a graphics processing unit (GPU), a digital signal processor (DSP), a reduced-instruction set computer (RISC), an application specific integrated circuit (ASIC), a field programmable gate array (FPGA), a field programmable logic device (FPLD), a logic circuit, and / or another logic-based device executing various functions including the ones described herein.

[0371] The image processing module 3144 may utilize any of a numb er of techniques to classify or otherwise analyze images of cells captured by camera 3142. For instance, cell image data may be analyzed to plot a plurality of cells into a cell clustering map. The image data may comprise tag-free images of single cells. In other examples, the image data may comprise images of single cells that are tagged (e.g., with a heterologous marker). The image data may be processed to generate a cell morphology map. The cell morphology map may comprise a plurality of morphologically distinct clusters corresponding to different types or states of the cells. In some cases, a classifier (e.g., a cell clustering machine learning algorithm or deep learning algorithm) may be trained by using the cell morphology map. The classifier may be configured to classify a cell image sample based on its proximity, correlation, or commonality with one or more of the morphologically distinct clusters. Thus, in some cases, the classifier may be used to classify 1he sample cell image sample accordingly. This classification may be fully automatic, such that the classification is accomplished solely by software executed through the image processing module 3144, without additional human operator review of the sample cell image. In other examples, the classification may be at least partially manual such that a human operator verifies or otherwise intervenes to inform or approve the classification of the sample cell image.

[0372] Regardless of the technique(s) used by the image processing module 3144 to classify or otherwise analyze images of cells captured by camera 3142, the system 3100 may provide sorting of cells in the cartridge 3120 based on such image processing. In some examples, the cartridge 3120 may include two or more outlet channels from flow channel, and the system 3100 may automatically activate one or more valves to direct an imaged cell through a selected one of those outlet channels based on the image analysis of the cell by the image processing module 3144. For instance, a certain outlet channel may be selected if classification or other analysis by image processing module 3144 determines that the cell appears to be a certain cell type of interest. In other examples, the system 3100 may provide cell sorting in any other suitable fashion and based on any suitable criterion or criteria. In some other examples, the system 3100 may provideimaging and analysis of cells without subsequent sorting of cells. In such examples, the imaged cells may remain contained in the cartridge 3120 after imaging or may exit the cartridge 3120 via an outlet port after imaging.

[0373] As noted above, the remaining components of the system 3100 that do not get replaced each time the cartridge 3120 is replaced may be collectively referred to as “the instrument.” In some examples, the instrument may include a light source 3130, an optical assembly 3132, an objective lens assembly 3140, a camera 3142, and various other components that removably receive the cartridge 3120 and provide any fluidic couplings, etc., that are needed for the system 3100 to perform properly. The instrum entmay further include the image processingmodule 3144. In other examples, the image processing module 3144 may be provided as a separate component (e.g., computer, etc.) that is coupled with the camera 3142 of the instrument to process images captured by the camera 3142. As further noted above, the instrument may further include or omit either or both of the pump 3110 and / or the reservoir 3112.

[0374] A. Example of Cartridge

[0375] FIGS. 34-38 show an example of a form that may be taken by the cartridge 3120. In particular, FIGS. 34-38 show an example of a cartridge 3200 that may be used in the system 3100 to provide imaging, analysis, and sorting of cells flowed through the cartridge 3200. The cartridge 3200 of this example may include a first layer 3300, a second layer 3400, and a third layer 3500. In the present example, each of layers 3300 and 3400 may comprise a polymer (e.g., a siloxane- containing polymer, such as polydimethylsiloxane (PDMS), thermoset plastic, hydrogel, thermoplastic elastomer (TPE), thermoplastic polyurethane (TPU), polycarbonate (PC), polystyrene (PS), poly(methyl methacrylate) (PMMA), cyclic olefin copolymer (COC), etc.). Layer 3500 may comprise a glass (e.g., borosilicate or other silicate glass, etc.) or a polymer (e.g, polycarbonate (PC), polystyrene (PS), poly(methyl methacrylate) (PMMA), cyclic olefin copolymer (COC), etc.). In other examples, each of layers 3300, 3400, and 3500 may comprise any other suitable material or combination of materials. Layers 3300, 3400, and 3500 may be arranged such that a top surface 3302 of layer 3300 may be exposed, a bottom surface 3304 of layer 3300 may be apposed with a top surface 3402 of layer 3400, and a bottom surface 3404 of layer 3400 may be apposed with a top surface 3502 of layer 3500. Layer 3500 may act as a substrate, providing structural support to layers 3300 and 3400, with a bottom surface 3502 of layer 3500 being placed upon a mounting surface (not shown) in an instrument of system 3100.

[0376] As shown in FIGS. 34-36, layer 3300 may be substantially thicker than layer 3400. As also shown in FIGS. 34-36, layer 3300 may include a plurality of fluid input ports 3310, a plurality of fluid output ports 3312, a plurality of pneumatic ports 3320, a plurality of well channels 3340,and a pair of tabs 3306. Ports 3310, 3312, and 3320 may be in the form of channels formed through the entire thickness of layer 3300, such that each port 3310, 3312, and 3320 may be open at the top surface 3302 and the bottom surface 3304. In some examples, fluid input conduits of the system 3100 may be inserted into fluid input ports 3310. Fluid output conduits of system 3100 may be inserted into fluid output ports 3312. Pneumatic input conduits of system 3100 may also be inserted into pneumatic ports 3320. An instrument of system 3100 may thus communicate liquids to cartridge 3200 via fluid input ports 3310, receive liquids from cartridge 3200 via fluid output ports 3312, and / or provide pneumatic pressure to cartridge 3200 via pneumatic ports 3320. In some examples, the conduits of system 3 lOOthat are coupled with ports 3310, 3312, and 3320 may comprise flexible tubes. In other examples, such conduits may take any other suitable form.

[0377] As shown in FIG. 36, bottom surface 3304 of layer 3300 may include a plurality of pneumatic channels 3322, with each pneumatic channel 3322 beingin fluidic communication with a corresponding pneumatic port 3320. Pneumatic channels 3322 may thus receive pneumatic pressure communicated through pneumatic ports 3320. Such pneumatic pressure maybe used to provide deflection of regions of layer 3400 underlying pneumatic channels 3322, such thatthose regions of layer 3400 may be operated as pinch valves to close fluidic communication between layers 3400 and 3500, as described in greater detail below. Each pneumatic channel 3322 may be formed as a recess in bottom surface 3304, such thatpneumatic pressure may be communicated alongthe space defined collectively by top surface 3402 oflayer 3400and eachpneumatic channel 3322. In other words, top surface 3402 of layer 3400 may define a bottom of each pneumatic channel 3322.

