Methods and systems for cell analysis

Abstract

A cartridge has a first layer, a first fluid input port to receive fluid to flow through the cartridge, a first fluid output port to convey fluid from the cartridge, and a first pneumatic port to convey pneumatic pressure to the cartridge. The first fluid input port includes a first opening in the first layer. The first fluid output port includes a second opening in the first layer. The first pneumatic port includes a third opening in the first layer. A first fluid conduit, including a first flexible tube, may be removably inserted into the first fluid input port via the first opening. A second fluid conduit, including a second flexible tube, may be removably inserted into the first fluid output port via the second opening. A first pneumatic conduit, including a third flexible tube, may be removably inserted into the first pneumatic port via the third opening.

Description

METHODS AND SYSTEMS FOR CELL ANALYSISCROSS-REFERENCE

[0001] This application claims the benefit of U.S. Provisional Application No. 63 / 539,614, filed September 21, 2023; U.S. Provisional Application No. 63 / 539,615, filed September 21, 2023; Application Serial No. NL 2036036, filed October 13, 2023; and Application Serial No. NL 2036035, filed October 13, 2023, which applications are incorporated herein by reference.BACKGROUND

[0002] The properties of cells may be analyzed to diagnose diseases and other conditions. Such analysis may include evaluation of cell morphology to determine cell type (e.g., stem cell or differentiated cell) or cell state (e.g., healthy state or disease state). In some cases, cells may be directed through a channel of a cartridge, under fluidic guidance, through a microscope imaging field. The images captured through the microscope maybe processed to evaluate cell morphology.SUMMARY

[0003] The present disclosure provides an apparatus comprising: a cartridge including: a first layer, a first fluid input port to receive fluid to flow through the cartridge, the first fluid input port including a first opening in the first layer, a first fluid output port to convey fluid from the cartridge, the first fluid output port including a second opening in the first layer, and a first pneumatic port to convey pneumatic pressure to the cartridge, the first pneumatic port including a third opening in the first layer; a first fluid conduit to removably insert into the first fluid input port via the first opening, the first fluid conduit including a first flexible tube; a second fluid conduit to removably insert into the first fluid output port via the second opening, the second fluid conduit including a second flexible tube; and a first pneumatic conduit to removably insert into the first pneumatic port via the third opening, the first pneumatic conduit including a third flexile tube. In some embodiments, the first fluid input port provides a friction fit with the first fluid conduit; the first fluid output port providing a friction fit with the second fluid conduit; and the first pneumatic port providing a friction fit with the first pneumatic conduit. In some embodiments, the apparatus further comprises a cartridge support assembly to removably receive the cartridge. In some embodiments, theapparatus further comprises a stage assembly supporting the cartridge support assembly, and the stage assembly moves the cartridge support assembly along one or more dimensions and thereby moves the cartridge along the one or more dimensions. In some embodiments, the cartridge support assembly includes a fluid conduit guide to receive and guide one or both of the first fluid conduit or the second fluid conduit. In some embodiments, the fluid conduit guide includes a head, and the one or both of the first fluid conduit or the second fluid conduit passes through the head. In some embodiments, the head includes a channel having a tapered passageway, and the one or both of the first fluid conduit or the second fluid conduit passes through the tapered passageway. In some embodiments, the fluid conduit allows the one or both of the first fluid conduit or the second fluid conduit to enter the head along one dimension and exit the head along another dimension. In some embodiments, the head rotates about an axis with the one or both of the first fluid conduit or the second fluid conduit disposed in the head. In some embodiments, the apparatus further comprises a first resilient member to resiliently bias the head toward a neutral angular position. In some embodiments, the first resilient member includes a torsion spring. In some embodiments, the first resilient member resiliently biases the head in a first angular direction toward the neutral angular position, and the apparatus further comprises a second resilient member to resiliently bias the head in a second angular direction toward the neutral angular position. In some embodiments, the cartridge support assembly includes a pneumatic conduit guide to receive and guide the first pneumatic conduit. In some embodiments, the pneumatic conduit guide includes a head, and the first pneumatic conduit passes through the head. In some embodiments, the head rotates about an axis with the first pneumatic conduit disposed in the head. In some embodiments, the apparatus further comprises a first resilient member to resiliently bias the head toward a neutral angular position. In some embodiments, the first resilient member includes a torsion spring. In some embodiments, the first resilient member resiliently biases the head in a first angular direction toward the neutral angular position, and the apparatus further comprises a second resilient member to resiliently bias the head in a second angular direction toward the neutral angular position. In some embodiments, the cartridge support assembly includes: a platform, the cartridge fitting on the platform, and a plurality of retainers, the plurality of retainers retaining the cartridge on the platform. In some embodiments, the platform includes an optically transmissive material to allow a camera to image a region of the cartridge through the platform. In some embodiments, at least one retainer of the plurality of retainers is movable relative to the platform to selectively engage the cartridge. In some embodiments, the cartridge support assembly further includes aresilient member to resiliently urge the at least one retainer of the plurality of retainers into engagement with the cartridge. In some embodiments, the first fluid conduit has an open free end and a grip spaced away from the open free end, the open free end fitting in the first fluid input port. In some embodiments, the grip restricts a depth of insertion of the first fluid conduit into the first fluid input port. In some embodiments, the grip includes a magnetic coupling element to magnetically couple with a complementary magnetic coupling element. In some embodiments, the apparatus further comprises a cartridge support assembly to removably receive the cartridge, and the cartridge support assembly includes the complementary magnetic coupling element. In some embodiments, the cartridge further includes a fluidic channel defining at least part of a fluid path between the first fluid input port and the first fluid output port. In some embodiments, the fluidic channel receives a fluid containing particles, the apparatus further including a camera to capture one or more images of one or more of the particles in the fluid as the fluid flows through the fluidic channel. In some embodiments, the cartridge further includes a second layer having a recess defining the fluidic channel.

[0004] The present disclosure provides an apparatus including: a cartridge having a plurality of fluidic ports; a plurality of flexible conduits coupled with the plurality of fluidic ports; a stage assembly to move the cartridge along a plane defined by a first axis and a second axis; and at least one flexible conduit guide having a head, at least one flexible conduit of the plurality of flexible conduits passing through the head, the head rotating about a third axis while the stage assembly moves the cartridge along the plane.

[0005] The present disclosure provides an apparatus including: a cartridge having a plurality of fluidic ports; a plurality of flexible conduits to couple with the plurality of fluidic ports, each flexible conduit including a magnetic coupling element; and a cartridge support assembly to removably receive the cartridge, the cartridge support assembly including one or more magnetic coupling elements, the magnetic coupling elements of the plurality of flexile conduits magnetically coupling with the one or more magnetic coupling elements of the cartridge support assembly. In some embodiments, the magnetic coupling elements of a first flexible conduit of the plurality of flexile conduits magnetically couple with the one or more magnetic coupling elements of the cartridge support assembly when the first flexible conduit is decoupled from the cartridge. In some embodiments, each flexible conduit includes a depth stop feature to restrict a depth of insertion of the flexible conduit into the cartridge.

[0006] The present disclosure provides a method comprising: moving a cartridge along a plane defined by a first axis and a second axis, the cartridge including a first fluidic conduitextending from the cartridge while the cartridge moves along the plane, the first fluidic conduit passing through a head of a fluidic conduit guide, the head rotating about a third axis while the cartridge moves along the plane and while the first fluidic conduit is disposed in the head. In some embodiments, the cartridge further includes a second fluidic conduit extending from the cartridge while the cartridge moves along the plane, the second fluidic conduit passing through the head of a fluidic conduit guide, and the head rotating about the third axis while the cartridge moves along the plane and while the second fluidic conduit is disposed in the head. In some embodiments, moving the cartridge along the plane includes moving the cartridge from a first position to a second position, the cartridge being located under an illumination head in the second position. In some embodiments, the cartridge is positioned for removal from a cartridge support assembly in the first position. In some embodiments, the method further comprises capturing an image of a cell in fluid in the cartridge while the cartridge is in the second position. In some embodiments, the fluidic conduit engages another component of an instrument, thereby inducing tension in the fluidic conduit, as the cartridge moves along the plane, the induced tension in the fluidic conduit causing the head to rotate about the third axis.

[0007] The present disclosure provides an apparatus comprising: a first fluidic path to receive a fluid containing particles; a first sorting region including: a second fluidic path, a third fluidic path, a first junction, the first fluidic path joining the second fluidic path and the third fluidic path at the first junction, a first valve to selectively permit or prevent communication of fluid along the second fluidic path downstream of the first junction, and a second valve to selectively permit or prevent communication of fluid along the third fluidic path downstream of the first junction, a second sorting region including: a fourth fluidic path, a fifth fluidic path, a second junction, the second fluidic path joining the fourth fluidic path and the fifth fluidic path at the second junction, the second junction being downstream of the first valve, a third valve to selectively permit or prevent communication of fluid along the fourth fluidic path downstream of the second junction, and a fourth valve to selectively permit or prevent communication of fluid along the fifth fluidic path downstream of the second junction; an outlet port to extract fluid from the third fluidic path, the outlet port being downstream of the second valve; a first well to receive fluid from the fourth fluidic path, the first well being downstream of the third valve; and a second well to receive fluid from the fifth fluidic path, the second well being downstream of the fourth valve. In some embodiments, the first valve includes a pneumatic channel and a deformable layer, and the pneumatic channel receives pneumatic pressure to deform the deformable layer. In some embodiments, the apparatusfurther comprises a camera to image particles conveyed along the first fluidic path. In some embodiments, the apparatus further comprises a processor, the processor classifying particles from images captured by the camera. In some embodiments, the processor controls operations of the first valve, the second valve, the third valve, and the fourth valve. In some embodiments, the processor selects one or more valves from the first valve, the second valve, the third valve, and the fourth valve for activation in response to classification of particles. In some embodiments, the apparatus further comprises a cartridge, the first fluidic path, the second fluidic path, the third fluidic path, the fourth fluidic path, the fifth fluidic path, the first junction, and the second junction extending along the cartridge. In some embodiments, the first valve, the second valve, the third valve, and the fourth valve are in the cartridge. In some embodiments, the outlet port provides a path for extraction of fluid from the cartridge via the fluidic path. In some embodiments, the first well and the second well are in the cartridge.

[0008] The present disclosure provides an apparatus comprising: a first layer including: a first surface, a second surface, a first fluidic path to receive a fluid containing particles, a second fluidic path, a third fluidic path, and a first junction, the first fluidic path joining the second fluidic path and the third fluidic path at the first junction; a first valve to selectively permit or prevent communication of fluid along the second fluidic path downstream of the first junction; a second valve to selectively permit or prevent communication of fluid along the third fluidic path downstream of the first junction; and a second layer including: a first surface, a second surface overlaying the first surface of the first layer, a first pneumatic channel to pneumatically pressurize the first valve and thereby transition the first valve to a closed state, a second pneumatic channel to pneumatically pressurize the second valve and thereby transition the first valve to a closed state, and a vent passageway, the vent passageway extending from the first surface to the second surface, the vent passageway being open to atmosphere. In some embodiments, the first fluidic path includes a first recess in the first surface, the second fluidic path includes a second recess in the first surface, and the third fluidic path includes a third recess in the first surface. In some embodiments, the first valve includes a region of the second fluidic path adjacent to a corresponding region of the first pneumatic channel, and the second valve includes a region of the third fluidic path adj acent to a corresponding region of the second pneumatic channel. In some embodiments, the first layer deforms in the region of the second fluidic path adj acent to the corresponding region of the first pneumatic channel in response to pneumatic pressurization of the first pneumatic channel, and the second layer deforms in the region of the third fluidic path adjacent to thecorresponding region of the second pneumatic channel in response to pneumatic pressurization of the second pneumatic channel. In some embodiments, the second layer further includes one or more vent channels extending from the vent passageway along the second surface of the second layer, and the one or more vent channels provide ventilation via the vent passageway.

[0009] The present disclosure provides an apparatus comprising: a first layer including: a first surface, a second surface, a first fluidic path to receive a fluid containing particles, and a second fluidic path; a first valve to selectively permit or prevent communication of fluid along the second fluidic path downstream of the first junction; and a second layer including: a first surface, a second surface overlaying the first surface of the first layer, a first pneumatic channel to pneumatically pressurize the first valve and thereby transition the first valve to a closed state, a vent passageway, the vent passageway extending from the first surface to the second surface, the vent passageway being open to atmosphere, and a vent channel extending from the vent passageway along the first surface, the vent channel to provide ventilation via the vent passageway. In some embodiments, the first layer further includes: a third fluidic path, and a first junction, the first fluidic path joining the second fluidic path and the third fluidic path at the first junction. In some embodiments, the apparatus further comprises: a second valve to selectively permit or prevent communication of fluid along the third fluidic path downstream of the first junction; and the second layer further including: a second pneumatic channel to pneumatically pressurize the second valve and thereby transition the first valve to a closed state. In some embodiments, the vent channel is positioned between the first pneumatic channel and the second pneumatic channel. In some embodiments, the first pneumatic channel includes a first recess in the second surface of the second layer, the vent channel includes a second recess in the second surface of the second layer, the first surface of the first layer defining a bottom of the first pneumatic channel, and the first surface of the first layer defining a bottom of the second vent channel.

[0010] The present disclosure provides an apparatus comprising: a first fluidic path to receive a fluid containing particles; a first fluid input port to receive a first conduit to convey fluid containing particles to the first fluidic path; a flow control fluidic path to receive a flow control fluid to focus a flow of the fluid containing particles along the first fluidic path; a second fluid input port to receive a second conduit to convey flow control fluid to the flow control fluidic path; and a flush assembly including: a third fluid input port, a fluid output port, and a fluidic flush channel extending between the third fluid input port and the fluid output port, the flush assembly to removably receive the first conduit and the second conduit,and the flush assembly to permit a flush fluid to be communicated along a fluid path defined by a combination of the first conduit, the second conduit, and the fluidic flush channel, such that the flush fluid enters the flush assembly via the third fluid input port and exits the flush assembly via the fluid output port. In some embodiments, the apparatus further comprises a cartridge, the first fluidic path, the flow control fluidic path, and the fluidic flush channel extending along the cartridge. In some embodiments, the first fluid input port, the second fluid input port, the third fluid input port, and the fluid output port extend into the cartridge. In some embodiments, the first conduit includes a first flexible tube, and the second conduit includes a second flexible tube.

[0011] The present disclosure provides a method comprising: inserting a first conduit into a first fluid input port of a cartridge; inserting a second conduit into a second fluid input of the cartridge; conveying a fluid containing particles along a first fluidic path of the cartridge via the first conduit and the first fluid input port; conveying a second fluid along a second fluidic path of the cartridge via the second conduit and the second fluid input port; removing the first conduit from the first fluid input port; removing the second conduit from the second fluid input port; inserting the first conduit into a third port of the cartridge; inserting the second conduit into a fourth port of the cartridge, the third port and the fourth port being coupled via a first fluidic flush channel to form a first flush assembly; and communicating a flushing fluid through the first conduit and the second conduit and further through the first flush assembly. In some embodiments, the method further comprises capturing images of particles conveyed along the first fluidic path. In some embodiments, the second fluid provides a focus to flow of the fluid containing particles along the first fluidic path. In some embodiments, the third port defines an output port of the first flush assembly, the fourth port defines an input port of the first flush assembly that communicates a flushing fluid through the first conduit and the second conduit and further through the first flush assembly including: communicating the flush fluid into the flush assembly via the first conduit, and communicating the flush fluid out of the flush assembly via the second conduit. In some embodiments, the method further comprises: inserting a fourth conduit into a fifth fluid input port of the cartridge; inserting a fifth conduit into a sixth fluid input port of the cartridge; conveying the fluid containing particles from the first fluidic path to a receptacle via the fourth conduit and the fifth fluid input port; and conveying a third fluid along a third fluidic path of the cartridge via the fifth conduit and the sixth fluid input port. In some embodiments, the method further comprises: removing the fourth conduit from the fifth fluid input port; removing the fifth conduit from the sixth fluid input port; inserting the fourth conduit into a seventh port of the cartridge;insertingthe fifth conduit into an eighth port of the cartridge, the seventh port and the eighth port being coupled via a second fluidic flush channel to form a second first flush assembly; and communicating a flushing fluid through the fourth conduit and the fifth conduit and further through the second flush assembly.

[0012] The present disclosure provides an apparatus comprising: a cartridge, the cartridge including: a first fluidic path to receive a fluid containing particles, the first fluidic path providing an imaging region to capture images of particles conveyed along the first fluidic path, and an optical fiducial region including a plurality of fiducial elements, each fiducial element of the plurality of fiducial elements having a shape that differs from shapes of the other fiducial elements of the plurality of fiducial elements; and a camera having a field of view, the cartridge being positionable to provide the imaging region and the optical fiducial region simultaneously within the field of view. In some embodiments, the plurality of fiducial elements has elliptical shapes, each elliptical shape having a major axis and a minor axis, major axes and minor axes varying among the plurality of fiducial elements. In some embodiments, the apparatus further comprises a processor, the processor processing an image of the optical fiducial region captured by the camera, to thereby determine whether the cartridge is aligned with the camera. In some embodiments, the processor further processes an image of a particle in the fluidic path captured by the camera, to thereby classify the particle. In some embodiments, the camera captures images of particles in the fluidic path at different positions along a height of the fluidic path, and the processor processes the images of particles in the fluidic path at different positions along the height of the fluidic path to thereby determine a focus location. In some embodiments, the height of the fluidic path has a vertical center position, the processor determining the focus location at the vertical center position. In some embodiments, the height of the fluidic path has a vertical center position, the processor determining the focus location at a vertical position below the vertical center position. In some embodiments, the particles include beads. In some embodiments, the cartridge further includes a layer having a first surface and a second surface, and the plurality of fiducial elements includes recesses in the first surface. In some embodiments, the cartridge further includes a focusing region having a focusing feature, the cartridge being positionable to provide the imaging region, the optical fiducial region, and the focusing feature simultaneously within the field of view, and the camera has an optical axis extending along a first dimension, the focusing feature having a depth along the first dimension. In some embodiments, the cartridge further includes a layer having a first surface and a second surface, and the focusing feature includes a recess in the first surface. In some embodiments,the focusing feature has a curved wall, the curved wall providing a cross-sectional area along a first plane that varies along the first dimension, and the first plane being perpendicular to the first dimension. In some embodiments, the apparatus further comprises a processor, the camera capturing images of the focusing feature at different positions along a height of the focusing feature, and the processor processing the images of the focusing feature at different positions along the height of the focusing feature to thereby determine a focus location.

[0013] The present disclosure provides an apparatus comprising: a first layer; a second layer positioned over the first layer, the second layer including: a first fluidic channel, the first fluidic channel including a first portion and a second portion adjacent to the first portion, the first portion having a rectangular cross-section, the second portion having a rounded crosssection; and a third layer positioned over the second layer, the third layer including a first pneumatic channel, the first pneumatic channel applying pneumatic pressure against the second portion of the first fluidic channel to thereby deform the second portion against the first layer and thereby prevent communication of fluid through the first fluidic channel. In some embodiments, the second layer includes resilient material to return the second portion to a non-deform ed state in response to removal of pneumatic pressure in the first pneumatic channel. In some embodiments, the first fluidic channel conveys a fluid containing particles. In some embodiments, the second layer has a first surface adjacent to the first layer and a second surface adjacent to the third layer, and the first fluidic channel includes a recess in the first surface of the second layer. In some embodiments, the third layer has a first surface adj acent to the second layer and a second surface, and the first pneumatic channel includes a recess in the first surface of the third layer. In some embodiments, the first pneumatic channel is positioned over the second portion such that the first pneumatic channel overlaps the second portion. In some embodiments, the first portion is positioned such that the first pneumatic channel does not overlap the first portion. In some embodiments, the first layer further includes: a junction upstream of the first fluidic channel, a second fluidic channel upstream of the junction, and a third fluidic channel downstream of the junction. In some embodiments, the third fluidic channel includes a third portion and a fourth portion adjacent to the third portion, the third portion having a rectangular cross -section, and the fourth portion having a rounded cross-section. In some embodiments, the third layer further includes a second pneumatic channel, the second pneumatic channel applying pneumatic pressure against the fourth portion of the third fluidic channel to thereby deform the fourth portion against the first layer and thereby prevent communication of fluid through the third fluidic channel.BRIEF DESCRIPTION OF THE DRAWINGS

[0014] FIG. 1 depicts a schematic view of an example of a cell analysis system.