[0378] As shown in FIGS. 34-35 and 37, layer 3400 may include a plurality of fluid inputports 3410, a plurality of fluid output ports 3412, and a plurality ofwell openings 3440. Ports 3410 and 3412 and well openings 3440 may be in the form of openings formed through the entire thickness of layer 3400. Fluid input ports 3410 of layer 3400 may be positioned to align with fluid input ports 3310 of layer 3300, such that fluid may be communicated from an instrument of system 3100 through layer 3400 via fluid input ports 3310 and 3410. Fluid output ports 3412 of layer 3400 may be positioned to align with fluid outputports 3312 of layer 3300, such that fluid may be communicated through layer 3400 to an instrument of system 3100 via fluid output ports 3312 and 3412. Well openings 3440 of layer 3400 may be positioned to align with well channels 3340 of layer 3300, such that fluid may be communicated through layer 3400 via well openings 3440 into well channels 3340.

[0379] Well openings 3440, well channels 3340, and top surface 3502 of layer 3500 thus may cooperate to define a plurality of wells, in which particles in fluid may be stored. In someexamples, a removable layer (e.g., tape, film, foil, etc.) or other removable cover may be provided over openings 3440, such as to minimize, or even prevent, evaporation from the underlying wells or contamination of the underlying wells and / or for other reasons. In some such examples, an operator may remove such a layer or cover from a well to retrieve fluid from the well (e.g., via pipette, etc.). Layer 3400 may not include pneumatic openings or ports, such that pneumatic pressure is not communicated through layer 3400.

[0380] As shown in FIG. 37, bottom surface 3404 of lay er 3400 may include a fluidic test input region 3450, a pair of fluidic flush input regions 3460, a pair of fluidic flush output regions 3462, a sample fluid receiving region 3600, a flow control fluid receiving region 3620, a flow drive fluid receiving region 3670, and / or a sample output region 3680. A plurality of fluidic channels 3442, 3452, 3464, 3604, 3662. 3664, and 3672 may be formed as recesses in bottom surface 3304, such that fluid may be communicated along the space defined collectively by top surface 3502 of layer 3500 and each fluidic channel 3442, 3452, 3464, 3604, 3662. 3664, and 3672.

[0381] Fluidic channel 3452 may terminate within layer 3400, such that fluidic channel 3452 may lack any kind of fluidic outlet. In some scenarios, a fluid input conduit may be coupled with the fluid inputport 3310 over fluidic test input region 3450, and fluid may be communicated into fluidic channel 3452 via the fluid input ports 3310 and 3410 over fluidic test input region 3450. This may be done to provide a quality control check to ensure that layers 3400 and 3500 are properly sealed together. In other words, if back pressure quickly accumulates in the fluid input conduitthatis coupled with the fluid inputport 3310 over fluidic testinputregion 3450, such back pressure may indicate that layers 3300 and 3400 are properly sealed together. If such back pressure does not sufficiently accumulate, this may indicate that layers 3400 and 3500 are not properly sealed together. It should be understood that similar quality control testing may be performed with pneumatic pressurizationthrough a pneumatic port 3320 into a pneumatic channel 3322 to ensure that layers 3300 and 3400 are properly sealed together.

[0382] A fluidic channel 3462 may extend between each fluidic flush input regions 3460 and a corresponding fluidic output region 3462. In some scenarios, a fluid input conduit may be coupled with the fluid input port 3310 over fluidic flush input regions 3460, and a fluid output conduit may be coupled with the fluid output port 3312 over fluidic flush output region 3462. Fluid may be communicated into flush input region 3460 via fluid input ports 3310 and 3410 over fluidic flush input region 3460, may flow along fluidic channel 3462, then may exit fluidic output region 3462 via fluid output ports 3312 and 3412 over fluidic output region 3462. This may be done to provide flushing of the fluid conduits that are coupled with these ports 3310 and 3412, such as when a cartridge 3200 has been replaced, to remove any contaminants that might otherwise befound in those fluid conduits.

[0383] A fluidic channel 3604 may extend from sample fluid receiving region 3600 to a junction 3640. A fluid input conduit may be coupled with the fluid input port 3310 over sample fluid receiving region 3600. A fluid containing sample cells may be communicated to junction 3640 via the fluid input ports 3310 and 3410 over sample fluid receiving region 3600 and via fluidic channel 3604. A pair of fluidic channels 3626 may extend from flow control fluid receiving region 3620 to junction 3640, such that fluidic channels 3604, 3626 converge at junction 3640. A fluid input conduit may be coupled with the fluid input port 3310 over flow control fluid receiving region 3620. A flow control fluid may be communicated to junction 3640 via the fluid input ports 3310 and 3410 over flow control fluid receiving region 3620 and via fluidic channels 3626. The fluid from fluidic channels 3604 and 3626 may exit junction 3640 along a sampling channel 3650.

[0384] The fluid that may be communicated along sampling channel 3650 may contain sample cells as noted above. These cells may be imaged by the instrument of system 3100 as also noted above. Such imagingmay be performedasthe cellstraverse sampling channel 3650. Forinstance, FIG. 38 shows an example of an imaging region 3900 that may be positioned along sampling channel 3650. In some examples, light source 3130 and optical assembly 3132 may be positioned over cartridge 3200 to illuminate imaging region 3900. Objective lens assembly 3140 and camera 3142 may be positioned under cartridge 3200 to capture images of cells within imaging region 3900. Otherexamplesmay provide imaging region 3900 at any other suitablelocation or locations along sampling channel 3650. Some examples may also provide a plurality of imaging regions 3900 at different respective positions along sampling channel 3650.

[0385] Sampling channel 3650 may terminate in another junction 3660, which may allow fluid to flow from sampling channel 3650 to either a first outlet channel 3662 or a second outlet channel 3664. Each outlet channel 3662 and 3664 may be selectively opened and closed through pneumatic valving. In particular, a pneumatic channel 3322 may be positioned over each outlet channel 3662 and 3664, in a region just downstream of junction 3660, such that pneumatic pressurization within a selected pneumatic channel 3332 may cause the underlying region of layer 3400 to deform downwardly against top surface 3502 of layer 3500. This may thereby effectively provide a closed valve in that outlet channel 3662 and 3664. When the pneumatic pressure is relieved in the pneumatic channel 3322 over a given outlet channel 3662 and / or 3664, the underlying region of layer 3400 may return to a non-deformed (i.e., flat) state, thereby effectively opening the fluid pathway through that outlet channel 3662 and / or 3664.

[0386] If the pneumatic valve for outlet channel 3662 is opened while the pneumatic valve for outlet channel 3664 is closed, the fluid from sampling channel 3650 may flow through outletchannel 3662 via junction 3660. The fluid path from outlet channel 3662 may then continue through a selected fluidic channel 3442. Each fluidic channel 3442 may provide a fluidic communication path between outlet channel 3662 and a respective well formed by well openings 3440 and well channels 3340. The fluid path between outlet channel 3662 and each fluidic channel 3442 may be selectively opened and closed through pneumatic valving as described above. In particular, a pneumatic channel 3322 may b e positioned over each fluidic channel 3442, in a region just downstream of outlet channel 3662, such that pneumatic pressurization within a selected pneumatic channel 3332 may cause the underlying region of layer 3400 to deform downwardly against top surf ace 3502 of layer 3500. This thereby may effectively provide a closed valve in that fluidic channel 3442. When the pneumatic pressure is relieved in pneumatic channel 3322, the underlying region of layer 3400 may return to a non-deformed (i.e., flat) state, thereby effectively opening the fluid pathway through fluidic channel 3442.

[0387] In some scenarios, it may be beneficial to provide additional assistance to the flow of fluid from outlet channel 3662 through a selected fluidic channel 3442 to reach a selected well channel 3340 via an underlying well opening 3440. To that end, additional fluid may be communicated through a fluid input conduit that is coupled with the fluid input port 3310 over flow drive fluid receiving region 3670. This additional fluid may reach outlet channel 3662 via ports 3310 and / or 3410 over flow drive fluid receiving region 3670 and further via fluidic channel 3672. At the time this additional fluid is communicated to outlet channel 3662, the pneumatic valve between outlet channel 3662 and junction 3660 may be in a closed state. The additional fluid from flow drive fluid receiving region 3670 and fluidic channel 3672 may provide a “boost’ to fluid in outlet channel 3662, thereby further driving the fluid from outlet channel 3662 through the selected fluidic channel 3442 and ultimately to the selected well channel 3340 via an underlying well opening 3440.

[0388] If the pneumatic valve for outlet channel 3664 is opened while the pneumatic valve for outlet channel 3662 is closed, the fluid from sampling channel 3650 may flow through outlet channel 3664 via junction 3660. The fluid path from outlet channel 3664 may reach sample output region 3680. The fluid may exit sample output region 3680 via the fluid output ports 3412 and / or 3312 that are positioned over sample output region 3680. A fluid output conduit may b e coupled with the fluid output port 3412 over sample output region 3680, such that the fluid may exit cartridge 3200 via this fluid output conduit. The fluid output conduit may be further coupled with a reservoir that is either integrated into the instrument of system 3100 or is external to the instrument.

[0389] As noted above, a first set of pneumatic valves may be actuated to allow fluid to flowfrom sample channel 3650 to either outlet channel 3662 or outlet channel 3664. If the fluid flows through outlet channel 3662, a second set of pneumatic valves may be actuated to allow the fluid to flow through a selected fluidic channel 3442 to reach a selected well channel 3340 via an underlying well opening 3440. System 3100 may execute a control algorithm to automatically select which pneumatic valves to activate. This control algorithm may be executed in response to data from image processing module 3144. In other words, image processing module 3144 may classify or otherwise analyze images of cells captured by camera 3142 as the cell-containing fluid passes through imaging region 3900. The pneumatic valves described above may provide sorting of cells in the fluid based on such image processing. For instance, cells of a firsttype (as identified by image processing module 3144) may be routed via pneumatic valving to a first well channel 3340, cells of a second type (as identified by image processing module 3144) may be routed via pneumatic valving to a second well channel 3340, and cells of a third type (as identified by image processing module 3144) may be routed via pneumatic valving to sample output region 3680.

[0390] B. Example of Sorting Features of Cartridge

[0391] As noted above, system 3100 may provide sorting of cells in cartridge 3120 based on analysis performed by image processingmodule 3144 on images of cells captured by camera 3142. As also noted above, sampling channel 3650 may terminate in another junction 3660, which may allow fluid to flow from sampling channel 365 Oto either a first outlet channel 3662 or a second outlet channel 3664. Each outlet channel 3662 and / or 3664 maybe selectively opened and closed through pneumatic valving. In scenarios where fluid is routed to first outlet channel 3662, system 3100 may provide further sorting by selectively activating pneumatic valves along each fluidic channel 3442 that is downstream of first outlet channel 3662. This may thereby direct the fluid (and cell(s) contained in the fluid) to a selected well defined by well openings 3440 and well channels 3340. Thus, the region of cartridge 3120 at junction 3660 and the adjacent pneumatic valves may be viewed as a primary sorting region. By contrast, the region of cartridge 3120 downstream of first outlet channel 3662 (i.e., where first outlet channel 3662 may effectively branch off into the various fluidic channels 3442, with their respective pneumatic valves) may be viewed as a secondary sorting region.

[0392] FIGS. 39-40 show the primary sorting region of cartridge 3120 in greater detail. As shown, a first valve 3692 may be positioned along first outlet channel 3662 while a second valve 3690 may be positioned along second outlet channel 3664. Second valve 3690 may be defined by a portion of a first pneumatic channel 3322a that is positioned directly over second outlet channel 3664. A first pneumatic port 3320a may be pneumatically coupled with first pneumatic channel 3322a such that first pneumatic channel 3322a may be pressurized via first pneumatic port 3320a.First valve 3692 may be definedby a portion of a second pneumatic channel 3322b that may be positioned directly over first outlet channel 3662. A second pneumatic port 3320b may be pneumatically coupled with second pneumatic channel 3322b such that second pneumatic channel 3322b may be pressurized via second pneumatic port 3320b.

[0393] FIGS. 41A-41C show an example of a sequence of operation of valves 3690, 3692 during operation of system 3100) with cartridge 3200. In the state of operation shown in FIG. 41A, neither pneumatic channel 3322a, 3322b may be pressurized, such that each valve 3690 and 3692 may be in an open state. Fluid may thus freely flow through first outlet channel 3662 and second outlet channel 3664.