[0015] FIG. 2 depicts a perspective view of an example of a cartridge that may be used in examples of the cell analysis system of FIG. 1.

[0016] FIG. 3 depicts an exploded perspective view of the cartridge of FIG. 2.

[0017] FIG. 4 depicts a perspective view of an example underside of a first layer of the cartridge of FIG. 2.

[0018] FIG. 5 depicts a perspective view of an example underside of a second layer of the cartridge of FIG. 2.

[0019] FIG. 6 depicts a top plan view of the cartridge of FIG. 2.

[0020] FIG. 7 depicts a top schematic view of the cartridge of FIG. 2 with a plurality of fluid conduits coupled with the cartridge and a plurality of pneumatic conduits coupled with the cartridge.

[0021] FIG. 8 depicts a perspective view of an example instrument that may be incorporated into the system of FIG. 1.

[0022] FIG. 9 depicts a perspective view of example imaging components and an example cartridge support assembly of the instrument of FIG. 8.

[0023] FIG. 10 depicts a top plan view of the imaging components and cartridge support assembly of FIG. 9.

[0024] FIG. 11 depicts a side elevation view of the imaging components and cartridge support assembly of FIG. 9.

[0025] FIG. 12 depicts a front elevation view of the imaging components and cartridge support assembly of FIG. 9.

[0026] FIG. 13 depicts a perspective view of an example stage assembly of the instrument of FIG. 8.

[0027] FIG. 14 depicts a perspective view of the stage assembly of FIG. 13 with an upper member removed.

[0028] FIG. 15 depicts a right side elevation view of the stage assembly of FIG. 13.

[0029] FIG. 16 depicts a left side elevation view of the stage assembly of FIG. 13.

[0030] FIG. 17 A depicts a top plan view of the stage assembly of FIG. 13 , with the cartridge support assembly of FIG. 9 in an example first position along an x-y plane;

[0031] FIG. 17B depicts a top plan view of the stage assembly of FIG. 13, with the cartridge support assembly of FIG. 9 in an example second position along an x-y plane;

[0032] FIG. 17C depicts a top plan view of the stage assembly of FIG. 13 , with the cartridge support assembly of FIG. 9 in an example third position along an x-y plane;

[0033] FIG. 18 depicts a perspective view of the cartridge support assembly of FIG. 9, with the cartridge of FIG. 2 seated in the cartridge support assembly.

[0034] FIG. 19 depicts a perspective view of the cartridge support assembly of FIG. 9, with the cartridge of FIG. 2 removed from the cartridge support assembly.

[0035] FIG. 20 A depicts an enlarged top plan view of the cartridge support assembly of FIG.9, with the cartridge of FIG. 2 seated in the cartridge support assembly, and with an example cartridge retainer in an example first position.

[0036] FIG. 20B depicts an enlarged top plan view of the cartridge support assembly of FIG. 9, with the cartridge of FIG. 2 seated in the cartridge support assembly, and with the cartridge retainer in an example second position.

[0037] FIG. 21 depicts a perspective view of an example first fluid conduit guide assembly of the cartridge support assembly of FIG. 9.

[0038] FIG. 22 depicts a perspective view of an example head of the first fluid conduit guide assembly of FIG. 21.

[0039] FIG. 23 depicts a cross-sectional view of the head of FIG. 22, taken along line 23 -23 of FIG. 22.

[0040] FIG. 24 depicts a perspective view of an example pneumatic conduit guide assembly of the cartridge support assembly of FIG. 9.

[0041] FIG. 25 depicts an exploded perspective view of the pneumatic conduit guide assembly of FIG. 24.

[0042] FIG. 26 depicts atop plan view of an example head of the pneumatic conduit guide assembly of FIG. 24.

[0043] FIG. 27 depicts a rear elevation view of the head of FIG. 26.

[0044] FIG. 28 depicts a perspective view of an example second fluid conduit guide assembly of the cartridge support assembly of FIG. 9.

[0045] FIG. 29 depicts an exploded perspective view of the second fluid conduit guide assembly of FIG. 28.

[0046] FIG. 30 depicts a perspective view of an example head of the second fluid conduit guide assembly of FIG. 28.

[0047] FIG. 31 depicts a cross-sectional view ofthe head of FIG. 30, taken along line 30-30 of FIG. 30.

[0048] FIG. 32 depicts another cross-sectional view of the head of FIG. 30, taken along line 32-32 of FIG. 30.

[0049] FIG. 33 A depicts a top plan view of the cartridge support assembly of FIG. 9, with the first fluid conduit guide assembly of FIG. 21 at an example first angular position along an x-y plane, with the pneumatic conduit guide assembly of FIG. 24 at an example first angular position along the x-y plane, and with the second fluid conduit guide assembly of FIG. 28 at an example first angular position along the x-y plane.

[0050] FIG. 33B depicts a top plan view of the cartridge support assembly of FIG. 9, with the first fluid conduit guide assembly of FIG. 21 at an example second angular position along an x-y plane, with the pneumatic conduit guide assembly of FIG. 24 at an example second angular position along the x-y plane, and with the second fluid conduit guide assembly of FIG. 28 at an example second angular position along the x-y plane.

[0051] FIG. 33C depicts a top plan view of the cartridge support assembly of FIG. 9, with the first fluid conduit guide assembly of FIG. 21 at the first angular position of FIG. 33 A, with the pneumatic conduit guide assembly of FIG. 24 at an example third angular position along the x-y plane, and with the second fluid conduit guide assembly of FIG. 28 at the first angular position of FIG. 33 A.

[0052] FIG. 34 depicts an enlarged partial view of the cartridge the stage assembly of FIG. 13 with components removed to show routing of a fluid conduit through a fluid conduit guide assembly.

[0053] FIG. 35 depicts a schematic side view of an example fluid conduit that may be used with the cartridge of FIG. 2 and the instrument of FIG. 8.

[0054] FIG. 36 depicts a schematic cross-sectional side view of the fluid conduit of FIG. 35 inserted into a fluid port of the cartridge of FIG. 2.

[0055] FIG. 37 depicts a schematic side view of an example pneumatic conduit that may be used with the cartridge of FIG. 2 and the instrument of FIG. 8.

[0056] FIG. 38 depicts a schematic cross-sectional side view of the pneumatic conduit of FIG. 37 inserted into a pneumatic port of the cartridge of FIG. 2.

[0057] FIG. 39 depicts a schematic view of another example of a cartridge that may be used in examples of the cell analysis system of FIG. 1.

[0058] FIG. 40 depicts another top plan view of the cartridge of FIG. 2.

[0059] FIG. 41 depicts an enlarged view of an example fluid input region of the cartridge of FIG. 2.

[0060] FIG. 42 depicts an enlarged perspective view of the underside of the second layer of FIG. 5, showing part of a sample fluid receiving region of the fluid input region of FIG. 42.

[0061] FIG. 43 depicts an enlarged view of an example mixing structure of the fluid input region of FIG. 41.

[0062] FIG. 44 depicts a cross-sectional view of the mixing structure of FIG. 43, taken along line 9-9 of FIG. 43.

[0063] FIG. 45 depicts a perspective schematic view of a portion of the mixing structure of FIG. 43.

[0064] FIG. 46A depicts a schematic view of fluid flow dynamics in a portion of the fluid input region of FIG. 41 just upstream of the mixing structure of FIG. 43.

[0065] FIG. 46B depicts a schematic view of fluid flow dynamics in a portion of the fluid input region of FIG. 41 just downstream of the mixing structure of FIG. 43.

[0066] FIG. 47 depicts an enlarged top plan view of an example of a primary sorting region of the cartridge of FIG. 2.

[0067] FIG. 48 A depicts a cross-sectional view of the primary sorting region of FIG. 47, taken along line 14-14 of FIG. 47, with an example of a first valve in an open state and an example of a second valve in an open state.

[0068] FIG. 48B depicts a cross-sectional view of the primary sorting region of FIG. 47, taken along line 14-14 of FIG. 47, with the second valve in a closed state and the first valve in the open state.

[0069] FIG. 48C depicts a cross-sectional view of the primary sorting region of FIG. 47, taken along line 14-14 of FIG. 47, with the second valve in the open state and the first valve in a closed state.

[0070] FIG. 49 depicts an enlarged top plan view of an example of a secondary sorting region of the cartridge of FIG. 2.

[0071] FIG. 50 depicts an enlarged top plan view of a region of the cartridge of FIG. 2 including an example set of wells downstream of the secondary sorting region of FIG. 49.

[0072] FIG. 51 depicts an enlarged top plan view of a region of the cartridge of FIG. 2 including examples of venting features.

[0073] FIG. 52 depicts an enlarged perspective view of the underside of the first layer of FIG. 4, showing the venting features of FIG. 51.

[0074] FIG. 53 depicts an enlarged top plan view of a region of another example of a cartridge that may be used in examples of the cell analysis system of FIG. 1, with examples of other venting features.

[0075] FIG. 54A depicts enlarged top plan view of a region of the cartridge of FIG. 2 including example flush ports and example fluid input ports, with a schematic representation of a set of fluid conduits coupled with the fluid input ports.

[0076] FIG. 54B depicts an enlarged top plan view of the region of FIG. 54, with a schematic representation of a set of fluid conduits coupled with the flush ports.

[0077] FIG. 55 A depicts enlarged top plan view of another region of the cartridge of FIG. 2 including other example flush ports, an example fluid input port, and an example fluid output port, with a schematic representation of a set of fluid conduits coupled with the fluid input port and the fluid output port.

[0078] FIG. 55B depicts an enlarged top plan view of the region of FIG. 54, with a schematic representation of a set of fluid conduits coupled with the flush ports.

[0079] FIG. 56 depicts enlarged top plan view of a region of the cartridge of FIG. 2 including an example optical fiducial region.

[0080] FIG. 57 depicts an enlarged top plan view of a first corner of the optical fiducial region of FIG.56.

[0081] FIG. 58 depicts an enlarged top plan view of a second comer of the optical fiducial region of FIG. 56.

[0082] FIG. 59 depicts an enlarged top plan view of a third corner of the optical fiducial region of FIG. 56.

[0083] FIG. 60 depicts an enlarged top plan view of a fourth comer of the optical fiducial region of FIG. 56.

[0084] FIG. 61 depicts an enlarged cross-sectional view of the cartridge of FIG. 2, taken along line 27-27 of FIG. 56, showing example focusing features.

[0085] FIG. 62 depicts a schematic representation of particles flowing along a fluidic channel of the cartridge of FIG. 2, with the particles separated in an example of two vertical regions.

[0086] FIG. 63 depicts an enlarged top plan view of an example sorting region of another example of a cartridge that may be used in examples of the cell analysis system of FIG. 1.

[0087] FIG. 64 A depicts a cross-sectional view of a valve of the sorting region of FIG. 63, taken along line 30-30 of FIG.63, with the valve in an open state.

[0088] FIG. 64B depicts a cross-sectional view of a valve of the sorting region of FIG. 63, taken along line 30-30 of FIG. 63, with the valve in a closed state.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, maybe 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] I. Terminology

[0091] Throughout this specification and the claims whichfollow, 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 any other 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, subcomponents, 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.

[0092] 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 “ / ”.

[0093] 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 asbeing “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.

[0094] 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 encompass both 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.

[0095] 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.

[0096] 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 isdisposed “adjacent” another feature may have portions that overlap or underlie the adjacent feature.

[0097] As used herein in the specification and claims, including as used in the examples and unless otherwise expressly specified, the terms “about” or “approximately” for any numerical values or ranges indicate a suitable dimensional tolerance, or other form of reasonable expected range, that allows the part or collection of components to function for its intended purpose as described herein. More specifically, “about” or “approximately” may refer to the range of values that are within ±10% of the recited value (e.g., “about 100” may refer to the range of values from 90 to 110, including 90, 110, 100, and all other values within the range of 90 and 110). Any numerical values given herein should also be understood to include about or approximately that value unless the context indicates otherwise. For example, if the value “10” is disclosed, then “about 10” is also disclosed. Any numerical range recited herein is intended to include all sub-ranges subsumed therein. The terms “approximately” and “about” are thus utilized herein to represent the degree by which a quantitative representation may vary from a stated reference without resulting in a change in the basic function of the subject matter at issue.

[0098] The term “substantially” is also utilized herein to represent the degree by which a quantitative representation may vary from a stated reference without resulting in a change in the basic function of the subject matter at issue. The term “substantially” shall therefore be understood to include a range of conditions or results that provide a functional equivalent to an explicitly stated condition or result. For instance, if a task is “substantially complete,” the result of the task having been substantially completed is functionally equivalent to the result that would have been achieved if the task had been perfectly completed. As another non- limiting example, a component that is “substantially straight” or “substantially flat,” an apparatus including a component that is “substantially straight” or “substantially flat” may provide a result or effect that is functionally equivalent to a result or effect that would be achieved by the same apparatus including the same component in a perfectly straight or perfectly flat configuration. The range implied by the term “substantially” should also be read to include the perfect result that is within that range. 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 other form of reasonable expected range, that allows a part or collection of components to function for its intended purpose as described herein.

[0099] 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.).

[0100] It is also understood that when a value is disclosed that “less than or equal to” the value, “greater than or equal to the value,” and possible ranges between values are also disclosed, as appropriately understood by the skilled artisan. For example, if the value “X” is disclosed the “less than or equal to X” as well as “greater than or equal to X” (e.g., where X is a numerical value) is also disclosed. It is also understood that the throughout the application, data is provided in a number of different formats, and that this data, represents endpoints and starting points, and ranges for any combination of the data points. For example, if a particular data point “10” and a particular data point “15” are disclosed, it is understood that greater than, greater than or equal to, less than, less than or equal to, and equal to 10 and 15 are considered disclosed as well as between 10 and 15. It is also understood that each unit between two particular units are also disclosed. For example, if 10 and 15 are disclosed, then 11, 12, 13, and 14 are also disclosed.

[0101] 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 / element from 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 not intended to impose numerical requirements on their objects.

[0102] 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.

[0103] 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.

[0104] 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 may comprise one or more aspects of a cell’s appearance, such as, for example, shape, size, arrangement, form, structure, pattern(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 may include, but are not limited to, circular, elliptic, 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). In other examples, the morphological feature of the cell may not and need not require any treatment to be visualized in an image or video.

[0105] The terms “unstructured” or “unsorted,” as used interchangeably herein, generally refers to a mixture of cells (e.g., an initial mixture of cells) that is not substantially sorted (or rearranged) into separate partitions. An unstructured population of cells may 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 may be a random (or randomized) mixture of the at least two types of cells. The cells as disclosed herein may be viable cells. A viable cell, as disclosed herein, may be a cell that is not undergoing necrosis or a cell that is notin an early or late apoptotic state. In other examples, the cells may not and need not be viable (e.g., fixed cells).

[0106] The term “resilient” as used herein refers to a material property where the material has shape memory and stiffness such that it is structurally biased toward a neutral shape or structural arrangement. As an example, a resilient member may have a resilient bias toward a neutral shape or structural arrangement where the resilient member is straight along a central longitudinal axis. That same resilient member may be deformed relative to the neutral shape or structural arrangement, such as by being bent away from that central longitudinal axis, in response to a force (e.g., when a force is imparted on the resilient member, where the force has a directional component that is transverse to the central longitudinal axis). While the resilient member is being deformed relative to the neutral shape in response to the force, the resilient member may be under stress whereby the resilient property of the material of theresilient member generates a force in a direction that is opposite to the force that is causing the deformation of the resilient member. In other words, the resilient property of the material of the resilient member may impart a mechanical bias urging the resilient member back toward the neutral shape or structural arrangement. After the force causing the deformation of the resilient member is removed, the resilient bias of the material of the resilient member may cause the resilient member to return to (or at least toward) the neutral shape or structural arrangement. While the foregoing example provides a straight configuration as a neutral shape or structural arrangement, other examples of resilient members may have other kinds of neutral shapes or structural arrangements.

[0107] II. Example of Cell Analysis System

[0108] 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.

[0109] FIG. 1 shows an example of a cell analysis system (100), which may be used to capture images of cells, and apply machine learning or artificial intelligence to analyze the captured images of the cells, and automatically sort the cells based on the analysis. System (100) of this example may include a pump (110) that may be operable to drive a sample cellcontaining fluid from a reservoir (112) into a cartridge (120). Cartridge (120) may be provided as a modular component, such that cartridge (120) may be readily replaced within system (100) (e.g., to analyze different batches of sample cells, etc.). The remaining components of system (100) that do not get replaced each time cartridge (120) is replaced may be collectively referred to as “the instrument.” The instrument of system (100) may include pump (110); or pump (110) may be considered as a separate component such that a different pump (110) may be used when a different batch of sample cells is being analyzed. Similarly, the instrument of system (100) may include reservoir (112); or reservoir (112) may be considered as a separate component such that a different reservoir (112) may be used when a different batch of sample cells is being analyzed.

[0110] In some embodiments, reservoir (112) comprises a syringe barrel; and pump (110) comprises a syringe pump. In other embodiments, pump (110) may take any other suitableform, including but not limited to a gravity feed, a peristaltic pump, etc. Reservoir (112) may also take any other suitable form, including but not limited to a vial, tube, etc. The sample in reservoir (112) may be preparedby 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.

[0111] Cartridge (120) may include a flow channel (122) fluidically coupled with pump (110), such that pump (110) maybe operable to drive the sample cell-containing fluid from reservoir (112) through flow channel (122). Cartridge (120) may comprise a microfluidic 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 (130) may generate light for such imaging. In particular, an optical assembly (132) may direct light from light source (130) toward an imaging region of flow channel (122). In some embodiments, light source (130) may comprise a source of incoherent white light, such as an arc lamp, etc. In other examples, light source (130) may take any other suitable form. Optical assembly (132) 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.

[0112] The light from light source (130), as directed by optical assembly (132), may illuminate cells as the cells pass through the imaging region of flow channel (122). An objective lens assembly (140) may be positioned on the opposite side of the imaging region of flow channel (122), may magnify the images of cells passing through the imaging region of flow channel (122), and may direct the magnified images to a camera (142). Objective lens assembly (140) and camera (142) thus may cooperate to capture high resolution images of cells that pass through the imaging region of flow channel (122), as illuminated by light source (130) and optical assembly (132). By way of example only, objective lens assembly (140) may provide magnification ranging from approximately 10x to approximately 200*. In other examples, objective lens assembly (140) may provide any other suitable level of magnification. By way of further example only, camera (142) may provide an exposure time ranging from approximately 0.001 ps to approximately 1 ms. In other examples, camera (142) may provide any other suitable exposure time. In some example, objective lens assembly (140) and camera (142) have an optical axis along the z-dimension.

[0113] An image processing module (144) may receive images from camera (142) and processes those received images in real time. Image processing module (144) may include one or more processors, one or more memories, and various other suitable electrical components. Image processing module (144) may also include software, firmware and / orhardware. In some embodiments, image processing module (144) is in communication with a remote server and / or with other components. The one or more processors of image processing module (144) 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.

[0114] Image processing module (144) may utilize any of a number of techniques to classify or otherwise analyze images of cells captured by camera (142). 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 the sample cell image sample accordingly. This classification may be fully automatic, such that the classification is accomplished solely by software executed through image processing module (144), without additional human operator review of the sample cell image. In some other examples, the classification is at least partially manual such that a human operator verifies or otherwise intervenes to inform or approve the classification of the sample cell image.

[0115] Regardless of the technique(s) usedby image processing module (144) to classify or otherwise analyze images of cells captured by camera (142), system (100) may provide sorting of cells in cartridge (120) based on such image processing. In some embodiments, cartridge (120) may include two or more outlet channels from flow channel, and system (100) 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 image processing module (144). For instance, a certain outlet channel may be selected if classification or other analysis by image processing module (144) determines that the cell appears to be a certain cell type of interest. In other examples, system (100) may provide cell sorting in any other suitablefashion; and based on any suitable criterion or criteria. In some other examples, system (100) provides imaging and analysis of cells without subsequent sorting of cells. In such examples, the imaged cells may remain contained in cartridge (120) after imaging or may exit cartridge (120) via an outlet port after imaging.