[0394] In the state of operation shown in FIG. 41B, first pneumatic channel 3322a may be pressurized by pressurized air (or any other suitable fluid) that may be communicated to first pneumatic channel 3322a via first pneumatic port 3320a. This pressurization of first pneumatic channel 3322a may cause layer 3400 to deform and thereby deflect downwardly in the region underneath first pneumatic channel 3322a, such that the bottom surface 3402 of layer 3400 may bear against the top surface 3502 of layer 3500 in the region underneath first pneumatic channel 3322a. This may effectively transition secondvalve 3690to aclosed state, suchthatthe deformed region of layer 3400 under first pneumatic channel 3322a may minimize, and in some instances even prevent, fluid from passing through second outlet channel 3664. First valve 3692 may be in the open state in the state of operation shown in FIG. 41B, such that fluid may freely flowthrough first outlet channel 3662.

[0395] In the state of operation shown in FIG. 41C, second pneumatic channel 3322b may be pressurized by pressurized air (or any other suitable fluid) that may be communicated to second pneumatic channel 3322b via second pneumatic port 3320b. This pressurization of second pneumatic channel 3322b may cause layer 3400 to deform and thereby deflect downwardly in the region underneath second pneumatic channel 3322b, such that the bottom surface 3402 of layer 3400 may bear against the top surface 3502 of layer 3500 in the region underneath second pneumatic channel 3322b. This may effectively transition first valve 3692 to a closed state, such that the deformedregion of layer 3400 under second pneumatic channel 3322b may minimize, and in some instances even prevent, fluid from passing through first outlet channel 3662. Second valve 3690 may be in the open state in the state of operation shown in FIG. 41C, such that fluid may freely flow through second outlet channel 3664.

[0396] Thus, if analysis performed by image processing module 3144 on images of cells captured by camera 3142 reveals that a cell should be directed to first outlet channel 3662 for sorting into one of the wells defined by defined by well openings 3440 and well channels 3340,second valve 3690 may be automatically pressurized and thereby transitioned to a closed state while first valve 3692 may remain in an open state as shown in FIG. 41B. The pneumatic valves formed at the regions where pneumatic channels 3322 overlie fluidic channels 3442 may be selectively actuated in the manner described above with reference to FIGS. 41 A-C to further route the cell along the appropriate fluidic channel 3442 to reach the desired well. In other words, the pneumatic valves formed at the regions where pneumatic channels 3322 overlie fluidic channels 3442 may be structurally configured and operable just like valves 3690 and 3692. If analysis performed by image processing module 3144 on images of cells captured by camera 3142 reveals that a cell should be directed to second outlet channel 3664 for extraction from cartridge 3200 via sample output region 3680, first valve 3692 may be automatically pressurized and thereby transitioned to a closed state while second valve 3690 may remain in an open state as shown in FIG. 41C

[0397] C. Example of Optical Cell Detector

[0398] In some examples, it may be desirable to provide confirmation that a cell has been routed at the primary sorting region with the intended result. In other words, it may be desirable in some examples to confirm that a cell intended to be routed into first outlet channel 3662 at junction 3660 was in fact routed into first outlet channel 3662, or that a cell intended to be routed into second outlet channel 3664 at junction 3660 was in fact routed into second outlet channel 3664. One technique that may be used for such confirmation is optical cell detection.

[0399] FIG. 42 shows an example of an optical emission assembly 4000 and an optical collection assembly 5000 that may cooperate to form an optical cell detectorthat optically detects individual cells passing along first outlet channel 3662 or second outlet channel 3664. As shown in FIG. 40, a first detection region 3696 may be positioned along the path of first outlet channel 3662 in the region between junction 3660 and first valve 3662. A second detection region 3694 may be positioned alongthe path of second outlet channel 3664 in the region between junction 3660 and second valve 3690. In some examples, detection regions 3694 and 3696 may have a center-to-center separation of approximately 250 micrometers. As fluid carrying a cell enters first outlet channel 3662 (e.g., due to closure of second valve 3690), that cell may be optically detected at first detection region 3696. As fluid carrying a cell enters second outlet channel 3664 (e.g, due to closure of first valve 3692), that cell may be optically detected at second detection region 3694.

[0400] As shown in FIG. 42, cartridge 3200 may be positioned in relation to assemblies 4000 and / or 5000 such that detection regions 3694 and / or 3696 are within an emission path (EP) of emission assembly 4000 and within a collection path (CP) of collection assembly 5000. Emission assembly 4000 may thus emit beams of light through each detection region 3694 and / or 3696along emission path (EP), while collection assembly 5000 may collect light from each detection region 3694 and / or 3696 along collection path (CP). In the present example, emission assembly 4000 may generate a first laser spot at first detection region 3696 and a second laser spot at second detection region 3696. Examples of components of assemblies 4000 and 5000 will be described in greater detail below.

[0401] D. Example of Optical Emission Assembly

[0402] As shown in FIGS. 43-44, emission assembly 4000 of this example may include a laser telescope assembly 4100, a Wollaston prism assembly 4200, a prism telescope assembly 4300, a pair of mirror assemblies 4400, 4450, a focus lens assembly 4500, and / or a dual mirror assembly 4600. Assemblies 4100, 4200, 4300, 4400, 4450, 4500, and / or 4600 may all be secured to a frame 4002, such that frame 4002 provides an optical bench. Frame 4002 may be fixed to a larger framework (not shown) of the instrument of system 3100. Assemblies 4100, 4200, 4300, and / or 4400 may all be aligned with each other along the x-dimension. Assemblies 4450, 4500, and / or 4600 may also all be aligned with each other along the x-dimension, though assemblies 4450, 4500 and 4600 may be offsetfrom assemblies 4100, 4200, 4300, 4400 along the z-dimension. Frame 4002 may include an opening 4004, which may provide a clear path for light to pass from mirror assembly 4400 to mirror assembly 4450 as described below.

[0403] As shown in FIGS. 45-46, telescope assembly 4100 of the present example may include a housing 4102 that has a distal opening 4104 and a lateral slot 4106. Telescope assembly 4100 may be secured to frame 4002 via housing4102. An adjustmentpin 4108 may be exposed through lateral slot 4106 and may be operable to translate along the arc of slot 4106. A laser source 4110 may be inserted through a proximal end of housing 4102 and may be fixed relative to housing 4110. Laser source 4110 may be operable to generate a laser beam and emit the laser beam along the x-dimension.