[0116] As noted above, the remaining components of system (100) that do not get replaced each time cartridge (120) is replaced may be collectively referred to as “the instrument.” In some embodiments, the instrument includes light source (130), optical assembly (132), objective lens assembly (140), camera(142), and various other components that removably receive cartridge (120) and provide any fluidic couplings, etc., that are needed for system (100) to perform properly. The instrument may further include image processing module (144). In other examples, image processing module (144) may be provided as a separate component (e.g., computer, etc.) that is coupled with camera (142) of the instrument to process images captured by camera (142). As further noted above, the instrument may further include or omit either or both of pump (110) and / or reservoir (112).

[0117] III. Example of Cartridge

[0118] FIGS. 2-6 show an example of a form that may be taken by cartridge (120). In particular, FIGS. 2-6 show an example of a cartridge (200) that may be used in system (100) to provide imaging, analysis, and sorting of cells flowed through cartridge (200). Cartridge (200) of this example may include a first layer (300), a second layer (400), and a third layer (500). In the present example, each of layers (300, 400) 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 (500) 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 layer (300, 400, 500) may comprise any other suitable material or combination of materials. Layers (300, 400, 500) may be arranged such that a top surface (302) of layer (300) is exposed. A bottom surface (304) of layer (300) may be apposed with a top surface (402) of layer (400), and a bottom surf ace (404) of lay er (400) is apposed with a top surface (502) of layer (500). Layer (500) may act as a substrate, providing structural support to layers (300, 400), with a bottom surface (502) of layer (500) being placed upon a mounting surface (not shown) in an instrument of system (100).

[0119] As shown in FIGS. 2-4, layer (300) may be substantially thicker than layer (400). As also shown in FIGS. 2-4, layer (300) may include a plurality of fluid input ports (310), a plurality of fluid output ports (312), plurality of pneumatic ports (320), and a plurality of pneumatic channels (322), and a pair of tabs (306). Ports (310, 312, 320) may be in the form of channels formed through the entire thickness of layer (300), such that each port (310, 312, 320) may be open attop surface (302) and at bottom surface (304). In some embodiments, fluid input conduits of system (100) may be inserted into fluid input ports (310), fluid output conduits of system (100) are inserted into fluid output ports (312), and pneumatic input conduits of system (100) are inserted into pneumatic ports (320). An instrument of system (100) may thus communicate liquids to cartridge (200) via fluid input ports (310), receive liquids from cartridge (200) via fluid output ports (312), and provide pneumatic pressure to cartridge (200) via pneumatic ports (320). In some embodiments, the conduits of system (100) that are coupled with ports (310, 312, 320) comprise flexible tubes. In other examples, such conduits may take any other suitable form.

[0120] As shown in FIG. 4, bottom surface (304) of layer (300) may include a plurality of pneumatic channels (322), with each pneumatic channel (322) being in fluidic communication with a corresponding pneumatic port (320). Pneumatic channels (322) thus may receive pneumatic pressure communicated through pneumatic ports (320). Such pneumatic pressure may be used to provide deflection of regions of layer (400) underlying pneumatic channels (322), such that those regions of layer (400) may be operated as pinch valves to close fluidic communication between layers (400, 500) as described in greater detail below. Each pneumatic channel (322) may be formed as a recess in bottom surface (304), such that pneumatic pressure maybe communicated along the space defined collectively by top surface (402) of layer (400) and each pneumatic channel (322). In other words, top surface (402) of layer (400) may define a bottom of each pneumatic channel (322).

[0121] As shown in FIGS. 2-3 and 5, layer (400) may include a plurality of fluid input ports (410), a plurality of fluid output ports (412), and a plurality of well openings (440). Ports (410, 412) and well openings (440) maybe in the form of openings formed through the entire thickness of layer (400). Fluid input ports (410) of layer (400) may be positioned to align with fluid input ports (310) of layer (300), such that fluid may be communicated from an instrument of system (100) through layer (400) via fluid input ports (310, 410). Fluid output ports (412) of layer (400) may be positioned to align with fluid output ports (312) of layer (300), such that fluid maybe communicated through layer (400) to an instrument of system (100) via fluid output ports (312, 412). Well openings (440) of layer (400) may be positionedto align with well channels (340) of layer (300), such that fluid may be communicated through layer (400) via well openings (440) into well channels (340).

[0122] Well openings (440), well channels (340), and top surface (502) of layer (500) thus may cooperate to define a plurality of wells (750, 752, 754, 756, 758, 760), in which particles in fluid may be stored. In some embodiments, a removable layer (e.g., tape, film, foil, etc.) or other removable cover is provided over openings (440), such as to minimize, and in some instances even prevent, evaporation from the underlying wells, to minimize, and in some instances even prevent, 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.). It should be understood that layer (400) may not include pneumatic openings or ports in this example, such that pneumatic pressure is not communicated through layer (400).

[0123] As shown in FIG. 5, bottom surface (404) of layer (400) may include a fluidic test input region (450), a pair of fluidic flush input regions (460), a pair of fluidic flush output regions (462), a sample fluid receiving region (600), a flow control fluid receiving region (620), a flow drive fluid receiving region (670), and a sample output region (680). A plurality of fluidic channels (442, 452, 464, 604, 662. 664, 672) may be formed as recesses in bottom surface (304), such that fluid may be communicated along the space defined collectively by top surface (502) of layer (500) and each fluidic channel (442, 452, 464, 604, 662. 664, 672).

[0124] Fluidic channel (452) may terminate within layer (400), such that fluidic channel (452) may lack any kind of fluidic outlet. In some scenarios, a fluid input conduit may be coupled with the fluid input port (310) over fluidic test input region (450), and fluid may be communicated into fluidic channel (452) via the fluid input ports (310, 410) over fluidic test inputregion (450). This may be doneto provide a quality control check, to ensure that layers (400, 500) are properly sealed together. In other words, if back pressure quickly accumulates in the fluid input conduit that is coupled with the fluid input port (310) over fluidic test input region (450), such back pressure may indicate that layers (300, 400) are properly sealed together. If such back pressure does not sufficiently accumulate, this may indicate that layers (400, 500) are not properly sealed together. It should be understood that similar quality control testing may be performed with pneumatic pressurization through a pneumatic port (320) into a pneumatic channel (322), to ensure that layers (300, 400) are properly sealed together.

[0125] A fluidic channel (464) may extend between each flush input regions (460) and a corresponding flush output region (462). In some scenarios, a fluid input conduit may be coupled with the fluid input port (310) over flush input regions (460), and a fluid output conduit may be coupled the fluid output port (312) over flush output region (462). Fluid may be communicated into flush input region (460) via fluid input ports (310, 410) over flush input region (460), may flow along fluidic channel (464), then may exit flush output region (462) via fluid output ports (312, 412) over flush output region (462). This may be done to provide flushing of the fluid conduits that are coupled with these ports (310, 412), such as when a cartridge (200) has been replaced, to remove any contaminants that might otherwise be found in those fluid conduits. The combination of a flush input region (460), a fluidic channel (464) a flush output region (462), fluid input port (310), and fluid outlet port (312) may be collectively understood to form a flush assembly. In some embodiments, the fluid communicated through the flush assembly includes a bio -compatible fluid such as an aqueous based buffer fluid or liquid culture medium; or a bio -compatible oil based fluid. In other examples, other kinds of flush fluid may be used.

[0126] A fluidic channel (604) may extend from sample fluid receiving region (600) to a junction (640). A fluid input conduit may be coupled with the fluid input port (310) over sample fluid receiving region (600), and a fluid containing sample cells may be communicated to junction (640) via the fluid input ports (310, 410) over sample fluid receiving region (600) and via fluidic channel (604). A pair of fluidic channels (626) may extend from flow control fluid receiving region (620) to junction (640), such that fluidic channels (604, 626) may converge at junction (640). A fluid input conduit may be coupled with the fluid input port (310) over flow control fluid receiving region (620), and a flow control fluid may be communicated to junction (640) via the fluid input ports (310, 410) over flow control fluid receiving region (620) and via fluidic channels (626). The fluid from fluidic channels (604, 626) exits junction (640) along a sampling channel (650).

[0127] The fluid communicated along sampling channel (650) may contain sample cells as noted above. These cells may be imaged by the instrument of system (100) as also noted above. Such imaging may be performed as the cells traverse sampling channel (650). For instance, FIG. 6 shows an example of an imaging region (652) that may be positioned along sampling channel (650). In some embodiments, light source (130) and optical assembly (132) are positioned over cartridge (200) to illuminate imaging region (652); while objective lens assembly (140) and camera (142) are positioned under cartridge (200) to capture images of cells within imaging region (652). Other examples may provide imaging region (652) atany other suitable location or locations along sampling channel (650). Some examples may also provide a plurality of imaging regions (652) at different respective positions along sampling channel (650).

[0128] FIG. 7 shows an example of an arrangement where fluid conduits (802) are coupled with fluid input ports (310), a fluid conduit (802) is coupled with fluid output port (312), and pneumatic conduits (804) are coupled with pneumatic ports (320). As described in greater detail below, each fluid conduit (802) may comprise a flexible tube that is inserted into the corresponding port (310, 312), with the material of layer (300) providing a friction fit to retain and seal each fluid conduit (802) relative to cartridge (200). Similarly, each pneumatic conduit (804) may comprise a flexible tube that is inserted into the corresponding port (320), with the material of layer (300) providing a friction fit to retain and seal each pneumatic conduit (804) relative to cartridge (200).

[0129] In the example shown in FIG. 7, a fluid conduit (802) is inserted into fluid input port (310) over sample fluid receiving region (600) and is further coupled with a source (810) of a fluid containing one or more sample cells. For instance, source (810) may constitute pump (110) and reservoir (112) of system (100) as described above. Another fluid conduit (802) may be inserted into fluid input port (310) over flow control fluid receiving region (620) and is further coupled with a source (812) of flow control fluid. In some embodiments, the flow control fluid includes a buffer fluid. In some examples the flow control fluid further includes beads; while in other examples the flow control fluid does not include beads. The flow control fluid may include a bio-compatible fluid. In some embodiments, the flow control fluid has a viscosity that differs from the viscosity of the fluid containing sample cells. In other examples, other kinds of fluid may be used for flow control fluid.

[0130] Another fluid conduit (802) may be inserted into fluid input port (310) over flow control flow drive fluid receiving region (670) and may be further coupled with a source (814) of flow drive fluid. In some embodiments, the same fluid that is communicated to flow control fluid receiving region (620) for flow control in cartridge (200) is also communicated to flow drive fluid receiving region (670) to boost fluid flow through and past secondary sorting region (204). In some such examples, source (812) and source (814) may be the same source. In some embodiments, the additional boosting fluid provided via flow drive fluid receiving region (670) may include any bio-compatible fluid, such as liquid culture medium, cell lysis solution, or an oil based fluid. In other examples, other kinds of fluid may be used. In the present example, another fluid conduit (802) is inserted into fluid output port (312) over sample output region (680) and is further coupled with a receptacle (816) (e.g., vial,tube, etc.) that receives fluid communicated from cartridge (200) via sample output region (680).

[0131] As also shown in FIG. 7, each pneumatic conduit (804) may be coupled with a respective pneumatic port (320); and all pneumatic conduits (804) are also coupled with a pneumatic pressure source (820). Pneumatic pressure source (820) may be operable to provide pneumatic pressure in the form of pressurized air or some other gas. Pneumatic pressure source (820) may include various features such as a pump, a manifold, a set of valves (e.g., to selectively provide pneumatic pressure to different pneumatic conduits (802)), and / or other features. In some embodiments, pneumatic pressure source (820) is integrated into the instrument of system (100). In some other examples, the instrument of system (100) is pneumatically coupled with an otherwise separate pneumatic pressure source (820).

[0132] IV. Example of Instrument

[0133] As noted above system (100) may include an instrument, which may removably receive cartridge (200) and may include various other features of system (100) as described herein. FIG. 8 shows one example of an instrument (900) that may be part of system (100). Instrument (900) of this example may comprise a support frame (902) on a base (904), a microscope assembly (910), an illumination head (912), a stage assembly (1000), and a cartridge support assembly (1100). Cartridge support assembly (1100) may be structurally configured to removably receive cartridge (200). Stage assembly (1000) may be operable to move cartridge support assembly (1100) (with cartridge (200)) along the x-y plane.Microscope assembly (910) may be operable to capture images of cells or other particles flowing along sampling channel (650) as described above, with illumination head (912) providing illumination of at least imaging region (652) of cartridge. Microscope assembly (910) may include the components and functionality of at least objective lens assembly (140) and camera (142) as described above. Illumination head (912) may include at least some of the components and functionality of optical assembly (132); and may be optically coupled with (or integrate) light source (130). It should be understood that instrument (900) may further include various other components not shown in FIG. 8, including but not limited to an outer housing, etc.

[0134] As best seen in FIGS. 9-12, when instrument (900) is arranged to allow microscope assembly (910) to capture images of cells or other particles flowing along sampling channel (650), illumination head (912) may be positioned directly over cartridge (200) and in close proximity to cartridge (200). This may provide a reduced length of the optical path between illumination head (912) and imaging region (652), which may in turn provide opticalefficiency in the illumination of imaging region (652). However, this position and proximity of illumination head (912) in relation to cartridge (200) may, In some embodiments, warrant movement of cartridge (200) away from illumination head (912) along the x-y plane to facilitate removal of cartridge (200) from instrument (900). In some examples where cartridge (200) is movable relative to illumination head (912) along the x-y plane, and where other components (e.g., fluid conduits (802) and / or pneumatic conduits (804) as described above in the context of FIG. 7) are inserted into cartridge (200), it may be desirable in some examples to avoid having any features of instrument (900) interfering with such components inserted into cartridge (200) as cartridge (200) moves along the x-y plane. For instance, in some examples some interfering components of instrument (900) may tend to create tension in conduits (802, 804), which may create a risk of conduits (802, 804) being pulled out of ports (310, 320) of cartridge (200), of conduits (802, 804) kinking or rupturing, of conduits (802, 804) snagging, or other results that might not be desirable in some examples.

[0135] The following description provides examples of features of instrument (900) that may allow cartridge (200) to move along the x-y plane relative to illumination head (912), thereby facilitating replacement of cartridge (200) in cartridge support assembly (1100) while still providing a reduced distance between illumination head (912) and imaging region (652) while fluid containing cells or other particles flows along sampling channel (650). The following description also provides examples of features of instrument (900) that may reduce, and in some cases may prevent, a risk of interference between components of instrument (900) and conduits that are inserted into cartridge (200) as cartridge (200) moves along the x- y plane.

[0136] A. Example of Cartridge Stage Assembly

[0137] As shown in FIG. 8, stage assembly (1000) maybe secured to frame assembly (902), which may be secured to base (904). Frame assembly (902) and base (904) thus may support stage assembly (1000) in this example. FIGS. 13-17C show examples of features and operability of stage assembly (1000) in further detail. As shown in FIG. 13, stage assembly (1000) may include an upper member (1010), and a lower member (1020), with a plurality of struts (1030) extending between members (1010, 1020) to thereby support upper member (1010) above lower member (1020) along the z-dimension. Upper member (1010) may include a rigid plate in this example, though upper member (1010) may include any other suitable components. Similarly, lower member (1020) may include a rigid plate in this example, though lower member (1020) may include any other suitable components.Cartridge support assembly (1100) may be positioned in the space between members (1010,1020) along the z-dimension; and maybe movable within this space along the x-y dimension as will be described in greater detail below.

[0138] As best seen in FIGS. 14-16, stage assembly (1000) may further include a pair of y- drive assemblies (1040). Y-drive assemblies (1040) maybe positioned at each side of upper member (1010) along the x-dimension. Each y-drive assembly (1040) may include an actuator (1042) and a rail assembly (1044) extending distally from actuator (1042). Each rail assembly (1044) may extend along the y-dimension, from one end of upper member (1010) along the y-dimension to the other end of upper member (1010) along the y-dimension.

[0139] As shown in FIGS. 15-16, cartridge support assembly (1100) may be coupled with each rail assembly (1044) via a respective bracket (1046). In some embodiments, one or more other components (e.g., one or more components of x-drive assembly (1050), as described below) maybe interposed between cartridge support assembly (1100) and brackets (1046). It should be understood that a strut (1030) may be omittedin FIG. 15 and in FIG. 16 to provide an unobstructed view of each bracket (1046). In some embodiments, each actuator (1042) may include a motor, each rail assembly (1044) may include a screw gear, and an upper portion of each bracket (1046) may include a nut or may be secured to a nut. In some such examples, the motor of actuator (1042) drives rotation of the screw gear of rail assembly (1044), and the rotation of the screw gear of rail assembly (1044) drives translation of the nut of bracket (1046) along the y-dimension. Actuators (1042) may be operated simultaneously to drive simultaneous movement of brackets (1046) along the y-dimension, thereby driving cartridge support assembly (1100) along the y-dimension. An example of such movement is shown in FIGS. 17A-17B, in which y-drive assemblies (1040) may cooperate to drive cartridge support assembly (1100) from a first position along the y-dimension (FIG. 17 A) to a second position along the y-dimension (FIG. 17B). While the example described above includes motors, screw gears, and nuts being included in y-drive assemblies (1040), other examples of y-drive assemblies (1040) may have any other suitable components and arrangements to drive movement of cartridge support assembly (1100) along the y- dimension.

[0140] Stage assembly (1000) of this example may further include an x-drive assembly (1050), portions ofwhich are shown in FIG. 17C. X-drive assembly (1050) of this example may include a platform (1052) and a rail (1054). In some embodiments, cartridge support assembly (1100) may be secured to brackets (1046) via rail (1054) and / or via other components of x-drive assembly (1050). Platform (1052) maybe fixedly secured to cartridge support assembly (1100); and slidably supported on rail (1054). X-drive assembly (1050)may further include an actuator (not shown), which may be structurally configured and operable similar to actuator (1042) described above. In other examples, the actuator of x- drive assembly (1050) may have any other suitable structural configuration or operability. In the present example, x-drive assembly (1050) may be operable to drive movement of cartridge support assembly (1100) along the x -dimension. An example of such movement is shown in FIGS. 17B-17A, in which -drive assembly (1050) drives cartridge support assembly (1100) from a first position along the x-dimension (FIG. 17B) to a second position along the x-dimension (FIG. 17C).

[0141] As described above, stage assembly (1000) may be operable to provide structural support to cartridge support assembly (1100), drive movement of cartridge support assembly (1100) along the y-dimension, and drive movement of cartridge support assembly (1100) along the x-dimension. As also described above, FIGS. 17A-17C show cartridge support assembly (1100) at three different positions along the x-y plane, as driven by stage assembly (1000). However, it should be understood that the positions along the x-y plane are only depicted in FIGS. 17A-17C for purpose of illustration, to show the operability of stage assembly (1000) to move cartridge support assembly (1100) along the x-y plane. During use of instrument (900), cartridge support assembly (1100) maybe positioned at various different positions along the x-y plane, including positions not depicted in FIGS. 17A-17C. Similarly, during some examples of use of instrument (900), cartridge support assembly (1100) might not reach one or more of the positions along the x-y plane depicted in FIGS. 17A-17C.Similarly, cartridge support assembly (1100) may encounter different ranges of movement along the x-dimension and / or along the y-dimension during use of instrument (900), including ranges of movement that are smaller or larger than those depicted in FIGS. 17A- 17C.

[0142] In the state shown in FIG. 17 A, cartridge support assembly (1100) may be positioned in relation to stage assembly (1000) such that a portion of cartridge (200) is underneath a slot (1012) in upper member (1010) along the z-dimension. Slot (1012) extends along the x- dimension and the y-dimension; and may be positioned to allow illumination head (912) to illuminate imaging region (652) without being obstructed when cartridge (200) is in the position shown in FIG. 17 A. For instance, a portion of illumination head (912) may be fixedly positioned within slot (1012). In some embodiments, other components that provide illumination via illumination head (912) may be fixedly positioned within slot (1012). In some embodiments, other components of instrument (900) may be positioned within slot (1012).

[0143] In some embodiments, it may be relatively difficult to remove cartridge (200) from cartridge support assembly (1100) when cartridge support assembly (1100) is in the position shown in FIG. 17A. In some such examples, y-drive assemblies (1040) may be activated to drive cartridge support assembly (1100) to the position shown in FIG. 17B. In some embodiments, with cartridge support assembly (1100) in the position shown in FIG. 17B, it may be relatively easier for an operator to remove cartridge (200) from cartridge support assembly (1100) than such removal would be when cartridge support assembly (1100) is in the position shown in FIG. 17A.