[0404] A waveplate 4120 may be positioned in front of laser source 4110 along the optical path (i.e., along the laser beam in the x-dimension). In the present example, waveplate 4120 may be a half-wave plate. Waveplate 4120 may be structurally configured to alter the polarization of the laser light passing through waveplate 4120. Adjustment pin 4108 may be secured to waveplate 4120 such that adjustment pin 4108 may be manipulated to rotate waveplate 4120 about the x- axis through the angular range of motion permitted by lateral slot 4106. Such rotation of waveplate 4120 about the x-axis may adjust the polarization provided by waveplate 4120 to the laser beam emitted by laser source 4110. For instance, waveplate 4120 may be rotated about the x-axis to achieve a desired intensity of two laser spots on cartridge 3200, with each laser spot being in a respective detection region 3692, 3694 on cartridge 3200. Waveplate 4120 may thusbe adjusted to balance the polarization states of the two beams that may ultimately be emitted by emission assembly 4000. In some examples, waveplate 4120 may have a design wavelength that matches the wavelength of laser source 4110. In some examples, waveplate 4120 maybe a zero order waveplate.

[0405] A neutral density filter 4130 may be positioned in front of waveplate 4120 to reduce the intensity of the light emitted from telescope assembly 4100. In some examples, neutral density filter 4130 may control back-reflections that might otherwise occur in the absence of neutral density filter 4130. In some examples, neutral density filter 4130 may be tilted at an angle of at least approximately 6 degrees relativ...

Claims

CLAIMSWHAT IS CLAIMED IS:

1. A system comprising: a sample unit to receive and hold a container comprising a sample, which sample comprises a plurality of particles in a solution; a tube to travel and extend through a first opening of the sample unit and into the container, wherein the tube is further to direct the plurality of cells to flow out of the container for processing by a microfluidic cartridge; and a pressurizer line to extend through a third opening of the sample unit, wherein the pressurizer line is to direct a pressurizing fluid into the sample unit to thereby pressurize the sample unit.

2. The system of claim 1, wherein the sample unit comprises a sealed interior volume for enclosing the container.

3. The system of claim 1, wherein the tube extends along a first longitudinal axis, and the washing fluid line extends along a second longitudinal axis different from the first longitudinal axis.

4. The system of claim 3, wherein the first longitudinal axis and the second longitudinal axis are substantially perpendicular to one another.

5. The system of claim 1, wherein the first opening is located at a distal end portion of the sample unit, and wherein the second opening is located at a side portion of the sample unit.

6. The system of claim 1, further comprising a washing solution source comprising the washing solution, wherein the washing solution source is to direct the washing solution through the washing fluid line towards the tube within the sample unit.

7. The system of claim 1, further comprising the microfluidic cartridge, wherein the microfluidic cartridge comprises a sorting junction to sort the plurality of particles using at least particle types.

8. The system of claim 1, wherein the sample unit comprises a housing having a plurality of sections that are to move relative to one another along a vertical axis of the sample unit, wherein the first opening and the second opening are disposed over a same section.

9. The system of claim 8, wherein the housing comprises a seal at a contact surface between the plurality of sections.

10. The system of claim 1, wherein the pressurizing fluid is a compressed gas.11 . The system of claim 10, further comprising a pressurizing fluid source comprising the pressurizing fluid, wherein the pressurizing fluid source is in fluidic communication with the pressurizer line.

12. The system of claim 10, wherein the pressurizing fluid is to create pressure within the sample unit so as to direct flow of the plurality of particles from the container and through the tube.

13. The system of claim 1, further comprising a motor unit coupled to the sample unit, wherein the motor unit comprises a rotatable shaft to impart a rotational motion to the container when the container is held within the sample unit, to thereby generate a substantially uniform suspension of particles in the container.

14. The system of claim 13, wherein the motor unit is disposed within the sample unit.

15. The system of claim 13, wherein the motor unit is disposed outside of the sample unit.

16. The system of claim 1, wherein the tube is to travel and extend to an inner volume of the container.

17. The system of claim 1, wherein when the tube is disposed within the inner volume of the container, a distance between (i) a distal end of the tube and (ii) a bottom surface of the container ranges between about 0. 1 millimeters (mm) and about 1 mm.

18. The system of claim 1 , wherein a length of the tube ranges between about 1 inch and about 6 inches.

19. The system of claim 1, wherein an inner diameter of the tube ranges between about 1 / 500 inch and about 1 / 100 inch.

20. The system of claim 1, wherein an outer diameter of the tube ranges between about 1 / 100 inch and about 1 / 10 inch.21 . The system of claim 1, wherein the system further comprises a washing fluid line to extend through a second opening of the sample unit, wherein the washing fluid line is to direct a washing solution to clean the tube within the sample unit in-between two or more sample processing runs.

22. A method for sample processing, the method comprising:(a) moving a container or a sample unit relative to each other thereby causing the container to be secured in the sample unit, wherein the container comprises a sample, which sample comprises a plurality of particles in a solution;(b) directing the plurality of particles to flow through a tube and out of the container for processing by a microfluidic cartridge, wherein the tube extends through a first opening of the sample unit and is disposed in the container; and(c) prior to or subsequent to (b), directing a washing solution to flow through a washing fluid line to clean the tube within the sample unit, wherein the washing fluid line extends through a second opening of the sample unit.

23. The method of claim 22, further comprising, subsequent to (c), replacing the container with a different container comprising a different plurality of particles for processing of the different plurality of particles by the microfluidic cartridge.

24. The method of claim 22, wherein (b) is performed when the container is enclosed within a sealed interior volume of the sample unit.

25. The method of claim 22, wherein in (b) the tube extends through the first opening along a first longitudinal axis, and in (c) the washing fluid line extends along a second longitudinal axis different from the first longitudinal axis.

26. The method of claim 25, wherein the first longitudinal axis and the second longitudinal axis are substantially perpendicular to one another.

27. The method of claim 22, wherein the first opening is located at a distal end portion of the sample unit, and wherein the second opening is located at a side portion of the sample unit.

28. The method of claim 22, wherein (c) comprises directing the washing solution from a washing solution source, through the washing fluid line, and towards the tube disposed within the sample unit.

29. The method of claim 22, further comprising, subsequent to (b), sorting the plurality of particles using at least particle types using a sorting junction of the microfluidic cartridge.

30. The method of claim 22, wherein the sample unit comprises a housing comprising a plurality of sections, wherein the first opening and the second opening are disposed over a same section, and wherein the method further comprises moving the plurality of sections relative to one another along a vertical axis of the sample unit to close or seal the sample unit.31 . The method of claim 30, wherein the housing comprises a seal at a contact surface between the plurality of sections.