[0144] In addition to including slot (1012), upper member (1010) may also include slot (1014). Slot (1014) may extend along the x-dimension and the y-dimension. In some embodiments, slot (1014) further facilitates removal of cartridge (200) from cartridge support assembly (1100) when cartridge support assembly (1100) is in the position shown in FIG. 17B. In some embodiments, slot (1014) may provide spatial clearance for other components of instrument (900); and / or may serve any other purpose(s).

[0145] As noted above, FIGS. 17B-17C show movement of cartridge support assembly (1100) along the x-dimension. As also noted above, the movements and positions of cartridge support assembly (1100) along the x-y plane shown in FIGS. 17A-17C may not necessarily be the same movements and positions that would be executed during use of instrument (900). In some embodiments, cartridge support assembly (1100) only moves along the x-dimension when cartridge support assembly (1100) is positioned in the vertical space (i.e., alongthe z-dimension) between members (1010, 1012). In some embodiments, such movement of cartridge support assembly (1100) alongthe x-dimension during a path of movement when cartridge support assembly (1100) moves from the position shown in FIG. 17B to the position shown in FIG. 17A. In some such examples, a combination of movement of cartridge support assembly (1100) alongthe y-dimension and the alongthe z-dimension is provided to prevent, minimize, or reduce strain on one or more conduits (802, 804) as will be described in greater detail below.

[0146] B. Example of Cartridge Support Assembly

[0147] FIGS. 18-20B show cartridge support assembly (1100) in greater detail. As shown, cartridge support assembly (1100) of this example may include a base assembly (1110), a frame assembly (1120), a cartridge seat assembly (1140), a first fluid conduit guide assembly (1300), a pneumatic conduit guide assembly (1400), and a second fluid conduit guide assembly (1500). Base assembly (1110) may support cartridge seat assembly (1140) and couples cartridge support assembly (1100) with stage assembly (1000) via platform (1052).Frame assembly (1120) may support a pneumatic assembly (1130) and other components; and may be fixed to base assembly (1110) such that frame assembly (1120) and base assembly (1110) move together unitarily along the x-y plane.

[0148] Pneumatic assembly (1130) may include a plurality of pneumatic ports (1132). Each pneumatic port (l 132) may be structurally configured to couple with a respective pneumatic conduit, such as pneumatic conduits (804) described above. Each pneumatic port (1132) may be further operable to communicate pressurized air (or other gas) to pneumatic conduits via pneumatic ports (1132). Pneumatic assembly (1130) may further include various other components, such as a pump, a manifold, a set of valves (e.g., a separate valve for each pneumatic port (1132), etc.). In some embodiments, pneumatic assembly (1130) may serve as pneumatic pressure source (820) described above with reference to FIG. 7. Pneumatic assembly (1130) may thus drive pneumatic valves in cartridge (200).

[0149] As best seen in FIGS. 19-20B, cartridge seat assembly (1140) may include a recessed platform (1142) on which cartridge (200) may be seated. Platform (1142) may include an optically transmissive material (e.g., glass, etc.), such that microscope assembly (910) may view imaging region (652) through platform (1142), from beneath platform (1142).

[0150] As best seen in FIGS. 20A-20B, cartridge seat assembly (1140) may further include a first lateral guide (1144) and a second lateral guide (1146), which may be separated from each other along the x-dimension by a width approximating the width of cartridge (200) along the x-dimension. Guides (1144, 1146) may provide appropriate positioning of cartridge (200) along the x-dimension when cartridge (200) is seated on platform (1142) with the side edges of cartridge engaging guides (1144, 1146). In some embodiments, cartridge seat assembly (1140) further includes resilient features that bias guides (1144, 1146) toward each other along the x-dimension; and / or some other kind(s) of feature(s) that allow(s) guides (1144, 1146) to be separated further from each other along the x-dimension during loading of cartridge (200) and then urged toward each other after cartridge (200) has been placed on platform (1142). In some such examples, guides (1144, 1146) may further promote appropriate positioning of cartridge (200) along the x-dimension.

[0151] Cartridge seat assembly (1140) of the present example may further include a first cartridge retainer assembly (1150) and a second cartridge retainer assembly (1160). First cartridge retainer assembly (1150) may be positioned at the rear of cartridge seat assembly (1140); and may include a frame (1152) that is fixed to base assembly (1110). A pair of retainers (1156) may be secured to frame (1152). In this example, each retainer (1156) may include a beam that is cantilevered over platform (1142). Each retainer (1156) may define aspace with platform (1142) along the z-dimension that corresponds to a thickness of layer (500) along the z-dimension. Thus, as shown in FIGS. 20A-20B, a portion near the rear edge of layer (500) may be positioned under retainers (1156); and retainers (1156) may thereby retain the region of cartridge (200) engaged by retainers (1156). In other words, retainers (1156) may restrict movement of the rear portion of cartridge (200) along the z-dimension. Frame (1152) may also include a set of stops (1151) that restrict movement of cartridge along the y-dimension, as stops (1151) may be positioned to engage the rear edge of layer (500) while the rear portion of layer (500) is disposed under retainers (1156).

[0152] Second cartridge retainer assembly (1160) may be positioned at the front of cartridge seat assembly; and may include a frame (1162) that may be secured to fixed to base assembly (1110). A movable retainer assembly (1164) may be coupled with frame (1162). Movable retainer assembly (1164) may include a pair of retainers (1164), a handle (1168), and a pair of stops (1169). In this example, each retainer (1164) may include a beam that may be cantilevered over platform (1142). Each retainer (1164) may define a space with platform (1142) along the z-dimension that may correspond to a thickness of layer (500) along the z- dimension. One or more resilient members (not shown) may be interposed between movable retainer assembly (1164) and frame (1162) to resiliently urge retainer assembly (1164) along the y-dimension to the position shown in FIG. 20B. Such one or more resilient members may include one or more leaf springs, one or more coil springs, etc.

[0153] With retainer assembly (1164) in the position shown in FIG. 20B, a portion near the front edge of layer (500) may be positionedunder retainers (1164); and retainers (1164) may thereby retain the region of cartridge (200) engaged by retainers (1164). In other words, retainers (1164) may restrict movement of the front portion of cartridge (200) along the z- dimension. Stops (1169) may be positioned to restrict movement of cartridge along the y- dimension, as stops (1169) may be positioned to engage the front edge of layer (500) while the rear portion of layer (500) may be disposed under retainers (1164). An operator may manipulate handle (1168) to move retainer assembly (1164) along the y-dimension from the position shown in FIG. 20B to the position shown in FIG. 20A.

[0154] With retainer assembly (1164) in the position shown in FIG. 20 A, retainers (1164) may be no longer positioned over layer (500); and stops (1169) may no longer engage the front edge of layer (500). This may facilitate removal of cartridge (200) from cartridge seat assembly (1140). For instance, while retainer assembly (1164) is held in the position shown in FIG. 20A, cartridge (200) may be slid along the y-dimension to move the rear portion of layer (500) from the space under retainers (1156), and then cartridge (200) may be removedfrom platform (1142) along the z-dimension. To seat another cartridge (200) in cartridge seat assembly (1140), the other cartridge (200) may be placed on platform (1142) while retainer assembly (1164) is held in the position shown in FIG. 20A. Cartridge (200) may then be slid along the y-dimension to move the rear portion of layer (500) into the space under retainers (1156), with the rear edge of layer (500) engaging stops (1151). Handle (1168) may then be released, allowing the resilient member(s) to return retainer assembly (1164) to the position shown in FIG. 20B. At that stage, the front region of layer (500) may again be positioned in the space under retainers (1166); and stops (1167) may engage the front edge of layer (500).

[0155] In some embodiments, each retainer (1156, 1166) has a resilient bias toward a relaxed position where the gap defined between at least part of each retainer (1156, 1166) and platform (1142) alongthe z-dimensionis smaller than the thickness of layer (500) along the z-dimension. In some such examples, retainers (1156, 1166) deflect upwardly along the z- dimension when layer (500) is positioned between retainers (1156, 1166) and platform (1142), such that retainers (1156, 1166) resiliently bear downwardly on the front and rear regions of layer (500). In some such examples, retainers (1156, 1166) may provide a firm seating of cartridge (200) on platform (1142). Such firm seating of cartridge (200) on platform (1142) may further promote appropriate positioning of cartridge (200) on platform (1142) as cartridge support assembly (1100) is moved alongthe x-y plane by stage assembly (1000).

[0156] Referring back to FIG. 18, base assembly (1110) of the present example may further include integral jack screws (1112). Jack screws (1112) may be positioned at each of three corners of base assembly (1110) to form a core geometry of a kinematic mount. In some embodiments, jack screws (1122) are also provided at each rear corner of base assembly (1110). Jack screws (1112) may be adjusted to change the height the corresponding corner of base assembly (1110) alongthe z-dimension. In some embodiments, such adjustments may be provided to fine tune the orientation of platform (1142), such as to make platform (1142) coplanar with a predefined x-y plane. In some embodiments, each jack screw (1112) includes a spherical feature that permits base assembly (1110) to move freely within limits without binding, providing the repeatability of a kinematic constraint. Each jack screw (111) may further include a fastener that runs concentrically through the center of jack screw (1112) that allows base assembly (1110) to be locked down after adjustment and preserving the kinematic mounting arrangement. This may in turn provide appropriate orientation of cartridge (200) relative to the predefined x-y plane. Such orientation of cartridge (200) relative to the predefined x-y plane may facilitate appropriate imaging of imaging region(652) by microscope assembly (912) and / or may provide appropriate performance of other optical components (and / or non-optical components) of instrument (900).

[0157] C. Examples of Conduit Guide Assemblies

[0158] As described above with reference to FIG. 7, in some examples several fluid conduits (802) coupled with cartridge (200) (e.g., via fluid output port (312) and fluid input ports (310)) while also being coupled with components that are external to cartridge (e.g., fluid sources (810, 812, 814) and receptacle (816)). As also described above with reference to FIG. 7, in some examples several pneumatic conduits (804) are coupled with cartridge (200) (e.g., via pneumatic ports (320)) while also being coupled with a component that is external to cartridge (e.g., pneumatic pressure source (820) or pneumatic assembly (1130)). As described above with reference to FIGS. 17A-17C base assembly (1110) (including cartridge (200)) may move along the x-y plane relative to stage assembly (1000) and relative to various other components of instrument (900). In some embodiments, such movement may tend to create a risk of interference between the various conduits (802, 804) coupled with cartridge (200) and one or more other components of instrument (900). It may therefore be desirable in some examples to guide conduits (802, 804), provide strain relief to conduits (802, 804), and / or otherwise mitigate any risks of damage or decoupling from cartridge (200) that conduits (802, 804) might otherwise face as base assembly (1110) (including cartridge (200)) moves along the x-y plane relative to stage assembly (1000) and relative to various other components of instrument (900).

[0159] FIGS. 8 and 13-17C show one fluid conduit guide assembly (920) that may provide some degree of guidance and / or protection to one or more fluid conduits (802). In some embodiments, fluid conduit guide assembly (920) engages a fluid conduit (802) that is coupled with fluid input port (310) of sample fluid receiving region (600) and source (810); and with a fluid conduit (802) that is coupled with fluid input port (310) of flow control fluid receiving region (620) and source (812). Fluid conduit guide assembly (920) of this example may include a bracket (922), a shaft (924), and a head (926). Bracket (922) may be secured to bottom member (1020) of stage assembly (1010). Shaft (924) may extend upwardly from bracket (922) along the z-dimension. Head (926) maybe mounted to the top of shaft (924). Head (926) may include a cylindraceous body defining a passageway (928). In some embodiments, head (926) may freely rotate relative to shaft (924) about a z-axis. In some other examples, head (926) and shaft (924) may rotate together relative to bracket (922) about a z-axis.

[0160] In some embodiments, one or more fluid conduits (802) is / are positioned within passageway (928) en route between one or more of sources (810, 812) and cartridge support assembly (1100). Also In some embodiments, shaft (924) includes one or more central channels and / or one or more side channels extending along at least part of the length of shaft (924), with such channel(s) also being structurally configured to receive one or more fluid conduits (802). In the present example, fluid conduit guide assembly (920) provides guidance and / or protection to the one or more fluid conduits (802) that is / are engaged with fluid conduit guide assembly (920), including during movement of cartridge support assembly (1100) (and cartridge (200)) along the x-y plane.

[0161] FIG. 34 shows an example of a fluid conduit (802) engaged with fluid conduit guide assembly (920). Fluid conduit (802) of this example may be coupled with source (810) of a fluid containing one or more sample cells; and with fluid input port (310) over sample fluid receiving region (600) of cartridge (200). Fluid conduit (802) of this example may include a flexible tube. In the example shown in FIG. 34, fluid conduit (802) extends generally upwardly from source (810) along the z-dimension and is positioned along shaft (924) of fluid conduit guide assembly (920). A set of retainers (925) may secure fluid conduit (802) relative to shaft (924). Retainers (925) may include hose clamps in this example, though retainers (925) may take any other suitable form. In some other examples, retainers (925) are omitted. While fluid conduit (802) is shown extending alongside an exterior surface of shaft (924) in FIG. 34, in some other examples fluid conduit (802) extends along a hollow interior region of shaft (924). In some other examples, fluid conduit (802) is at least partially seated within a side channel extending along at least part of the length of shaft (924).

[0162] Continuing with the example shown in FIG. 34, fluid conduit (802) continues through passageway (928) of head (926) and descends downwardly along the z-dimension to enter head (1320) of fluid conduit guide assembly (1300) as described in greater detail below. While FIG. 34 shows fluid conduit (802) positioned along a substantially straight path between head (926) and head (1320), in some examplesthis path may be substantially curved or have some other configuration. After passing through head (1320), fluid conduit (802) may terminate in fluid input port (310) over sample fluid receiving region (600) of cartridge (200) as described herein.

[0163] As described above and shown in FIG. 34, fluid conduit (802) may traverse a path that extends upwardly along the z-dimension and then downwardly along the z-dimension between source (810) and cartridge (200). In some embodiments, this path substantially lacks any horizontal regions. In other words, to the extent that any region of the length offluid conduit (802) traverses a path having a substantially horizontal component (e.g., through head (926)), such a region of the length of fluid conduit (802) may be substantially short. By minimizing the length of fluid conduit (802) that traverses a substantially horizontal path, this arrangement may tend to minimize or otherwise reduce a tendency of cells or other particles in fluid conduit (802) to settle along an inner sidewall of fluid conduit (802). By minimizing or otherwise reducing a tendency of cells or other particles in fluid conduit (802) to settle along an inner sidewall of fluid conduit (802), this arrangement may tend to minimize or otherwise reduce an effective loss of cells or other particles in fluid conduit (802) during transit from source (810) to cartridge (200).

[0164] FIGS. 13-16 show another fluid conduit guide assembly (930) that may provide some degree of guidance and / or protection to one or more fluid conduits (802). Fluid conduit guide assembly (930) of this example includes a shaft (932) and a head (934). Shaft (932) may be secured to bottom member (1020) of stage assembly (1010). Shaft (932) extends upwardly from bottom member (1020) along the z-dimension. Head (934) may be mounted to the top of shaft (932). In some embodiments, head (934) includes one or more pivoting links or other pivoting features. Such pivoting features may pivot about a z-axis, an x-axis, a y-axis, and / or any other axis / axes. In some embodiments, one or more fluid conduits (802) is / are coupled with head (934) en route between source (814) and cartridge support assembly (1100) and / or en route between receptacle (816) and cartridge support assembly (1100). In the present example, fluid conduit guide assembly (930) provides guidance and / or protection to the one or more fluid conduits (802) that is / are engaged with fluid conduit guide assembly (930), including during movement of cartridge support assembly (1100) (and cartridge (200)) along the x-y plane.

[0165] FIGS. 21-23 show fluid conduit guide assembly (1300) in greater detail. Fluid conduit guide assembly (1300) of this example may include a shaft (1310) and a head (1320). The bottom of shaft (1310) may be secured to base assembly (1110). Head (1320) may be mounted to the top of shaft (1310). In some embodiments, head (1320) is rotatable relative to shaft (1310) about a z-axis, as shown in FIGS. 33 A-33B. In some other examples, head (1320) and shaft (1310) are rotatable together unitarily relative to base assembly (1110) about the z-axis. In examples where head (1320) and / or shaft (1310) is / are rotatable about the z- axis, one or more resilient members (e.g., torsion springs, etc.) may resiliently bias head (1320) and / or shaft (1310) toward a neutral angular position about the z-axis. In other words, the one or more resilient members may allow head (1320) and / or shaft (1310) to be rotated away from the neutral angular position about the z-axis when a force is applied to (1320)and / or shaft (1310) when an external force is applied to head (1320) (e.g., when tension is applied to one or more fluid conduits (802) disposed in head (1320)). However, when an externally applied force is removed from head (1320) (e.g., when tension in one or more fluid conduits (802) disposed in head (1320) is relieved), the resilient bias of the one or more resilient members may drive head (1320) and / or shaft (1310) back toward the neutral angular position.

[0166] Head (1320) includes a body (1322) having a first opening (1320) and a second opening (1334). Second opening (1334) may be recessed within body (1322) relative to first opening (1320), with an inner surface (1332) providing a tapered channel from opening (1330) to opening (1334). A recess (1342) may be in a curved surface (1340) of body (1322). As best seen in FIG. 23, second opening (1334) may be positioned at a top region of recess (1342). Each opening (1330, 1334) may have a stadium shape in this example. Openings (1320, 1334) may be sized to slidably receive one or more fluid conduits (802). Recess (1342) may also be sized to accommodate one or more fluid conduits (802). In some embodiments, one or more fluid conduits (802) enter head (1320) in a generally vertical orientation (via recess (1342)) and exit head (1320) in a generally horizontal orientation (via openings (1334, 1330). In some other examples, one or more fluid conduits (802) enter head (1320) in a generally horizontal orientation (via openings (1330, 1334)) andexit head (1320) in a generally vertical orientation (via recess (1342)).

[0167] Fluid conduit guide assembly (1300) may provide some degree of guidance and / or protection to one or more fluid conduits (802). In some embodiments, fluid conduit guide assembly (1300) engages a fluid conduit (802) that is coupled with fluid input port (310) of sample fluid receiving region (600) and source (810); and with a fluid conduit (802) that is coupled with fluid input port (310) of flow control fluid receiving region (620) and source (812). Such fluid conduit(s) (802) may enter head (1320) (e.g., from fluid conduit guide assembly (920)) via recess (1342) pass through second opening (1334) and then through first opening (1330) before connecting with cartridge (200).

[0168] The rotatability of head (1320) about the z-axis, combined with the stadium shapes of openings (1330, 1334) and the tapered channel defined by surface (1332), may provide guidance some degree of guidance and / or protection to the one or more fluid conduits (802) thatis / are engaged with fluid conduit guide assembly (1330), including during movement of cartridge support assembly (1100) (and cartridge (200)) along the x-y plane. For instance, in the event that one or more components of instrument (900) engage the one or more fluid conduits (802) passing through head(1320) during movement of cartridge support assembly(1100) (and cartridge (200)) along the x-y plane and create tension in the one or more engaged fluid conduits (802), head (1320) may rotate about the z-axis to at least partially relieve such tension and thereby reduce strain that might otherwise occur in the one or more engaged fluid conduits (802) (and / or at the couplings of the one or more engaged fluid conduits (802)). By way of further example, the guidance and / or protection provided by fluid conduit guide assembly (1300) may tend to reduce a risk of fluid conduits (802) being pulled out of ports (310) of cartridge (200), of fluid conduits (802) kinking or rupturing, of fluid conduits (802) snagging, or other results that might not be desirable in some examples.

[0169] FIGS. 24-27 show pneumatic conduit guide assembly (1400) in greater detail. Pneumatic conduit guide assembly (1400) of this example includes a base (1410), a shaft (1430), a first clamp-on flange (1440), a second clamp-on flange (1460), a head assembly (1470), and pins (1420, 1422, 1450). Base (1410) may be secured to base assembly (1110) and may include a pair of circular pin openings (1412, 1414). Pins (1420, 1422) may be disposed in pin openings (1412, 1414). The bottom of shaft (1430) may be pivotably disposed within base (1410). A pair of torsion springs (1432, 1434) may be disposed about shaft (1430). First clamp-on flange (1440) may include a central opening (1442) and an arcuate opening (1444). Shaft(1430) maybe disposed in central opening (1442); and clampon flange (1440) may be securely clamped onto shaft (1430). Pin (1450) may be disposed in arcuate opening (1444) and is operable to move along the arcuate path defined by arcuate opening (1444). Second clamp-on flange (1460) may include a central opening (1462) and a circular opening (1464). Shaft (1430) may be disposed in central opening (1462); and clampon flange (1460) may be securely clamped onto shaft (1430). Pin (1450) may be secured within circular opening (1464).

[0170] Head assembly (1470) may be secured to the top of shaft (1430). As best seen in FIGS. 26-27, head assembly (1470) may include a first body (1472) and a second body (1474) secured to first body (1472). An arm (1476) may extend from first body (1472) and defines a plurality of openings (1478), with each opening (1478) being surrounded by a corresponding lead-in surface (1477). Each lead-in surface (1477) may taper downwardly toward the corresponding opening (1478) along the z-dimension. As shown in FIG. 27, bodies (1472, 1474) may cooperate to define a gap (1480), with a pair of pins (1490, 1492) spanning across gap (1480). A first space (1482) may be defined between pin (1490) and body (1474) along the z-dimension; and a second space (1484) may be defined between pin (1492) and pin (1490) along the z-dimension.

[0171] Each opening (1478) maybe sized to slidably receive a respective pneumatic conduit (804). One or both of spaces (1482, 1484) may also slidably receive one or more pneumatic conduits (804). For instance, pneumatic conduits (804) may pass through one or both of spaces (1482, 1484) en route from pneumatic ports (1132) toward cartridge (200). In some embodiments, pneumatic conduits (804) pass through space (1484) en route from pneumatic ports (1132) toward cartridge (200). Pins (1490, 1492) may serve to guide and neatly arrange pneumatic conduits (804) to prevent kinking; while permitting each pneumatic conduit (804) to move and slide to adjustforthe movement of head assembly (1470); while also providing for a service loop of each pneumatic conduit (804) that may reduce the risk of pneumatic conduits (804) of being undesirably pull out of from cartridge (200) due to interference with other components of instrument (900) during operation. Pneumatic conduits (804) may continue through respective openings (1478) beforebeing inserted into pneumatic ports (320) of cartridge (200). Further, each opening (1478) may be sized in diameter, and each space (1484) may be sized in width, to control the movement of pneumatic conduits (804) by adding just enough friction to permit the user to move pneumatic conduits (804) in and out of position to reach cartridge (200) and stay in-place when user is finished.

[0172] Head assembly (1470) and shaft (1430) may be rotatable about a z-axis relative to base (1410). An example of such rotation is shown in shown in FIGS. 33A-33C. Torsion springs (1432, 1434) maybe structurally configured to impart a bi-directional angular bias to head assembly (1470) and shaft (1430) about the z-axis. In other words, if head assembly (1470) and shaft (1430) rotate in a first angular direction about the z-axis relative to base (1410), away from a neutral angular position about the z-axis, one torsion spring (1432, 1434) may resiliently urge head assembly (1470) and shaft (1430) in a second angular direction about the z-axis relative to base (1410), toward the neutral angular position about the z-axis. If head assembly (1470) and shaft (1430) rotate in the second angular direction aboutthe z-axis relative to base (1410), away from the neutral angular position about the z- axis, the other torsion spring (1432, 1434) may resiliently urge head assembly (1470) and shaft (1430) in the first angular direction aboutthe z-axis relative to base (1410), toward the neutral angular position aboutthe z-axis. In this example, pins (1420, 1422) may provide a grounding structure for torsion springs (1432, 1434) while pin (1450) and a structural feature of clamp-on flange (1440) may provide a bearing structure for torsion springs during rotation of head assembly (1470) and shaft (1430) about the z-axis.

[0173] The rotatability of head assembly (1470) aboutthe z-axis, combined with the stadium positioning of pneumatic conduits (804) in openings (1478) and the tapered lead-in surfaces(1477) around openings (1478) may provide guidance some degree of guidance and / or protection to the pneumatic conduits (804) that are engaged with pneumatic conduit guide assembly (1400), including during movement of cartridge support assembly (1100) (and cartridge (200)) along the x-y plane. For instance, in the event that one or more components of instrument (900) engage one or more pneumatic conduits (804) during movement of cartridge support assembly (1100) (and cartridge (200)) along the x-y plane and create tension in the one or more engaged pneumatic conduits (804), head assembly (1470) may rotate about the z-axis to at least partially relieve such tension and thereby reduce strain that might otherwise occur in the one or more engaged pneumatic conduits (804) (and / or at the couplings of the one or more engaged pneumatic conduits (804)). By way of further example, the guidance and / or protection provided by pneumatic conduit guide assembly (1400) may tend to reduce a risk of pneumatic conduits (804) being pulled out of ports (320) of cartridge (200), of pneumatic conduits (804) kinking or rupturing, of pneumatic conduits (804) snagging, or other results that might not be desirable in some examples.

[0174] FIGS. 28-32 show fluid conduit guide assembly (1500) in greater detail. Fluid conduit guide assembly (1500) of this example may include a base (1510), a shaft (1530), a first clamp-on flange (1540), a second clamp-on flange (1560), a head (1570), and pins (1520, 1522, 1550). Base (1510) may be secured to base assembly (1110). Pins (1520, 1520) may be secured within base (1510). The bottom of shaft (1530) may be pivotably disposed within base (1510). A pair of torsion springs (1532, 1534) may be disposed about shaft (1530). First clamp-on flange (1540) may include a central opening (1542) and an arcuate opening (1544). Shaft (1530) may be disposed in central opening (1542); and clamp-on flange (1540) may be securely clamped onto shaft (1530). Pin (1550) may be disposed in arcuate opening (1544) and may be operable to move along the arcuate path defined by arcuate opening (1544). Second clamp-on flange (1560) may include a central opening (1562) and a circular opening (1564). Shaft (1530) may be disposed in central opening (1562); and clamp-on flange (1560) may be securely clamped onto shaft (1530). Pin (1550) may be secured within circular opening (1564).

[0175] Head (1570) may be secured to the top of shaft (1530). As best seen in FIGS. 30-32, head (1570) may include a body (1572) with a first surface (1574) having a first opening (1580) and a channel (1582) extending into body (1572) from first opening (1580). A second opening (1590) is in a second surface (1576) of body (1572). Channel (1582) may pass through body (1572), from first opening (1580) to second opening (1590). As shown in FIG. 31, channel (1582) may have a tapered cross-sectional profile along the x-y plane, flaringoutwardly toward opening (1580). As shown in FIG. 32, channel (1582) may have a curved profile along the x-z plane, providing a bend angle of approximately 90 degrees in view of first surface (1574) being perpendicular to second surface (1576). Openings (1580, 1590) may be sized to slidably receive one or more fluid conduits (802). Channel (1582) may also be sized to accommodate one or more fluid conduits (802). In some embodiments, one or more fluid conduits (802) may enter head (1570) in a generally vertical orientation (via opening (1590)) and exit head (1570) in a generally horizontal orientation (via opening (1580). In some other examples, one or more fluid conduits (802) may enter head (1570) in a generally horizontal orientation (via opening (1580)) and may exit head (1570) in a generally vertical orientation (via opening (1590)).

[0176] Head (1570) and shaft (1530) may be rotatable abouta z-axis relative to base (1510). An example of suchrotation is shown in shown in FIGS. 33 A-33B. Torsion springs (1532, 1534) may be structurally configured to impart a bi-directional angular bias to head (1570) and shaft (1530) about the z-axis. In other words, if head (1570) and shaft (1530) rotate in a first angular direction about the z-axis relative to base (1510), away from a neutral angular position aboutthe z-axis, one torsion spring (1532, 1534) may resiliently urge head (1570) and shaft (1530) in a second angular direction aboutthe z-axis relative to base (1510), toward the neutral angular position about the z-axis. If head (1570) and shaft (1530) rotate in the second angular direction about the z-axis relative to base (1510), away from the neutral angular position aboutthe z-axis, the other torsion spring (1532, 1534) may resiliently urge head (1570) and shaft (1530) in the first angular direction about the z-axis relative to base (1510), toward the neutral angular position about the z-axis. In this example, pins (1520, 1522) may provide a grounding structure for torsion springs (1532, 1534) while pin (1550) and a structural feature of clamp-on flange (1540) may provide a bearing structure for torsion springs during rotation of head (1570) and shaft (1530) about the z-axis.

[0177] Fluid conduit guide assembly (1500) may provide some degree of guidance and / or protection to one or more fluid conduits (802). In some embodiments, fluid conduit guide assembly (1500) engages a fluid conduit (802) that is coupled with fluid input port (310) of flow drive fluid receiving region (670) and source (814); and with a fluid conduit (802) that is coupled with fluid output port (310) of sample output region (680) and receptacle (816). Such fluid conduit(s) (802) may enter head (1570) (e.g., from fluid conduit guide assembly (930)) via opening (1580) pass through channel (1582) and then through opening (1590) before connecting with cartridge (200).

[0178] The rotatability of head (1570) about the z-axis, combined with the wide shape of opening (1580) and the tapered configuration of channel (1582), may provide guidance some degree of guidance and / or protection to the one or more fluid conduits (802) that may be engaged with fluid conduit guide assembly (1500), including during movement of cartridge support assembly (1100) (and cartridge (200)) along the x-y plane. For instance, in the event that one or more components of instrument (900) engage the one or more fluid conduits (802) passing through head (1570) during movement of cartridge support assembly (1100) (and cartridge (200)) along the x-y plane and create tension in the one or more engaged fluid conduits (802), head (1570) may rotate about the z-axis to at least partially relieve such tension and thereby reduce strain that might otherwise occur in the one or more engaged fluid conduits (802) (and / or at the couplings of the one or more engaged fluid conduits (802)). By way of further example, the guidance and / or protection provided by fluid conduit guide assembly (1500) may tend to reduce a risk of fluid conduits (802) being pulled out of ports (310, 320) of cartridge (200), of fluid conduits (802) kinking or rupturing, of fluid conduits (802) snagging, or other results that might not be desirable in some examples.

[0179] As noted above, FIGS. 33A-33C show rotation of heads (1320, 1570) and head assembly (1470) about respective z-axes relative to base assembly (1100). However, it should be understood that the angular positions of heads (1320, 1570) and head assembly (1470) about respective z-axes are only depicted in FIGS. 33 A-33C for purpose of illustration, to show the operability of conduit guide assemblies (1300, 1400, 1500) to provide rotation about respective z-axes to relieve tension in conduits. During use of instrument (900), heads (1320, 1570) and head assembly (1470) may be positioned at various different angular orientations about their respective z-axes, including angular orientations not depicted in FIGS. 33A-33C. Similarly, during some examples of use of instrument (900), heads (1320, 1570) and / or head assembly (1470) might not reach one or more of the angular orientations about their respective z-axes as depicted in FIGS. 33A-33C. Similarly, heads (1320, 1570) and / or head assembly (1470) may encounter different ranges of angular movement about the respective z-axes during use of instrument (900), including ranges of angular movement that are smaller or larger than those depicted in FIGS. 33 A-33C.

[0180] In some embodiments, heads (1320, 1570) and head assembly (1470) are at the respective angular positions about respective z-axes shown in FIG. 33 A when cartridge support assembly (1100) is at the position along the x-y plane shown in FIG. 17B. Also In some embodiments, heads (1320, 1570) and head assembly (1470) are at the respective angular positions about respective z-axes shown in FIG. 33C when cartridge supportassembly (1100) is at the position along the x-y plane shown in FIG. 17 A. In some such examples, the presence of illumination head (912) over cartridge (200) in the operational state shown in FIG. 17A causes head assembly (1470) to be in the angular position about its z-axis as shown in FIG. 33C; while the presence of illumination head (912) over cartridge (200) in the operational state shown in FIG. 17A does not cause a change in the respective angular positions of heads (1320, 1570) about their respective z-axes to change relative to those angular positions shown in FIG. 33 A. However, In some embodiments, heads (1320, 1570) may nevertheless rotate through some respective range(s) of angular motion about their respective z-axes during a transition between the operational state shown in FIG. 17B and the operational state shown in FIG. 17 A.

[0181] D. Examples of Conduits

[0182] As noted above, a fluid conduit (802) may be inserted directly into a port (310, 312) of cartridge (200) to provide a fluidic coupling between cartridge (200) and a fluid source (810, 812, 814) or a receptacle (816). FIG. 35 shows an example of a fluid conduit (1600) that may be used in such a fashion. Fluid conduit (1600) may thus be used in accordance with the above descriptions of fluid conduits (802). Fluid conduit (1600) of this example may include a flexible tube (1602) with an open free end (1604). A grip (1610) may be secured to fluid conduit (1600) in a region proximal to free end (1604). Grip (1610) may include a body (1612) and a hilt (1614). Hilt (1614) may be positioned at a first distance (DI) from free end (1604).

[0183] As shown in FIG. 36, first distance (DI) may correspond with a position of a fluidic channel (650) within cartridge (200). Thus, when fluid conduit (1600) is inserted into fluid input port (310), fluid conduit (1600) may be advanced along the z-dimension until hilt (1614) engages top surface (302) of layer (300). Due to the length of first distance (DI), free end (1604) may be positioned at or in fluidic channel (650) when hilt (1614) is engaged with top surface (302) of layer (300). Hilt (1614) may thus provide a depth stop that positions fluid conduit (1600) deeply enough into cartridge (200) to achieve a suitable fluid seal with layer (300) while also allowing fluid to be communicated from free end (1604) to fluidic channel (650). While fluid conduit (1600) is shown as being inserted in a fluid input port (310) in FIG. 36, fluid conduit (1600) may also be inserted into a fluid output port (312).

[0184] A magnetic coupling member (1616) may be provided in body (1612). In some embodiments, magnetic coupling member (1616) comprises a permanent magnet. In some other examples, magnetic coupling member (1616) comprises a ferrous member (e.g., a piece of steel, etc.). Referring back to FIGS. 18-20B, base assembly (1110) ofthe present examplemay include a first sidewall (1 170) with a first magnetic coupling member (1172) at a first side of cartridge seat assembly (1140); and a second sidewall (1180) with a second magnetic coupling member (1182) at a second side of cartridge seat assembly (1140). In some examples where coupling member (1616) of fluid conduit (1600) comprises a permanent magnet, each magnetic coupling member (1172, 1182) may comprise a ferrous member (e.g., a piece of steel, etc.). In some examples where coupling member (1616) of fluid conduit (1600) comprises a ferrous member (e.g., a piece of steel, etc.), each magnetic coupling member (1172, 1182) comprises a permanent magnet. In either scenario, grip (1610) may be removably coupled to first magnetic coupling member (1172) via magnetic attraction between magnetic coupling members (1616, 1172); or to second magnetic coupling member (1182) via magnetic coupling between magnetic coupling members (1616, 1182).

[0185] During some examples of use of instrument (900), there may be scenarios where one or more fluid conduits (1600) is / are not coupled with cartridge (200). For instance, such a scenario may occur when a cartridge (200) is being replaced. During such scenarios, the one or more fluid conduits (1600) that is / are not coupled with cartridge (200) may be temporarily coupled with first magnetic coupling member (1172) or second magnetic coupling member (1182), by moving grip (1610) within sufficient proximity to magnetic coupling member (1172, 1182) to allow magnetic coupling members (1616) to magnetically couple with magnetic coupling member (1172, 1182). By having grip (1610) temporarily secured to a magnetic coupling member (1172, 1182) via magnetic coupling member (1616), the associated fluid conduit (1600) may be retained away from the space directly above cartridge seat assembly (1140), providing clearance for removal of a cartridge (200) from cartridge seat assembly (1140) and / or insertion of a cartridge into cartridge seat assembly (1140) without interference from any decoupled fluid conduits (1600). In some embodiments, fluid conduits (1600) that are routed through head (1300) may be selectively coupled with magnetic coupling member (1182); while fluid conduits (1600) that are routed through head (1500) may be selectively coupled with magnetic coupling member (1172).

[0186] In some other examples of fluid conduit (1600), magnetic coupling member (1616) is omitted. Similarly, in some other examples of base assembly (1110), magnetic coupling members (1172, 1182) are omitted.

[0187] FIG. 37 shows an example of a pneumatic conduit (1650) that may be used in accordance with the above descriptions of pneumatic conduits (804). Pneumatic conduit (1650) of this example may include a flexible tube (1652) with an open free end (1654). A grip (1660) may be secured to fluid conduit (1650) in a region proximal to free end (1654).Grip (1660) may include a body (1662) and a hilt (1664). Hilt (1664) may be positioned at a second distance (D2) from free end (1654).

[0188] As shown in FIG. 38, second distance (D2) may correspond with a position of a pneumatic channel (322) within cartridge (200). Thus, when pneumatic conduit (1650) is inserted into pneumatic input port (320), pneumatic conduit (1650) may be advanced along the z-dimension until hilt (1664) engages top surface (302) of layer (300). Due to the length of second distance (D2), free end (1654) maybe positioned at orin pneumatic channel (322) when hilt (1664) is engaged with top surface (302) of layer (300). Hilt (1664) may thus provide a depth stop that positions pneumatic conduit (1650) deeply enough into cartridge (200) to achieve a suitable fluid seal with layer (300) while also allowing pneumatic pressure to be communicated from free end (1654) to pneumatic channel (322).

[0189] A magnetic coupling member (1666) may be provided in body (1662). In some embodiments, magnetic coupling member (1666) comprises a permanent magnet. In some other examples, magnetic coupling member (1666) comprises a ferrous member (e.g., a piece of steel, etc.). In either scenario, grip (1660) may be removably coupled to first magnetic coupling member (1172) via magnetic attraction between magnetic coupling members ( 1666, 1172); or to second magnetic coupling member (1182) via magnetic coupling between magnetic coupling members (1666, 1182).

[0190] During some examples of use of instrument (900), there may be scenarios where one or more pneumatic conduits (1650) is / are not coupled with cartridge (200). For instance, such a scenario may occur when a cartridge (200) is being replaced. During such scenarios, the one or more pneumatic conduits (1650) that is / are not coupled with cartridge (200) may be temporarily coupled with first magnetic coupling member (1172) or second magnetic coupling member (1182), by moving grip (1660) within sufficient proximity to magnetic coupling member (1172, 1182) to allow magnetic coupling members ( 1666) to magnetically couple with magnetic coupling member (1172, 1182). By having grip (1660) temporarily secured to a magnetic coupling member (1172, 1182) via magnetic coupling member (1666), the associated pneumatic conduit (1650) may be retained away from the space directly above cartridge seat assembly (1140), providing clearance for removal of a cartridge (200) from cartridge seat assembly (1140) and / or insertion of a cartridge into cartridge seat assembly (1140) without interference from any decoupled pneumatic conduits (1650).

[0191] In some other examples of pneumatic conduit (1650), magnetic coupling member (1666) is omitted.

[0192] V. Example of Another Cartridge

[0193] FIG. 39 shows an example of another cartridge (3000) that may be used with system (100) in place of cartridge (200). Except as otherwise noted below, cartridge (3000) of this example may be structurally configured and operable like cartridge (200). Cartridge (3000) of this example may include a sample fluid receiving region (3002) and a flow control fluid receiving region (3004). A flow channel (3006) may lead from sample fluid receiving region (3002) to a junction (3006). A pair of flow channels (3008) may lead from flow control fluid receiving region (3004) to junction (3006). A sampling channel (3012) may extend from junction (3006) to a bend (3014), which leads to a sample output region (3018) via an outlet channel (3016).

[0194] A cell containing fluid may be communicated through sample fluid receiving region (3002), and a flow control fluid may be communicated through flow control fluid receiving region (3004). These two fluids may meet at junction (3010), which may provide a flow focusing feature, with the merged fluids being conveyed along sampling channel (3012). Light source (130) and optical assembly (132) may illuminate imaging region (3020); while objective lens assembly (140) and camera (142) may capture images of cells within imaging region (3020). The fluid may continue around bend (3014), through outlet channel (3016), and exits cartridge (3000) at sample output region (3018). The fluid that exits cartridge (3000) at sample output region (3018) may be further conveyed to a reservoir that is either integrated into the instrument of system (100) or is external to the instrument.