32. The method of claim 22, further comprising directing a pressurizing fluid into the sample unit through a pressurizer line to pressurize the sample unit, wherein the pressurizer line extends through a third opening of the sample unit.

33. The method of claim 32, wherein the pressurizing fluid is a pressurized gas.

34. The method of claim 32, wherein the pressurizing fluid is directed from a pressurizing fluid source in fluidic communication with the pressurizer line.

35. The method of claim 32, further comprising using a pressure exerted by the pressurizing fluid to create pressure within the sample unit to direct flow of the plurality of particles from the container and through the tube.

36. The method of claim 22, further comprisingusing a motor unit coupled to the sample unit to impart a rotational motion to the container when the container is held within the sample unit, to generate a substantially uniform suspension of particles in the container.

37. The method of claim 36, wherein the motor unit is disposed within the sample unit.

38. The method of claim 36, wherein the motor unit is disposed outside of the sample unit.

39. The method of claim 22, further comprising, prior to (b), extending the tube to an inner volume of the container.

40. The method of claim 39, wherein, when the tube is disposed within the inner volume of the container, a distance between (i) a distal end of the tube and (ii) a bottom surface of the container ranges between about 0.2 millimeters (mm) and about 1 mm.41 . The method of claim 22, wherein a length of the tube ranges between about 1 inch and about 6 inches.

42. The method of claim 22, wherein an inner diameter of the tube ranges between about 1 / 500 inch and about 1 / 100 inch.

43. The method of claim 22, wherein an outer diameter of the tube ranges between about 1 / 100 inch and about 1 / 10 inch.

44. A system comprising: a platform to hold a container comprising a sample, which sample comprises a plurality of particles in a solution; a top portion disposed above the platform; a vertical actuator coupled to at least one of the platform or the top portion, wherein the vertical actuator is to direct a relative movement between the platform and the top portion, tobringthe platform and the top portion into contact with one another to enclose the container on the platform; a motor unit coupled to the platform, wherein the motor unit comprises a rotatable shaft to impart a rotational motion to the container, to thereby generate a substantially uniform suspension of particles in the container; and a joint that partially couples the top portion and the vertical actuator to each other, wherein the joint is to permit a relative movement between the top portion and the vertical actuator, to thereby de-couple the rotational motion of the container from the vertical actuator.

45. The system of claim 44, wherein the relative movement between the top portion and the vertical actuator has at least two degrees-of-freedom.

46. The system of claim 44, wherein the relative movement between the top portion and the vertical actuator is via at least three degrees-of-freedom.

47. The system of claim 44, wherein the joint comprises a ball-and-socket joint.

48. The system of claim 44, wherein the vertical actuator is coupled to the top portion.

49. The system of claim 44, further comprising a vertical guide rail coupled to the top portion, wherein the vertical guide rail is to limit movement of the top portion along an axis that is different from a vertical axis of the vertical guide rail, to provide an alignment between the top portion and the platform during their relative movement.

50. The system of claim 45, further comprising a base for holding at least the motor unit, wherein the base comprises at least one damper to de-couple rotational motion of the motor unit from the base.51 . The system of claim 50, wherein the at least one damper comprises a plurality of dampers.

52. The system of claim 50, wherein the at least one damper comprises a spring damper.

53. The system of claim 44, wherein the motor unit is coupled to a bottom surface of the platform.

54. A method for sample processing, the method comprising:(a) securing a container on a platform and below a top portion, wherein the container comprises a sample, which sample comprises a plurality of particles in a solution;(b) moving the platform and the top portion relative to one another using a vertical actuator to (i) bring the platform and the top portion into contact with one another and (ii) enclose the container on the platform;(c) imparting a rotational motion to the container using a motor unit comprising a rotatable shaft, to thereby generate a substantially uniform suspension of particles in the container, wherein the top portion and the vertical actuator are partially coupled to one another via a joint, wherein the joint permits a relative movement between the top portion and the vertical actuator, to de-couple the rotational motion of the container from the vertical actuator during (c).

55. The method of claim 54, wherein the relative movement between the top portion and the vertical actuator is via at least two degrees-of-freedom.

56. The method of claim 55, wherein the relative movement between the top portion and the vertical actuator is via at least three degrees-of-freedom.

57. The method of claim 54, wherein the joint comprises a ball-and-socket joint.

58. The method of claim 54, wherein the vertical actuator is coupled to the top portion.

59. The method of claim 54, wherein the top portion is coupled to a vertical guide rail, wherein, in (b), the vertical guide rail (i) limits movement of the top portion along an axis that is different from a vertical axis of the vertical guide rail and (ii) provides an alignment between the top portion and the platform during their relative movement.

60. A system comprising: a sample unit comprising a bottom portion, wherein the bottom portion is disposed within an inner volume of the sample unit and to hold a container comprising a sample, which sample comprises a plurality of particles in a solution;a motor unit coupled to the platform and disposed within the inner volume of the sample unit, wherein the motor unit comprises a rotatable shaft configured impart a rotational motion to the container when the container is disposed over the platform, thereby to generate a substantially uniform suspension of particles in the container; and a pressurizer line to extend through an opening of the sample unit, wherein the pressurizer line is to direct a pressurizing fluid into the sample unit, thereby to pressurize the inner volume of the sample unit.

61. The system of claim 60, wherein the motor unit is coupled to a bottom surface of the platform.

62. The system of claim 60, wherein the pressurizing fluid is a pressurized gas.

63. The system of claim 61, further comprising a pressurizing fluid source comprising the pressurizing fluid, wherein the pressurizing fluid source is in fluidic communication with the pressurizer line.

64. The system of claim 60, further comprising a tube to travel and extend through an additional opening of the sample unit and into the container, wherein the tube is further to direct the plurality of particles to flow out of the container for processing by a microfluidic cartridge.

65. The system of claim 63, wherein a pressure exerted by the pressurizing fluid is sufficient to pressurize the sample unit and direct flow of the plurality of particles from the container and through the tube.

66. The system of claim 64, further comprising the microfluidic cartridge, wherein the microfluidic cartridge comprises a cell sorting junction to sort the plurality of particles using at least particle types.

67. A method for sample processing, the method comprising:(a) securing a container on a platform of a sample unit, wherein the platform is disposed within an inner volume of the receptable, and wherein the container comprises a sample, which sample comprises a plurality of particles in a solution;(b) imparting, using a motor unit coupled to the platform, a rotational motion to the container when the container is disposed over the platform, to generate a substantially uniform suspension of particles in the container, wherein the motor unit is disposed within the inner volume of the sample unit; and(c) directing a pressurizing fluid into the sample unit through a pressurizer line to pressurize the inner volume of the sample unit, wherein the pressurizer line is extended through an opening of the sample unit.

68. The method of claim 66, wherein the motor unit is coupled to a bottom surface of the platform.

69. The method of claim 66, wherein the pressurizing fluid is a pressurized gas.

70. The method of claim 69, wherein the pressurizing fluid is directed from a pressurizing fluid source in fluidic communication with the pressurizer line.

71. The method of claim 66, further comprising directing the plurality of particles to flow through a tube and out of the container for processing by a microfluidic cartridge, wherein the tube is extended through an additional opening of the sample unit and disposed in the container.

72. The method of claim 71 , wherein a pressure exerted by the pressurizing fluid is sufficient to pressurize the sample unit and direct flow of the plurality of particles from the container and through the tube.

73. The method of claim 71, further comprising, subsequent to (b), sorting the plurality of particles using at least particle types using a cell sorting junction of the microfluidic cartridge.

74. A system for sample processing, the system comprising: a platform to hold a container comprising a sample, which sample comprises a plurality of particles in a solution; a motor unit coupled to the platform, wherein the motor unit comprises a rotatable shaft configured impart a rotational motion to the container when the container is disposed over the platform; anda controller coupled to the motor unit, wherein the controller is to direct the motor unit to impart the rotational motion to the container, to generate a substantially uniform suspension of particles in the container, wherein the rotational motion comprises: a first rotation along a direction at a first speed; and a second rotation along a different direction at a second speed, wherein the first speed or the second speed is between about 200 rotations per minute (RPM) and about 1,000 RPM.

75. The system of claim 74, wherein the direction and the different direction are opposite to one another.

76. The system of claim 75, wherein each of the first speed and the second speed is between about 200 RPM and about 1,000 RPM.

77. The system of claim 74, wherein the first speed or the second speed is greater than or equal to about 400 RPM.

78. The system of claim 74, wherein the first speed or the second speed is greater than or equal to about 500 RPM.

79. The system of claim 74, wherein the rotational motion further comprises: a third rotation along the direction at a third speed, wherein the first speed and the third speed are different; or a fourth rotation along the additional direction at a fourth speed, wherein the second speed and the fourth speed are different.

80. The system of claim 79, wherein the rotational motion comprises the third rotation and the fourth rotation.

81. The system of claim 80, wherein the rotational motion comprises, in a sequential order, the first rotation, the third rotation, the second rotation, and the fourth rotation.

82. The system of claim 79, wherein each of the third speed and the fourth speed is between about 200 RPM and about 1,000 RPM.

83. The system of claim 79, wherein each of the third speed and the fourth speed is greater than or equal to about 400 RPM.

84. The system of claim 79, wherein each of the third speed and the fourth speed is greater than or equal to about 500 RPM.

85. A method for sample processing, the method comprising:(a) holding a container on a platform, wherein the container comprises a sample, which sample comprises a plurality of particles in a solution;(b) imparting, using a motor unit coupled to the platform, a rotational motion to the container when the container is disposed over the platform, to generate a substantially uniform suspension of particles in the container, wherein the rotational motion comprises: a first rotation along a direction at a first speed; and a second rotation along a different direction at a second speed, wherein the first speed or the second speed is between about 200 rotations per minute (RPM) and about 1,000 RPM.

86. The method of claim 85, wherein the direction and the different direction are opposite to one another.

87. The method of claim 85, wherein each of the first speed and the second speed is between about 200 RPM and about 1,000 RPM.

88. The method of claim 85, wherein the first speed or the second speed is greater than or equal to about 400 RPM.

89. The method of claim 85, wherein the first speed or the second speed is greater than or equal to about 500 RPM.

90. The method of claim 85, wherein the rotational motion further comprises:a third rotation along the direction at a third speed, wherein the first speed and the third speed are different; or a fourth rotation along the additional direction at a fourth speed, wherein the second speed and the fourth speed are different.91 . The method of claim 90, wherein the rotational motion comprises the third rotation and the fourth rotation.

92. The method of claim 91 , wherein the rotational motion comprises, in a sequential order, the first rotation, the third rotation, the second rotation, and the fourth rotation.

93. The method of claim 90, wherein each of the third speed and the fourth speed is between about 200 RPM and about 1,000 RPM.

94. The method of claim 90, wherein each of the third speed and the fourth speed is greater than or equal to about 400 RPM.

95. The method of claim 90, wherein each of the third speed and the fourth speed is greater than or equal to about 500 RPM.

96. An apparatus comprising: a cartridge receiving region to receive a cartridge; an emission assembly including: a first light source, and a set of optical elements to redirect light from the first light source to illuminate a first fluid channel of the cartridge with a first beam of light and a second fluid channel of the cartridge with a second beam of light; and a collection assembly to receive light transmitted from the emission assembly through the first fluid channel and through the second fluid channel, the collection assembly to generate signals indicating presence of one or more particles in the first fluid channel or in the second fluid channel.

97. The apparatus of claim 96, the first light source comprising a laser.

98. The apparatus of claim 97, the laser comprising a collimated diode laser.

99. The apparatus of any of claims 96 through 98, the first beam of light to illuminate the first fluid channel with an illumination footprint having an elliptical shape, and the second beam of light to illuminate the second fluid channel with an illumination footprint having an elliptical shape.

100. The apparatus of any of claims 96 through 99, the first fluid channel having a width, the second fluid channel having a width, the first beam of light to illuminate an entirety of the width of the first fluid channel, and the second beam of light to illuminate an entirety of the width of the second fluid channel.

101. The apparatus of any of claims 96 through 100, the emission assembly further including a demagnifying telescope interposedbetween the first light source and the set of optical elements.

102. The apparatus of any of claims 96 through 101, the emission assembly further including a half wave plate interposed between the first light source and the set of optical elements.

103. The apparatus of any of claims 96 through 102, the set of optical elements including a Wollaston prism.

104. The apparatus of any of claims 96 through 103, the set of optical elements including a telescope to expand the first beam of light and the second beam of light.

105. The apparatus of claim 104, the set of optical elements including a focusing lens to focus the first beam of light and the second beam of light as expanded by the telescope.