[0195] Cartridge (3000) may thus be similar to cartridge (200) except that cartridge (3000) may lack the sorting capabilities of cartridge (200). Nevertheless, the other teachings provided above in the context of cartridge (200) may be readily applied to cartridge (3000).

[0196] The fluid communicated along sampling channel (650) may contain sample cells as noted above. These cells may be imaged by the instrument of system (100) as also noted above. Such imaging may be performed as the cells traverse sampling channel (650). For instance, FIG. 6 shows an example of an imaging region (2900) that may be positioned along sampling channel (650). In some embodiments, light source (130) and optical assembly (132) are positioned over cartridge (200) to illuminate imaging region (2900); while objective lens assembly (140) and camera (142) are positioned under cartridge (200) to capture images of cells within imaging region (2900). Other examples may provide imaging region (2900) at any other suitable location or locations along sampling channel (650). Some examples may also provide a plurality of imaging regions (2900) at different respective positions along sampling channel (650).

[0197] A. Example of Sorting Features of Cartridge

[0198] As noted above, system (100) may provide sorting of cells in cartridge (120) based on analysis performed by image processing module (144) on images of cells captured by camera (142). Cartridge (200) of the present example may provide a primary sorting region (202) and a secondary sorting region (204) to achieve such sorting.

[0199] FIG. 47 shows primary sorting region (202) of cartridge (200) in greater detail. Primary sorting region (202) may be located where sampling channel (650) terminates in a junction (660), which may allow fluid to flow from sampling channel (650) to either a first outlet channel (662) or a second outlet channel (664). As shown, a first valve (2692) may be positioned along first outlet channel (662) while a second valve (2690) is positioned along second outlet channel (664).

[0200] First valve (2692) may be defined by a portion of a pneumatic channel (322b) that may be positioned directly over first outlet channel (662), in a region just downstream of junction (660). Pneumatic port (320b) may be pneumatically coupled with pneumatic channel (322b) such that pneumatic channel (322b) may be pressurized via pneumatic port (320b). Second valve (2690) may be defined by a portion of a pneumatic channel (322a) that may be positioned directly over second outlet channel (664). Pneumatic port (320a) may be pneumatically coupled with pneumatic channel (322a) such that pneumatic channel (322a) may be pressurized via pneumatic port (320a). Each outlet channel (662, 664) may thus be selectively opened and closed through pneumatic valving via respective valves (692, 690) as described below.

[0201] FIGS. 48A-48C show an example of a sequence of operation of valves (2690, 2692) during operation of system (100) with cartridge (200). In the state of operation shown in FIG. 48 A, neither pneumatic channel (322a, 322b) is pressurized, such that each valve (2690, 2692) is in an open state. Fluid may thus freely flow through first outlet channel (662) and second outlet channel (664).

[0202] In the state of operation shown in FIG. 48B, pneumatic channel (322a) may be pressurized by pressurized air (or any other suitable fluid) that may be communicated to pneumatic channel (322a) via pneumatic port (320a). This pressurization of pneumatic channel (322a) may cause layer (400) to deform and thereby deflect downwardly in the region underneath pneumatic channel (322a), such that the bottom surface (402) of layer (400) may bear against the top surface (502) of layer (500) in the region underneath pneumatic channel (322a). This may effectively transition second valve (2690) to a closed state, such that the deformed region of layer (400) under pneumatic channel (322a) may prevent fluid from passing through second outlet channel (664). First valve (2692) may be inthe open state in the state of operation shown in FIG. 48B, such that fluid may freely flow through first outlet channel (662).

[0203] In the state of operation shown in FIG. 48C, pneumatic channel (322b) may be pressurized by pressurized air (or any other suitable fluid) that may be communicated to pneumatic channel (322b) via pneumatic port (320b). This pressurization of pneumatic channel (322b) may cause layer (400) to deform and thereby deflect downwardly in the region underneath pneumatic channel (322b), such that the bottom surface (402) of layer (400) may bear against the top surface (502) of layer (500) in the region underneath pneumatic channel (322b). This may effectively transition first valve (2692) to a closed state, such that the deformed region of layer (400) under pneumatic channel (322b) may prevent fluid from passing through first outlet channel (662). Second valve (2690) may be in the open state in the state of operation shown in FIG. 48C, such that fluid may freely flow through second outlet channel (664).

[0204] When the pneumatic pressure is relieved in the pneumatic channel (322a, 322b) over a given outlet channel (664, 662), the underlying region of layer (400) may return to a non- deformed (e.g., flat) state, thereby effectively opening the fluid pathway through that outlet channel (664, 662). In some embodiments, this return to the non-deformed state may be provided by resilient properties of layer (400). Each valve (2690, 2692) may thus be transitioned from an open state to a closed state by pressurizing the corresponding pneumatic channel (322a, 322b); and returned from the closed state to the open state by relieving pressure in the corresponding pneumatic channel (322a, 322b).

[0205] If analysis performed by image processing module (144) on images of cells captured by camera (142) reveals that a cell should be directed to first outlet channel (662) for further sorting via secondary sorting region (204), second valve (2690) may be automatically pressurized and thereby transitioned to a closed state while first valve (2692) remains in an open state as shown in FIG. 48B. System (100) may then provide further sorting via secondary sorting region (204) as will be described in greater detail below.

[0206] If analysis performedby image processing module (144) on images of cells captured by camera (142) reveals that a cell should be directed to second outlet channel (664) for extraction from cartridge (200) via sample output region (680)), first valve (2692) may be automatically pressurized and thereby transitioned to a closed state while second valve (2690) remains in an open state as shown in FIG. 48C. The fluid from sampling channel (650) may then flow through outlet channel (664) via junction (660). The fluid path from outlet channel (664) may reach sample output region (680). The fluid may exit sample output region (680)via the fluid output ports (412, 312) that maybe positioned over sample output region (680). A fluid output conduit may be coupled with the fluid output port ( 12) over sample output region (680), such that the fluid may exit cartridge (200) via this fluid output conduit. The fluid output conduit may be further coupled with a reservoir that may be either integrated into the instrument of system (100) or may be external to the instrument.

[0207] FIGS. 48-49 show the secondary sorting region (204) of cartridge (200) in greater detail. As shown, secondary sorting region (204) may receive fluid via outlet channel (662) from primary sorting region (202). Within secondary sorting region (204), outlet channel (662) may branch off into two additional fluidic channels (2700, 2702) at a junction (2704). Fluidic channel (2700) may branch off into three additional fluidic channels (2710, 2712, 2714) at another junction (2706). Similarly, fluidic channel (2708) may branch off into three additional fluidic channels (2716, 2718, 2720) at another junction (2708). Pneumatic channels (322c, 322d, 322e, 322f, 322g) may pass over fluidic channels (2710, 2712, 2714, 2716, 2718, 2720) within secondary sorting region (204). In this example, pneumatic channels (322c, 322d, 322e, 322f, 322g) may all extend along the x-dimension, and fluidic channels (2710, 2712, 2714, 2716, 2718, 2720) may all extend along the y-dimension, such that pneumatic channels (322c, 322d, 322e, 322f, 322g) may be perpendicular to pneumatic channels (322c, 322d, 322e, 322f, 322g). However, pneumatic channels (322c, 322d, 322e, 322f, 322g) may be positioned above fluidic channels (2710, 2712, 2714, 2716, 2718, 2720) along the z-dimension.

[0208] Pneumatic channel (322c) may provide a valve (2730) over fluidic channel (2710), a valve (2732) over fluidic channel (2712), and a valve (2734) over fluidic channel (2714). Thus, when pneumatic channel (322c) is pneumatically pressurized via a pneumatic port (320c) at the other end of pneumatic channel (322c) (see FIG. 51), the pneumatic pressure may cause the region of layer (400) over each fluidic channel (2710, 2712, 2714) to deform downwardly, thereby transitioning each valve (2730, 2732, 2724) to a closed state as described above with respect to valves (2690, 2692). The closed valves (2730, 2732, 2724) may prevent fluid from flowing through fluidic channels (2710, 2712, 2714) past valves (2730, 2732, 2724). In this example, valves (2730, 2732, 2724) may transition between the open and closed state simultaneously. As shown in FIG. 49, pneumatic channel (322c) may be narrower along the y-dimension in the regions where pneumatic channel (322c) passes over fluidic channels (2716, 2138, 2720). This narrowed width of pneumatic channel (322c) may prevent deformation of the region of lay er (400) over each fluidic channel (2716, 2138,2720) when pneumatic channel (322c) is pneumatically pressurized. Thus, pneumatic channel (322c) may not form valves over fluidic channels (2716, 2718, 2720).

[0209] Pneumatic channel (322d) may provide a valve (2736) over fluidic channel (2716), a valve (2738) over fluidic channel (2718), and a valve (2740) over fluidic channel (2720). Thus, when pneumatic channel (322d) is pneumatically pressurized via a pneumatic port (320d) at the other end of pneumatic channel (322d) (see FIG. 51), the pneumatic pressure may cause the region of lay er (400) over each fluidic channel (2716, 2718, 2720) to deform downwardly, thereby transitioning each valve (2736, 2738, 2740) to a closed state as described above with respect to valves (2690, 2692). The closed valves (2736, 2738, 2740) may prevent fluid from flowing through fluidic channels (2716, 2718, 2720) past valves (2736, 2738, 2740). In this example, valves (2736, 2738, 2740) may transition between the open and closed state simultaneously. As shown in FIG. 49, pneumatic channel (322d) may be narrower along the y-dimension in the regions where pneumatic channel (322d) passes over fluidic channels (2710, 2712, 2714). This narrowed width of pneumatic channel (322d) may prevent deformation of the region of lay er (400) over each fluidic channel (2710, 2712, 2714) when pneumatic channel (322d) is pneumatically pressurized. Thus, pneumatic channel (322d) may not form valves over fluidic channels (2710, 2712, 2714).

[0210] Pneumatic channel (322e) may provide a valve (752) over fluidic channel (2712), a valve (754) over fluidic channel (2714), a valve (2746) over fluidic channel (2716), and a valve (2748) over fluidic channel (2718). Thus, when pneumatic channel (322e) is pneumatically pressurized via pneumatic port (320e) at the other end of pneumatic channel (322e) (see FIG. 51), the pneumatic pressure may cause the region of layer (400) over each fluidic channel (2712, 2716, 2716, 2718) to deform downwardly, thereby transitioning each valve (752, 754, 2746, 2748) to a closed state as described above with respect to valves (2690, 2692). The closed valves (752, 754, 2746, 2748) may prevent fluid from flowing through fluidic channels (2712, 2716, 2716, 2718) past valves (752, 754, 2746, 2748). In this example, valves (752, 754, 2746, 2748) may transition between the open and closed state simultaneously. As shown in FIG. 49, pneumatic channel (322e) may be narrower along the y-dimension in the regions where pneumatic channel (322e) passes over fluidic channels (2710, 2720). This narrowed width of pneumatic channel (322e) may prevent deformation of the region of layer (400) over each fluidic channel (2710, 2720) when pneumatic channel (322e) is pneumatically pressurized. Thus, pneumatic channel (322e) may not form valves over fluidic channels (2710, 2720).

[0211] Pneumatic channel (322f) may provide a valve (2770) over fluidic channel (2710), a valve (2774) over fluidic channel (2714), a valve (2786) over fluidic channel (2716), and a valve (2790) over fluidic channel (2720). Thus, when pneumatic channel (322f) is pneumatically pressurized via a pneumatic port (320f) at the other end of pneumatic channel (322f) (see FIG. 51), the pneumatic pressure may cause the region of layer (400) over each fluidic channel (2710, 2714, 2716, 2720) to deform downwardly, thereby transitioning each valve (2770, 2774, 2776, 2790) to a closed state as described above with respect to valves (2690, 2692). The closed valves (2770, 2774, 2776, 2790) may prevent fluid from flowing through fluidic channels (2710, 2714, 2716, 2720) past valves (2770, 2774, 2776, 2790). In this example, valves (2770, 2774, 2776, 2790) may transition between the open and closed state simultaneously. As shown in FIG. 49, pneumatic channel (322f) may be narrower along the y-dimension in the regions where pneumatic channel (322f) passes over fluidic channels (2712, 2718). This narrowed width of pneumatic channel (322f) may prevent deformation of the region of layer (400) over each fluidic channel (2712, 2718) when pneumatic channel (322f) is pneumatically pressurized. Thus, pneumatic channel (322f) may not form valves over fluidic channels (2712, 2718).

[0212] Pneumatic channel (322g) may provide a valve (2771) over fluidic channel (2710), a valve (2773) over fluidic channel (2712), a valve (2798) over fluidic channel (2718), and a valve (2791) over fluidic channel (2720). Thus, when pneumatic channel (322g) is pneumatically pressurized via a pneumatic port (320e) at the other end of pneumatic channel (322g) (see FIG. 51), the pneumatic pressure may cause the region of layer (400) over each fluidic channel (2710, 2712, 2718, 2720) to deform downwardly, thereby transitioning each valve (2771, 2773, 2798, 2791) to a closed state as described above with respect to valves (2690, 2692). The closed valves (2771, 2773, 2798, 2791) may prevent fluid from flowing through fluidic channels (2710, 2712, 2718, 2720) past valves (2771, 2773, 2798, 2791). In this example, valves (2771, 2773, 2798, 2791) transition between the open and closed state simultaneously. As shown in FIG. 49, pneumatic channel (322g) may be narrower along the y-dimension in the regions where pneumatic channel (322g) passes over fluidic channels (2714, 2716). This narrowed width of pneumatic channel (322g) may prevent deformation of the region of layer (400) over each fluidic channel (2714, 2716) when pneumatic channel (322g) is pneumatically pressurized. Thus, pneumatic channel (322g) may not form valves over fluidic channels (2714, 2716).

[0213] As described above, when a pneumatic channel (322c, 322d, 322e, 322f, 322g) is in a pneumatically pressurized state, the valves (2730, 2732, 2734, 2736, 2738, 2740, 752, 754,2746, 2748, 2770, 2774, 2786, 2790, 2771, 2773, 2798, 2791) of that pneumatic channel (322c, 322d, 322e, 322f, 322g) may be in a closed state. When a pneumatic channel (322c, 322d, 322e, 322f, 322g) is in a non-pressurized state, the valves (2730, 2732, 2734, 2736, 2738, 2740, 752, 754, 2746, 2748, 2770, 2774, 2786, 2790, 2771, 2773, 2798, 2791) of that pneumatic channel (322c, 322d, 322e, 322f, 322g) may be in an open state. Fluid may be allowed to flow through, or prevented from flowing through, each fluidic channel (2710, 2712, 2714, 2716, 2718, 2720), and thereby reach the corresponding well (750, 752, 754, 756, 758, 760), based on whether all the valves (2730, 2732, 2734, 2736, 2738, 2740, 752, 754, 2746, 2748, 2770, 2774, 2786, 2790, 2771, 2773, 2798, 2791) along the fluidic channel (2710, 2712, 2714, 2716, 2718, 2720) are in an open state. If one or more valves (2730, 2732, 2734, 2736, 2738, 2740, 752, 754, 2746, 2748, 2770, 2774, 2786, 2790, 2771, 2773, 2798, 2791) along a fluidic channel (2710, 2712, 2714, 2716, 2718, 2720) is / are in a closed state, then fluid may not flow through fluidic channel (2710, 2712, 2714, 2716, 2718, 2720) and reach the corresponding well (750, 752, 754, 756, 758, 760).

[0214] The following table provides an example of the different pneumatic states that may be provided in pneumatic channels (322c, 322d, 322e, 322f, 322g) to permit or prevent fluid (and a cell contained therein) to flow to each well (750, 752, 754, 756, 758, 760):

[0215] TABLE

[0258] In some scenarios, it may be beneficial to provide additional assistance to the flow of fluid from outlet channel (662) through whichever fluidic channel (2710, 2712, 2714, 2716, 2718, 2720) is selected for routing via secondary sorting region (204) to reach a corresponding selected well (750, 752, 754, 756, 758, 760). To provide such assistance, additional fluid may be communicated through a fluid input conduit that is coupled with the fluid input port (310) over flow drive fluid receiving region (670) of cartridge (200). This additional fluid may reach outlet channel (662) via ports (310, 410) over flow drive fluid receiving region (670) and further via fluidic channel (672). At the time this additional fluid is communicated to outlet channel (662), the pneumatic valve between outlet channel (662) and junction (660) may be in a closed state. As shown in FIG. 51, a pneumatic valve (2795) may be positioned along fluidic channel (672) downstream of flow drive fluid receiving region (670). Pneumatic valve (2795) may be closed through pneumatic pressurization of pneumatic channel (322h) via pneumatic port (320h).

[0259] The additional fluid from flow drive fluid receiving region (670) and fluidic channel (672) may provide a “boost” to fluid in outlet channel (662), thereby further driving the fluid from outlet channel (662) through the selected fluidic channel (2710, 2712, 2714, 2716, 2718, 2720); and ultimately to the selected well (750, 752, 754, 756, 758, 760). Whichever valves (2730, 2732, 2734, 2736, 2738, 2740, 752, 754, 2746, 2748, 2770, 2774, 2786, 2790, 2771, 2773, 2798, 2791) are open to allow the sample cell carrying fluid to flow from outlet channel (662) to the selected well (750, 752, 754, 756, 758, 760) may remain open as needed to allow the boosting fluid from flow drive fluid receiving region (670) to adequately flow through the fluidic channel (2710, 2712, 2714, 2716, 2718, 2720) corresponding to the selected well (750, 752, 754, 756, 758, 760).

[0260] System (100) may execute a control algorithm to automatically select which pneumatic valves (2690, 2692, 2730, 2732, 2734, 2736, 2738, 2740, 752, 754, 2746, 2748, 2770, 2774, 2786, 2790, 2771, 2773, 2798, 2791)to activate. This control algorithm may be executed in response to data from image processing module (144). In other words, image processing module (144) may classify or otherwise analyze images of cells captured by camera (142) as the cell -containing fluid passes through imaging region (2900), and the pneumatic valves 2690, 2692, 2730, 2732, 2734, 2736, 2738, 2740, 752, 754, 2746, 2748, 2770, 2774, 2786, 2790, 2771, 2773, 2798, 2791) described above may provide sorting of cells in the fluid based on such image processing. For instance, cells of a first type (as identified by image processing module (144)) may be routed via pneumatic valving atprimary and secondary sorting regions (202, 204) to a first well (750), cells of a second type (as identified by image processing module (1 4)) may be routed via pneumatic valving at primary and secondary sorting regions (202, 204) to a second well (752), and cells of a third type (as identified by image processing module (144)) may be routed via pneumatic valving at primary sorting region (202) to sample output region (680).

[0261] B. Example of Flow Control Features of Cartridge

[0262] As noted above, a fluid containing sample cell may be communicated to cartridge (200) via a fluid input conduit that may be positioned over sample fluid receiving region (600); while a flow control fluid may be communicated to cartridge (200) via a fluid input conduit that may be positioned over flow control fluid receiving region (620). FIG. 41 shows these regions (600, 620) in greater detail. In some embodiments, the flow control fluid may include a buffer fluid. In some examples the flow control fluid may further include beads; while in other examples the flow control fluid may not include beads. The flow control fluid may include a bio-compatible fluid. In some embodiments, the flow control fluid may have a viscosity that differs from the viscosity of the fluid containing sample cells. In other examples, other kinds of fluid may be used for flow control fluid.

[0263] As shown, sample fluid receiving region (600) may comprise a teardrop shaped recess in the bottom surface (404) of layer (400), with an array of filtering elements (2602) positioned within the teardrop shape. As best seen in FIG. 42, each filtering element (2602) in this example may be in the form of a cylindraceous structure that extends down to top surface (502) of layer (500). Filtering elements (2602) may be spaced apart from each other with enough distance to allow cells to be carried by the cell-containing fluid through the recess of fluid receiving region (600) to fluidic channel (604). However, filtering elements (2602) may be close enough to each other to filter out any debris that may be present in the cell-containing fluid, such that filtering elements (2602) may prevent unwanted clogging of fluidic channel (604).