106. The apparatus of any of claims 96 through 105, the set of optical elements including at least two mirrors.

107. The apparatus of claim 106, the at least two mirrors to move via one or both of translational adjustment or tilt adjustment to thereby reposition the first beam of light or the second beam of light relative to the cartridge.

108. The apparatus of any of claims 96 through 107, the set of optical elements to provide separation of the first beam of light from the second beam of light by approximately 250 micrometers.

109. The apparatus of any of claims 96 through 108, the cartridge having a third fluid channel and a fluid junction, the third fluid channel leading into the fluid junction, and the first fluid channel and the second fluid channel each leading out of the fluid junction.

110. The apparatus of claim 109, the cartridge further including a first valve and a second valve, the first valve to selectively permit communication of fluid from the third fluid channel to the first fluid channel via the fluid junction, and the second valve to selectively permit communication of fluid from the third fluid channel to the second fluid channel via the fluid junction.

111. The apparatus of any of claims 96 through 110, the emission assembly further comprising a second light source, the second light source to provide alignment illumination to the cartridge.

112. The apparatus of claim 111, the second light source to illuminate the cartridge with white light.

113. The apparatus of any of claims 96 through 112, further comprising a processor, the processor to process signals from the collection assembly to thereby determine a number of particles communicated through one or both of the first fluid channel or the second fluid channel.

114. The apparatus of any of claims 96 through 113, the collection assembly including a first photosensor to generate a signal indicating presence of one or more particles in the first fluid channel.

115. The apparatus of claim 114, the collection assembly further including a second photosensor to generate a signal indicating presence of one or more particles in the second fluid channel.

116. The apparatus of claim 115, the collection assembly further including a beam splitter, the beam splitter to split light received from the first fluid channel and from the second fluidchannel, the beam splitter to direct light received from the first fluid channel toward the first photosensor, and the beam splitter to direct light received from the second fluid channel toward the second photosensor.

117. The apparatus of claim 116, the beam splitter comprising a polarizing beam splitter, the polarizing beam splitter to split light received from the first fluid channel and from the second fluid channel via polarization.

118. The apparatus of any of claims 96 through 117, the collection assembly including a camera, the camera to capture an image of the first fluid channel and the second image channel to verify alignment of the first beam of light with the first fluid channel and to verify alignment of the second beam of light with the second fluid channel.

119. The apparatus of claim 118, the collection assembly further including a first beam splitter, the first beam splitter to direct light received from the first fluid channel and from the second fluid channel simultaneously along a first path and a second path, the first path leading toward the camera, the second path leading toward a combination of a first photosensor a second photosensor, the first photosensor to generate a signal indicating presence of one or more particles in the first fluid channel, and the second photosensor to generate a signal indicating presence of one or more particles in the second fluid channel.

120. The apparatus of claim 119, the collection assembly further including a second beam splitter, the second beam splitter to split light received along the second path, the second beam splitter to direct light received from the first fluid channel toward the first photosensor, and the second beam splitter to direct light received from the second fluid channel toward the second photosensor.

121. The apparatus of any of claims 119 through 120, the first beam splitter comprising a beam splitter cube.

122. The apparatus of any of claims 119 through 121, the first path being longer than the second path.

123. The apparatus of any of claims 118 through 122, further comprising:a movable cartridge receiving stage, and a processor, the processor to provide movement of the movable cartridge receiving stage in response to an image captured by the camera indicating misalignment of the first beam of light with the first fluid channel or misalignment of the second beam of light with the second fluid channel.

124. A method comprising: activating a single light source; communicating light from the single light source through an emission assembly, the emission assembly including optical elements redirecting light from the first light source to illuminate a first fluid channel of a cartridge with a first beam of light and a second fluid channel of the cartridge with a second beam of light; communicating fluid through the cartridge, the fluid containing particles; and receiving signals from a collection assembly, the collection assembly receiving light transmitted from the emission assembly through the first fluid channel and through the second fluid channel, the received signals indicating presence of one or more particles in the first fluid channel or in the second fluid channel.

125. An apparatus comprising: a cartridge receiving region to receive a cartridge, the cartridge including: a first fluid channel, a second fluid channel, a third fluid channel, a fluid junction, the third fluid channel leading into the fluid junction, the first fluid channel and the second fluid channel each leading out of the fluid junction, a first valve, the first valve to selectively permit communication of fluid from the third fluid channel to the first fluid channel via the fluid junction, and a second valve, the second valve to selectively permit communication of fluid from the third fluid channel to the second fluid channel via the fluid junction; and an optical assembly, to generate signals indicating presence of one or more particles in the first fluid channel, the optical assembly further to generate signals indicating presence of one or more particles in the second fluid channel.

126. A method comprising: driving fluid through a cartridge, the cartridge including: a first fluid channel, a second fluid channel, a third fluid channel, a fluid junction, the third fluid channel leading into the fluid junction, the first fluid channel and the second fluid channel each leading out of the fluid junction, a first valve, the first valve to selectively permit communication of fluid from the third fluid channel to the first fluid channel via the fluid junction, and a second valve, the second valve to selectively permit communication of fluid from the third fluid channel to the second fluid channel via the fluid junction; and using an optical assembly to count one or both of: a number of particles flowing through the first fluid channel, or a number of particles flowing through the second fluid channel.

127. An apparatus comprising: a cartridge receiving region to receive a cartridge; an emission assembly, the emission assembly to illuminate at least one fluid channel of the cartridge with at least one beam of light; and a collection assembly, the collection assembly to receive light transmitted from the emission assembly through the at least one fluid channel, the collection assembly including: a camera, the camera to capture an image of the at least one fluid channel to verify alignment of the at least one beam of light with the at least one fluid channel, at least one photosensor, the at least one photosensor to generate signals indicating presence of one or more particles in the at least one fluid channel, and a beam splitter, the beam splitter to direct light received from the at least one fluid channel simultaneously along a first path and a second path, the first path leading toward the camera, the second path leading toward the at least one photosensor.

128. A method comprising: illuminating at least one fluid channel of a cartridge with at least one beam of light; receiving light transmitted from the emission assembly through the at least one fluid channel;splitting the received light along a first path and along a second path, the first path leading toward a camera, the second path leading toward at least one photosensor; capturing an image with the camera to verify alignment of the at least one beam of light with the at least one fluid channel; and generating one or more signals with the at least one photosensor to indicate presence of one or more particles in the at least one fluid channel.

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