[0264] Flow control fluid receiving region (620) may comprise a circle shaped recess in the bottom surface (404) of layer (400), with an array of filtering elements (2622) positioned within the circle shape. Filtering elements (2622) of flow control fluid receiving region (620) may be structurally configured and operable just like filtering elements (2602) described above. Filtering elements (2622) may thus prevent unwanted clogging of a fluidic channel (2624), which may provide a pathway from flow control fluid receiving region (620) to fluidic channels (626). As shown in FIG. 41, fluidic channels (626) may include a first fluidic channel (626a) and a second fluidic channel (626b), which may have mirror symmetrywith each other. Each fluidic channel (626) may have a serpentine configuration with a herringbone region (2630) and an outlet region (2638) leading to junction (640).

[0265] While sample fluid receiving region (600) and flow control fluid receiving region (620) are described above as including filtering elements (2602, 2622), other portions of cartridge (200) may also include filtering elements like filtering elements (2602, 2622). For instance, fluidic test input region (450), flush input regions (460), flush output regions (462), flow drive fluid receiving region (670), and / or sample output region (680) may each include filtering elements like filtering elements (2602, 2622).

[0266] In some embodiments, it may be desirable to carefully control the fluid flow dynamics within sampling channel (650) during operation of system (100) with cartridge (200).Controlling the fluid flow dynamics within sampling channel (650) may ensure that the cells in in the fluid communicated along sampling channel (650) have a desired spacing relative to each other and / or relative to the three-dimensional confines of sampling channel (650).Providing such control over the spacing of the cells relative to each other and / or relative to the three-dimensional confines of sampling channel (650) may optimize the imaging of the cells within imaging region (2900), which may in turn optimize the processing of the cell images and the results obtained through such image processing. The following description provides examples of how the fluid flow dynamics within sampling channel (650) may be controlled.

[0267] C. Examples of Mixing Structures in Side Channels Upstream of Junction

[0268] In some embodiments, it may be desirable to perform a calibration of camera (142) and objective lens assembly (140) before capturing images of cells in imaging region (2900). In some of those examples, it may be desirable to communicate beads (or other particles) having a known structural configuration along sampling channel (650), such that camera (142) may capture images of the beads as they pass through imaging region (2900) during a calibration routine. In some embodiments, such beads (or other particles) may also be communicated along sampling channel (650) while sample cells (or other sample particles) are also communicated along sampling channel (650). The presence of the beads in sampling channel (650) may allow image processing module (144) to detect changes in the structural configuration of sampling channel (650) during operation of system (100), such as expansion of sampling channel (650) caused by thermal expansion of cartridge (200) during operation of system (100). In some such examples, such changes in the structural configuration of sampling channel (650) during operation of system (100) may be detected due to a tendency of beads to flow along separate x-y planes that are separated from each other along the z-dimension by a distance that varies with the structural configuration of sampling channel (650).

[0269] In some cases where beads are used, it may be beneficial to communicate those beads through fluidic channels (626). Those beads may tend to arrange themselves within the fluid flowing along fluidic channels (626) in a predictable arrangement. Even though it may be desirable to have a predictable arrangement of particles (e.g., cells) as those particles travel along sampling channel (650) In some embodiments, it may be desirable for particles to have an unpredictable arrangement before entering junction (640) in some examples. An unpredictable arrangement of particles upstream of junction (640) may in fact lead to a more predictable arrangement of particles downstream of junction (640). It may therefore be desirable in some examples to provide a feature in fluidic channels (626) that will add chaos to the arrangement of beads in fluid that flows through fluidic channels (626).

[0270] As noted above, each fluidic channel (626) may include a herringbone region (2630). FIGS. 43-45 show herringbone region (2630) in greater detail. Herringbone region (2630) may serve as a mixing feature and thus provide chaos to the arrangement of beads in fluid that flows through herringbone region (2630). Each herringbone region (2630) may include a plurality of chevron shaped recesses (2634) above the flow channel (2632) through herringbone region (2630). Each recess (2634) may include a ceiling (2634) and set of sidewalls (2636). In some embodiments, as shown in FIG. 45, sidewalls (2636) may define a length (L2) of approximately 60 pm. Sidewalls (2636) may also form angles (0) with each other at approximately 45 degrees. Ceiling (2634) may be positioned at a height (H3) of approximately 33 pm relative to the bottom of each sidewall (2636). The specific dimensions provided above are not intended to be limiting. Other dimensions may be used.

[0271] FIG. 46 A shows an example of an arrangement of beads (652) in fluidic channel (626) upstream of herringbone region (2630); while FIG. 46B shows an example of an arrangement of beads (652) in fluidic channel (660) in outlet region (2638) of fluidic channel (626) downstream of herringbone region (2630). As shown, the arrangement of beads (652) upstream of herringbone region (2630) may be substantially orderly; whereas the arrangement of beads (652) downstream of herringbone region (2630) may be substantially stochastic or randomized. This stochastic or randomized arrangement of beads (652) in outlet region (2638) may provide a greater likelihood that beads (652) will be subject to the flow focusing phenomenon described herein than might otherwise be achieved in the absence of herringbone region (2630). In other words, without herringbone region (2630), beads (652) may be less likely to mimic the arrangement in imaging region (2900) that would be achievedby cells later passing through imaging region (2900). Herringbone region (2630) may thus facilitate replication of cell arrangements in imaging region (2900) by bead (660) arrangements in imaging region (2900) during calibration of system (100).

[0272] While FIG. 41 shows each fluidic channel (626) having only one herringbone region (2630), each fluidic channel (626) may have two or more herringbone regions (2630) in other examples. Some other examples may omit herringbone regions (2630).

[0273] D. Examples of Flow Resistance Relationships in Channels of Junction

[0274] In some embodiments, it may be desirable to maximize the stability of the flow rate of fluid along the entire length of sampling channel (650). For instance, in cases where pneumatic valves are actuated downstream of junction (660) to sort cells in response to image analysis of the cells as they pass through imaging region (2900), a stable flow rate of fluid may ensure that the cells are sorted as intended. In other words, a stable flow rate through sampling channel (650) may ensure appropriate synchronization between valve timing and image capture / analysis. The inclusion of flow focusing features such as those described below may tend to complicate the achievement of a stable flow rate through sampling channel (650).

[0275] In some embodiments, it may also be desirable to allow the flow rate of fluid being input through fluid input port (410) of sample fluid receiving region (600), and to allow the flow rate of fluid being input through fluid input port (410) of flow control fluid receiving region (620) to be adjusted, while still providing a stable flow rate through sampling channel (650). Allowing greater flexibility in input fluid flow rates may increase the versatility of cartridge (200), such as by allowing end users to meet different fluid flow requirements based on the process protocols at hand.

[0276] The above-described results may be achieved by providing tuned flow resistance through fluidic channels (604, 626, 650) as described below. In particular, the stability of flow along sampling channel (650) may be provided or promoted, in part, through precise control of the flow rate of fluid entering junction (640). In turn, the control of the flow rate of fluid entering junction (640) maybe provided, in part, by providing tuned flow resistance through fluidic channel (604) and each outlet region (2638) of each fluidic channel (626). By tuning the flow resistance through fluidic channel (604) and each outlet region (2638) of each fluidic channel (626), cartridge (200) may accommodate different flow rates of fluid received via sample fluid receiving region (600) and flow control fluid receiving region (620), while still maintaining a certain flow rate ratio through fluidic channel (604) and each outlet region (2638). This may allow cartridge (200) to accommodate different end user needs, which mayinclude different flow rates and driving pressures through sample fluid receiving region (600) and flow control fluid receiving region (620).

[0277] The pressure of sample-carrying fluid communicated through fluidic channel (604) may be expressed as “Pi,” the flow resistance of fluidic channel (604) may be expressed as “Ri,” and the flow rate through fluidic channel (604) may be expressed as “p ” The pressure of flow control fluid communicated through each fluidic channel (626) may be expressed as “P2,” the flow resistance of each fluidic channel (626) may be expressed as “R2,” and the flow rate through each fluidic channel (626) may be expressed as “I2” The pressure of the combined fluid communicated through sampling channel (650) may be expressed as “Po,” the flow resistance of sampling channel (650) may be expressed as “Ro ” and the flow rate through sampling channel (650) may be expressed as “Io ” With these parameters identified, a ratio of the flow rate p of fluidic channel (604) to the flow rate I2of each fluidic channel (626) may be expressed in the following equation (I):

[0279] The flow rate Ioof sampling channel (650) may be expressed in the following equation (II):

[0281] One or more pumps (110) and / or other components may be operated to drive the fluids through fluidic channels (604, 626, 650) may achieve a desired main flow rate Ioin sampling channel (650), and ratio of flow rates Ii / I2of fluidic channels (604, 626), based on the two equations (I, II) above. As can be seen above, these equations (I, II) factor in the flow resistance values R}, R2, Ro of fluidic channels (604, 626, 650). The outcomes of these equations (I, II) may thus be influenced by how fluidic channels (604, 626, 650) are structurally configured to tune the flow resistance value R}, R2, Ro of each fluidic channel (604, 626, 650), since the flow resistance value Ay, R2, Roof each fluidic channel (604, 626, 650) may be fixed by the structural configuration of each fluidic channel (604, 626, 650).

[0282] In the present example, channels (604, 626, 650) may be structurally configured such that the flow resistance R}of fluidic channel (604) is substantially lower than the flow resistances R2, A0of channels (626, 650); and such that the flow resistance R2of each fluidic channel (626) is substantially equal to (or on the same order as) the flow resistance Roof sampling channel (650). This relationship may thusbe expressed in in the following equation (III):

[0283] (III) R1« R2~ R0

[0284] By way of example only, the value of flow resistance R] of fluidic channel (604) may range from approximately 1 / 5 of the value of the flow resistance / ?0of sampling channel (650) to approximately i of the value of the flow resistance / ?0of sampling channel (650). Similarly, the value of flow resistance Ri of fluidic channel (604) may range from approximately 1 / 5 of the value of the flow resistance R of each fluidic channel (626) to approximately i of the value of the flow resistance R2 of each fluidic channel (626).

[0285] Channels (604, 626, 650) may be structurally configured such that the flow resistance Ri of fluidic channel (604) may be substantially lower than the flow resistances R , Roof channels (626, 650) by fluidic channel (604) having a substantially shorter length than the length of channels (626, 650). Similarly, channels (604, 626, 650) may be structurally configured such that the flow resistance R2 of each fluidic channel (626) may be substantially equal to (or on the same order as) the flow resistance Ro of sampling channel (650) by each fluidic channel (626) having a length that is substantially equal to (or on the same order as) the length of sampling channel (650). To achieve substantially equal length of each fluidic channel (626) and sampling channel (650) without creating unnecessary overall length in cartridge (200), each fluidic channel (626) may have a serpentine configuration. In some embodiments, the different flow resistances Rj, R2, Ro may be achieved by using different cross-sectional areas (e.g., different heights and / or widths) among channels (604, 626, 650).

[0286] With the relationships between / ?;, R2, Ro provided as expressed in equation (III), the ratio of the flow rateof each fluidic channel (626) to the flow rate I2of fluidic channel (604) may be simplified as the following equation (IV):

[0288] Similarly, with the relationships between / ?;, R2, Ro as expressed in equation (III), the flow rate Ioof sampling channel (650) may simplified as the following equation (IV):

[0290] The substantially lower flow resistance / ?; of fluidic channel (604) may be due, at least in part, to fluidic channel (604) having a substantially shorter length than the lengths of channels (626, 650). In some embodiments, the flow resistance R2of each fluidic channel (626) may range from approximately 10 times the flow resistance / ?; of fluidic channel (604) to approximately 50 times the flow resistance / ?; of fluidic channel (604); or more particularly, may be approximately 20 times the flow resistance / ?; of fluidic channel (604). In some embodiments, the flow resistance of sampling channel (650) may range from being approximately equal to the flow resistance R2of each fluidic channel (626) to beingapproximately 5 times the flow resistance R2of each fluidic channel (626); or more particularly, may be approximately 3 times the flow resistance R2of each fluidic channel (626).

[0291] Minimizing the flow resistance Ri of fluidic channel (604) may minimize the fluid pressure P}applied through sample fluid receiving region (600) and fluidic channel (604), which may in turn minimize the risk of damage to cells contained in the fluid that is communicated through sample fluid receiving region (600) and fluidic channel (604). Having a higher pressure P2of fluid in fluidic channels (626) (e.g., due to the substantially higher flow resistance of fluidic channels (626)) may not be problematic since the fluid communicated through flow control fluid receiving region (620) and fluidic channels (626) may not contain cells that might otherwise be damaged. Thus, in some examples of operation, the pressure of fluid in fluidic channels (626) may be set to be higher than the pressure Pi of fluid in fluidic channel (604). In addition, to provide positive inflow from fluidic channel (604) into junction (640), the pressure P2of fluid in fluidic channels (626) and the pressure P}of fluid in fluidic channel (604) may be controlled to adhere to the following equation (V): l0292l <v> S < S

[0293] E. Example of Ventilation Features in Cartridge

[0294] The air or other gas that is used to provide pneumatic pressurization in pneumatic channels (322) may hereinafter be referred to as “pneumatic pressure gas.” In some embodiments, after one or more pneumatic channels (322) have been pressurized during use of cartridge (200), it may be possible that some of the pneumatic pressure gas may tend to enter the space between layers (300, 400), between bottom surface (320) and top surface (402). This may tend to create separation between layers (300, 400). In some embodiments, the pneumatic pressure gas may tend to build up in one or more of pneumatic channels (322) and / or migrate from one pneumatic channel (322) to another pneumatic channel (322) after cartridge (200) is used for some time. Even if the pneumatic pressure gas does not migrate through the space between layers (300, 400) or otherwise cause separation between layers (300, 400), in some examples the material forming layer (400) may allow some pneumatic pressure gas to pass through layer (400) via diffusion. Regardless of whether the pneumatic pressure gas diffuses through layer (400) and / or between layers (300, 400), the pneumatic pressure gas may eventually reach one or more fluidic channels such as sampling channel (650). One or more of the above-described effects may occur in some cases where one ormore pneumatic valves of cartridge (200) is / are maintained in a closed state for a long period of time and / or in other scenarios.

[0295] To prevent or mitigate the risk of pneumatic pressure gas passing through layer (400) and / or between layers (300, 400), cartridge (200) of the present example may include venting features that allow the pneumatic pressure gas to escape to atmosphere. These venting features may not adversely affect the ability of the pneumatic pressure gas to achieve successful operation of the valves of cartridge (200) as described above. Venting features of the present example are shown in FIGS. 51-52, and include a set of vent passageways (2800, 2810) and vent channels (2802, 2804). Vent passageways (2800, 2810) may extend through the full thickness of layer (300) along the z-dimension, such that each vent passageway (2800, 2810) is open at the top surface (302) and at the bottom surface (304). Each vent passageway (2800, 2810) may further provides a path to the atmosphere to allow venting to the atmosphere.

[0296] Each vent channel (2802, 2804) may be formed as a recess in bottom surface (304). Vent channels (2802) may extend directly from vent passageway (2800) along the x-y plane; and vent channels (2804) may branch off from vent channels (2802) along the x-y plane. Top surface (402) of layer (400) may define a bottom of each vent channel (2802, 2804) in this example. Any pneumatic pressure gas that reaches vent channels (2802, 2804) (e.g., through layer (400) and / or through a space between layers (300, 400)) may be relieved to the atmosphere alongthe space defined collectively by top surface (502) of layer (500) and each vent channel (2802, 2804), with such space eventually reaching vent passageway (2800).

[0297] As shown in FIGS. 51-52, each vent channel (2802) may be positioned to be near one or more pneumatic channels (322). In particular, vent channel (2804a) may be positioned near pneumatic channel (322h); vent channel (2804b) maybe positioned between pneumatic channels (322h, 322c); vent channel (2804c) may be positioned between pneumatic channels (322c, 322d); vent channel (2804d) may be positioned between pneumatic channels (322d, 322e); vent channel (2804e) may be positioned between pneumatic channels (322d, 322e); vent channel (2804 f) may be positioned between pneumatic channels (322e, 322f); and vent channel (2804g) may be positioned near pneumatic channels (2804g). Vent channel (2804a) may be positioned to provide venting for pneumatic pressure gas that may tend to otherwise build up from pneumatic channel (322h); vent channel (2804b) may be positioned to provide venting for pneumatic pressure gas that may tend to otherwise build up from either or both of pneumatic channels (322h, 322c); vent channel (2804c) may be positioned to provideventing for pneumatic pressure gas that may tend to otherwise build up from either or both ofpneumatic channels (322c, 322d); vent channel (2804d) may be positioned to provideventing for pneumatic pressure gas that may tend to otherwise build up from either or both of pneumatic channels (322d, 322e); vent channel (2804e) maybe positioned to provideventing for pneumatic pressure gas that may tend to otherwise build up from either or both of pneumatic channels (322d, 322e); vent channel (2804 f) may be positioned to provide venting for pneumatic pressure gas that may tend to otherwise build up from either or both of pneumatic channels (322e, 322f); and vent channel (2804g) may be positioned to provide venting for pneumatic pressure gas that may tend to otherwise build up from pneumatic channel (2804g).

[0298] As described above, vent passageway (2800) may be positioned to relieve to atmosphere any pneumatic pressure gas that reaches any of vent channels (2802, 2804). Vent passageway (2810) may not have any associated vent channels in this example, though vent passageway (2810) may have one or more associated vent channels in some other examples. Even without any associated vent channels, vent passageway (2810) may still effectively relieve to the atmosphere any pneumatic pressure gas that reaches vent passageway via layer (400) or via the space between layers (300, 400).

[0299] FIG. 53 shows an example of another arrangement that may be used to provide ventilation in a cartridge (102) of system (100). Specifically, FIG. 53 shows features of another cartridge that may include a sampling channel (3650) that is like sampling channel (650), and a plurality of pneumatic channels (3322) that are like pneumatic channels (322). Specifically, pneumatic channel (3322b) may be like pneumatic channel (322b), pneumatic channel (3322c) may be like pneumatic channel (322c), pneumatic channel (3322d) may be like pneumatic channel (322d), pneumatic channel (3322e) may be like pneumatic channel (322e), pneumatic channel (3322f) may be like pneumatic channel (322f), and pneumatic channel (3322g) may be like pneumatic channel (322g). The cartridge venting arrangement of FIG. 53 may also include a plurality of vent passageways (3810) that may be like vent passageway (3810).

[0300] Vent passageway (3810a) may be positioned near pneumatic channels (3322b, 3322h), such that vent passageway (3810a) may provide venting for pneumatic pressure gas that may tend to otherwise build up from either or both of pneumatic channels (3322b, 3322h). Vent passageway (3810b) may be positioned near pneumatic channels (3322h, 3322c), such that vent passageway (3810b) may provide venting for pneumatic pressure gas that may tend to otherwise build up from either or both of pneumatic channels (3322h, 3322c). Vent passageway (3810c) may be positioned near pneumatic channels (3322d,3322e), such that vent passageway (3810c) may provide venting for pneumatic pressure gas that may tend to otherwise build up from either or both of pneumatic channels (3322d, 3322e). Vent passageway (3810d) may be positioned near pneumatic channels (3322e, 3322f), such that vent passageway (38 lOd) may provide venting for pneumatic pressure gas that may tend to otherwise build up from either or both of pneumatic channels (3322e, 3322f). Vent passageway (3810e) may be positioned near pneumatic channels (3322f, 3322g), such that vent passageway (3810e) may provide venting for pneumatic pressure gas that may tend to otherwise build up from either or both of pneumatic channels (3322f, 3322g). Vent passageway (38 lOf) may be positioned near pneumatic channel (3322g), such that vent passageway (381 Of) may provide venting for pneumatic pressure gas that may tend to otherwise build up from pneumatic channel (3322g).

[0301] While vent passageways (3810) of FIG. 53 do not have any corresponding vent channels like vent channels (2802, 2804), some other examples may include one or more vent channels that allow pneumatic pressure gas to flow toward one or more of vent passageways (3810) of FIG. 53.

[0302] F. Example of Conduit Flush Ports in Cartridge

[0303] In some embodiments, system (100) maybe used in different processes where one or more fluids are communicated through one or more cartridges (200) in different sessions of use. Some examples of system (100) may include integral fluid conduits that are reused with the same cartridge (200) and / or with different cartridges during different sessions of use of system (100). In such scenarios, such fluid conduits may be cleaned between different sessions of use of system (100), to avoid or mitigate any risk of contamination from residual fluids or materials that might otherwise remain in such fluid conduits between sessions of use of system (100). In cartridge (200), flush input regions (460) and flush output regions (462) may be used to flush fluid conduits that are otherwise used to communicate fluids to or from cartridge (200).

[0304] FIG. 54A shows an arrangement where a first conduit (2824) may be coupled with sample fluid receiving region (600) and with a source (2824) of a fluid containing one or more sample cells. For instance, source (2824) may constitute pump (110) and reservoir (112) of system (100) as described above. In the present example, first conduit (2824) comprises a flexible tube that is inserted into fluid input port (310a) directly over sample fluid receiving region (600), with the material of layer (300) providing a friction fit to retain and seal first conduit (2824) relative to cartridge (200). A second conduit (2822) may be coupled with flow control fluid receiving region (620) and with a source (2826) of flowcontrol fluid. In some embodiments, the flow control fluid includes a buffer fluid. In some embodiments, the flow control fluid further includes beads; while in other examples the flow control fluid does not include beads. The flow control fluid may include a bio -compatible fluid. In some embodiments, the flow control fluid has a viscosity that differs from the viscosity of the fluid containing sample cells. In other examples, other kinds of fluid may be used for flow control fluid. In the present example, second conduit (2822) comprises a flexible tube that is inserted into fluid input port (310b) directly over flow control fluid receiving region (620), with the material of layer (300) providing a friction fit to retain and seal second conduit (2822) relative to cartridge (200).

[0305] System (100) may be operated with cartridge (200) and conduits (2820, 2822) in the state shown in FIG. 54A, as described herein, to capture images of sample cells, classify the imaged sample cells, and sort the sample cells. Once this session of use is complete (e.g., after all of the sample cells from source (2824) have been processed), an operator may pull first conduit (2820) out of fluid input port (310a) and pull second conduit (2822) out of fluid input port (310b). The operator may then couple first conduit (2820) with flush output region (462a) by inserting first conduit (2820) into fluid output port (312a) directly over flush output region (462a). The material of layer (300) may provide a friction fit to retain and seal first conduit (2820) relative to cartridge (200) at fluid output port (312a). The other end of first conduit (2820) may be decoupled from source (2820) and coupled with a waste reservoir (2825). The operator may also couple second conduit (2822) with flush input region (460a) by inserting second conduit (2822) into fluid input port (310c) directly over flush input region (460a). The material of layer (300) may provide a friction fit to retain and seal second conduit (2822) relative to cartridge (200) at fluid input port (310c). The other end of second conduit (2822) may be decoupled from source (2826) and coupled with a source (2827) of flush fluid. An example of the resulting arrangement is shown in FIG. 54B.

[0306] As noted above, a fluidic channel (464a) may extend between flush input region (460a) and flush output region (462a). Flush fluid from source (2827) may thus be communicated through second conduit (2822) to flush input region (460a), through fluidic channel (464a), out flush output region (462a) and along first conduit (2820) to waste reservoir (2825). In some embodiments, the flush fluid may be pushed through this fluid circuit from the source (2827) side of the fluid circuit, such as by a pump. In some other examples, the flush fluid may be pulled through this fluid circuit from the waste reservoir (2825) side of the fluid circuit. In either of these arrangements, the wash fluid may flow through both conduits (2820, 2822), with cartridge (200) providing a connection path for thewash fluid to flow between conduits (2820, 2822). After conduits (2820, 2822) have been sufficiently flushed, conduits (2820, 2822) may be returned to the arrangement shown in FIG. 54A.

[0307] While first conduit (2820) may be coupled with flush output region (462a) and second conduit (2822) may be coupled with flush input region (460a) during the flushing stage shown in FIG. 54B and described above, in other examples second conduit (2822) may be coupled with flush output region (462a) and first conduit (2820) may be coupled with flush input region (460a) during the flushing stage.

[0308] FIG. 55 A shows an arrangement where a third conduit (2830) may be coupled with flow drive fluid receiving region (670) and with a source (2834) of flow drive fluid. In some embodiments, the same fluid that is communicated to flow control fluid receiving region (620) for flow control in cartridge (200) may also be communicated to flow drive fluid receiving region (670) to boost fluid flow through and past secondary sorting region (204). In some such examples, source (2824) and source (2834) may be the same source. In some embodiments, the additional boosting fluid provided via flow drive fluid receiving region (670) and fluidic channel (672) may include any bio-compatible fluid, such as liquid culture medium, cell lysis solution, or an oil based fluid. In other examples, other kinds of fluid may be used.

[0309] In the present example, third conduit (2830) comprises a flexible tube that is inserted into fluid input port (310c) directly over flow drive fluid receiving region (670), with the material of layer (300) providing a friction fit to retain and seal third conduit (2830) relative to cartridge (200). A fourth conduit (2832) may be coupled with sample output region (680) and with a receptacle (2836) (e.g., vial, tube, etc.) that receives fluid communicated from cartridge (200) via sample output region (680). In the present example, fourth conduit (2832) comprises a flexible tube that is inserted into fluid output port (312c) directly over sample output region (680), with the material of layer (300) providing a friction fit to retain and seal fourth conduit (2832) relative to cartridge (200).

[0310] System (100) may be operated with cartridge (200) and conduits (2830, 2832) in the state shown in FIG. 55 A, as described herein, to capture images of sample cells, classify the imaged sample cells, and sort the sample cells. Once this session of use is complete (e.g., after all of the sample cells from source (2824) have been processed), an operator may pull third conduit (2830) out of fluid input port (310c) and pull fourth conduit (2832) out of fluid output port (312c). The operator may then couple third conduit (2830) with flush output region (462b) by inserting third conduit (2830) into fluid output port (312b) directly overflush output region (462b). The material of layer (300) may provide a friction fit to retain and seal third conduit (2830) relative to cartridge (200) at fluid output port (312b). The other end of third conduit(2830) may be decoupledfrom source (2834) and coupled with a waste reservoir (2835). An example of the resulting arrangement is shown in FIG. 55B. In some embodiments, waste reservoir (2835) is the same as waste reservoir (2825). In examples where the same waste reservoir (2825, 2835) to receive waste from first and third conduits (2824, 2830), the fluidic path between first conduit (2824) and the shared reservoir (2825, 2835) may differ from the fluidic path between third conduit (2830) and the shared reservoir (2825, 2835).

[0311] The operator may also couple fourth conduit (2832) with flush input region (460b) by inserting fourth conduit (2832) into fluid input port (3 lOd) directly over flush input region (460b). The material of layer (300) may provide a friction fit to retain and seal fourth conduit (2832) relative to cartridge (200) at fluid input port (3 lOd). The other end of fourth conduit (2832) may be decoupled from receptacle (2836) and coupled with a source (2827) of flush fluid. An example of the resulting arrangement is shown in FIG. 55B. In some embodiments, source (2837) is the same as source (2827). In examples where the same source (2827, 2837) to is used to provide flush fluid to second and fourth conduits (2822, 2832), the fluidic path between second conduit (2822) and the shared source (2827, 2837) may differ from the fluidic path between fourth conduit (2832) and the shared source (2827, 2837).

[0312] As noted above, a fluidic channel (464b) may extend between flush input region (460b) and flush output region (462b). Flush fluid from source (2837) may thus be communicated through fourth conduit (2832) to flush input region (460b), through fluidic channel (464b), out flush output region (462b) and along third conduit (2830) to waste reservoir (2835). In some embodiments, the flush fluid is pushed through this fluid circuit from the source (2837) side of the fluid circuit, such as by a pump. In some other examples, the flush fluid is pulled through this fluid circuit from the waste reservoir (2835) side of the fluid circuit. In either of these arrangements, the wash fluid may flow through both conduits (2830, 2832), with cartridge (200) providing a connection path for the wash fluid to flow between conduits (2830, 2832). After conduits (2830, 2832) have been sufficiently flushed, conduits (2830, 2832) may be returned to the arrangement shown in FIG. 55A.

[0313] While third conduit (2830) may be coupled with flush output region (462b) and fourth conduit (2832) is coupled with flush input region (460b) during the flushing stage shown in FIG. 55B and described above, in other examples fourth conduit (2832) maybe coupled withflush output region (462b) and third conduit (2830) may be coupled with flush input region (460b) during the flushing stage.

[0314] G. Example of Visual Fiducials and Focusing Features of Cartridge

[0315] As noted above, objective lens assembly (140) and camera (142) may capture images of cells conveyed via fluid along sampling channel (650), with such images being captured within imaging region (2900). In some examples it may be beneficial to ensure that cartridge (200) is appropriately positioned in relation to objective lens assembly (140) and camera (142), to ensure that objective lens assembly (140) and camera (142) may adequately capture images of cells conveyed via fluid along sampling channel (650). This may include ensuring that cartridge (200) is appropriately seated in a cartridge mount of the instrument of system (100); that the cartridge mount is appropriately positioned within the instrument relative to objective lens assembly (140) and camera (142); and / or that objective lens assembly (140) and camera (142) are otherwise appropriately positioned relative to cartridge (200).

[0316] FIGS. 56-60 show an example optical fiducial region (2840) of cartridge (200). Optical fiducial region (2840) may be positioned near imaging region (2900) in this example. Optical fiducial region (2840) may include a plurality of fiducial elements (2844) arranged in a rectangle with four corners (2842a, 2842b, 2842c, 2842d). Fiducial elements (2844) may include recesses in bottom surface (404) of layer (400), such that fiducial elements (2844) may have optically detectable edges extending along the z-dimension, thereby defining optically detectable shapes along the x-y plane. These shapes may include ellipses.

[0317] The elliptical shape of each fiducial element (2844) may differ from the elliptical shape of the other fiducial elements (2844). For instance, as best seen in FIG. 57, fiducial elements (2844) in the upper left-hand comer (2842a) of optical fiducial region (2840) may have a major axis extending along the x-dimension, with the minor axis extending along the y-dimension. While the elliptical shapes of fiducial elements (2844) in the upper left-hand corner (2842a) of optical fiducial region (2840) may share this general characteristic, the lengths of the major and minor axes may still vary among fiducial elements (2844) in the upper left-hand corner (2842a).

[0318] As best seen in FIG. 58, fiducial elements (2844) may approach a circular shape at the upper right-hand corner (2842b) of optical fiducial region (2840). The length of the axis along the x-dimension of the elliptical shape for each fiducial element (2844) may gradually reduce per each fiducial element (2844) as the array of fiducial elements (2844) spans along the x-dimension, such that fiducial elements (2844) may have a longest axis along the x-dimension in the left-hand side of optical fiducial region (2840) and the shortest axis along the x-dimension in the right-hand side of optical fiducial region (2840).

[0319] As best seen in FIG. 59, which shows the lower left-hand corner (2842c) of optical fiducial region (2840), the length of the axis along the x-dimension of the elliptical shape for each fiducial element (2844) may remain the same per each fiducial element (2844) as the array of fiducial elements (2844) spans along the y-dimension. However, the length of the axis along the y-dimension of the elliptical shape for each fiducial element (2844) may gradually increase per each fiducial element (2844) as the array of fiducial elements (2844) spans along the y-dimension, such that fiducial elements (2844) may have a shortest axis along the y-dimension in the top side of optical fiducial region (2840) and the longest axis along the y-dimension in the bottom side of optical fiducial region (2840).

[0320] As best seen in FIG. 60, which shows the lower right-hand corner (2842c) of optical fiducial region (2840), the length of the axis along the y-dimension of the elliptical shape for each fiducial element (2844) may remain the same per each fiducial element (2844) as the array of fiducial elements (2844) spans along the x-dimension. However, the length of the axis along the x-dimension of the elliptical shape for each fiducial element (2844) may gradually decrease per each fiducial element (2844) as the array of fiducial elements (2844) spans along the x-dimension, such that fiducial elements (2844) may have a longest axis along the x-dimension in the left-hand side of optical fiducial region (2840) and the shortest axis along the x-dimension in the right-hand side of optical fiducial region (2840), as noted above with reference to FIG. 58.

[0321] In view of the foregoing, the elliptical shape of fiducial element (2844) at upper lefthand comer (FIG. 57) may have the longest length along the x-dimension and the shortest length along the y-dimension, the elliptical shape of fiducial element (2844) at the upper right-hand comer (FIG. 58) may have a circular shape representing the shortest axes along the x-dimension and y-dimension, the elliptical shape of fiducial element (2844) at the lower left-hand corner (FIG. 59) may have the longest axes along the x-dimension and y- dimension, and the elliptical shape of fiducial element (2844) at the lower right-hand corner (FIG. 60) may have the shortest length along the x-dimension and the longest length along the y-dimension. The elliptical shapes of the rest of fiducial elements (2844) may progressively transition from these extremes based on their positions along the x-dimension and y-dimension.

[0322] While objective lens assembly (140) and camera (142) may be primarily used to capture images of cells within imaging region (2900) during use of system (100) in someembodiments, optical fiducial region (2840) may nevertheless be within the field of view of objective lens assembly (140) and camera (142). Objective lens assembly (140) and camera (142) may thus capture an image of optical fiducial region (2840) during a setup or calibration procedure. The image processing module (144) may analyze this image to determine whether cartridge (200) is appropriately positioned within the x-y plane relative to objective lens assembly (140) and camera (142). The configuration and arrangement of the unique elliptical shapes of fiducial elements (2844) may facilitate image analysis by image processing module (144) to determine whether cartridge (200) is appropriately positioned within the x-y plane.

[0323] If the image analysis by image processing module (144) indicates that cartridge (200) is not appropriately positioned within the x-y plane, one or more adjustments may be made to ensure that cartridge (200) is appropriately positioned within the x-y plane. In some embodiments, cartridge (200) is secured to a mount that may be automatically moved by system (100) (e.g., via one or more actuators) to move cartridge (200) into the appropriate position within the x-y plane. In some other examples, system (100) may notify an operator to reposition cartridge within the x-y plane. In still other examples, objective lens assembly (140) and camera (142) may be moved along an x-y plane to ensure appropriate alignment with cartridge. Such movement of objective lens assembly (140) and camera (142) may be manual or automated (e.g., performed by one or more actuators).

[0324] In addition to providing appropriate positioning of cartridge (200) relative to objective lens assembly (140) and camera (142) and / or other components of system (100) along an x-y plane, it may be beneficial to provide appropriate focusing of objective lens assembly (140) and camera (142) relative to cartridge (200) along the z-dimension. In some embodiments, such focusing may be performed as part of an initial setup or calibration process. In the present example, and as shown in FIG. 56, cartridge (200) may include a focusing feature (2850) thatmay facilitate a focusing setup routine. Focusing feature (2850) may include a plurality of focusing elements (2852) that are positioned between optical fiducial region (2840) and sampling channel (650). Focusing elements (2852) may also be within imaging region (2900) in this example. It should therefore be understood that focusing feature (2850) may be already within the field of view of objective lens assembly (140) and camera (142) when cartridge (200) is appropriately positioned within the x-y plane.

[0325] As shown in FIG. 61, each focusing element (2852) of the present example may include a recess (2854) in bottom surface (404) of layer (400). Each recess (2854) may have a curved wall (2856) such that the cross-sectional size of recess (2854) along an x-y planevaries along the z-dimension. In some examples each recess (2854) has a paraboloid shape, though other shapes may be used, including but not limited to recesses having a rectangular cross-sectional profile. Camera (142) may capture images of recess (2854) at different positions along the z-dimension. Image processing module (144) may analyze these images to determine an appropriate focus along the z-dimension. For instance, image processing module (144) may determine the position of the bottom of recess (2854) along the z- dimension and the position of the top of recess (2854) along the z-dimension, and thereby identify the appropriate z-focus position (i.e., the position along the z-dimension at which to focus the image transmitted to camera (142)). In some embodiments, this appropriate z-focus position corresponds to the center of sampling channel (650) alongthe z-dimension. In some other examples, the appropriate z-focus position corresponds to a lower half of sampling channel (650) alongthe z-dimension or some other region of sampling channel (650) along the z-dimension.

[0326] In some embodiments, the position of cartridge (200) along the z-dimension may be adjusted in response to analysis of images focusing elements (2852) captured by camera (142). In some embodiments, the position of a focusing lens (between objective lens assembly (140) and camera (142)) alongthe z-dimension and / or the position of camera (142) alongthe z-dimension may be adjusted in response to analysis of images focusing elements (2852) captured by camera (142).

[0327] As another example of a focusing routine, referringto FIG. 62, camera (142) may be used to capture reference images of particles (2850) conveyed along sampling channel (650) during an initial setup or calibration stage. Particles (2850) may include cells, beads, or any other particles. In the example shown, flow control fluid conveyed along fluidic channels (626) may provide horizontal focus to the fluid conveyed through fluidic channel (604), such that particles (2850) are centered within sampling channel (650) along the y-dimension but are distributed across sampling channel (650) in the z-dimension within an upper vertical region (VRi) and a lower vertical region (VR2). Camera (142) may capture images of these particles (2850) in this arrangement as particles (2850) pass through imaging region (2900). These images of particles (2850) may be captured at different positions along the z- dimension.

[0328] By analyzing these images of particles (2850), image processing module (144) may determine the vertical center position (Zo) of sampling channel (650) in the z-dimension. The appropriate z-focus position may then be established based on this determination. In some embodiments, this appropriate z-focus position corresponds to the vertical center position(Zo) of sampling channel (650) in the z-dimension. In some other examples, the appropriate z-focus position corresponds to a lower half of sampling channel (650) along the z-dimension or some other region of sampling channel (650) along the z-dimension. In examples where images of particles (2850) rather than images of focusing elements (2852) are used to determine the appropriate z-focus position, the same kinds of adjustments may be made based on this determination as described above in the context of focusing elements (2852).

[0329] H. Example of Hybrid Fluidic Channels in Cartridge

[0330] As described above with reference to FIGS. 48A-48C, pneumatic valves (2690, 2692, 2730, 2732, 2734, 2736, 2738, 2740, 752, 754, 2746, 2748, 2770, 2774, 2786, 2790, 2771, 2773, 2798, 2791, 2795)may be provided for fluidic channels (662, 664, 672, 2710, 2712, 2714, 2716, 2718, 2720) having cross-sectional profiles that are rectangular shaped. In some embodiments, pneumatic valves may be provided for fluidic channels having cross-sectional profiles that are rounded rather than rectangular. A valve at a fluidic channel having a rounded cross-sectional profile may require less pneumatic pressure in an overhead pneumatic channel to achieve full closure of the valve. However, a fluidic channel having a square or rectangular cross-sectional profile may facilitate stable inertial flow focusing (e.g., along two focal planes in the z-dimension) more easily than a fluidic channel having a rounded cross-sectional profile. In addition, a fluidic channel having a square or rectangular cross-sectional profile may require less pressure to drive fluid flow through the fluidic channel. Thus, a “hybrid” cartridge may include fluidic channels that have regions with rounded cross-sectional profiles (e.g., where a valve would be positioned) and regions with rectangular cross-sectional profiles.

[0331] FIGS. 63-64 show an example of how cartridge (200) may be modified to include a hybrid fluidic channel configuration as described above. The cartridge of this example includes a sampling channel (4650) that may be like sampling channel (650) of cartridge (200), such that sampling channel (4650) may have a rectangular cross-sectional profile (along the y-z plane) along the entire length of sampling channel (4650). The features upstream of sampling channel (4650) may be the same as the features upstream of sampling channel (650). Sampling channel (4650) may terminate in a junction (4660) that is like junction (660) of cartridge (4660). This junction (4660) may further lead to a first outlet channel (4662) and a second outlet channel (4664). The features downstream of first outlet channel (4662) may be the same as the features downstream of first outlet channel (662): and the features downstream of second outlet channel (4664) may be the same as the features downstream of second outlet channel (664).

[0332] First outlet channel (4662) of this example may differ from first outlet channel (662) of cartridge (200) in that first outlet channel (662) may have a portion (4663) having a rounded cross-sectional profile and an adjacent portion (4665) having a rectangular cross- sectional profile. Portion (4663) may form part of a valve (4692), which receives pneumatic pressure via a pneumatic channel (4322b). Pneumatic channel (4322b) may be like pneumatic channel (322b). Portion (4665) may extend downstream of portion (4663). Second outlet channel (4664) of this example may differ from first outlet channel (662) of cartridge (200) in that first outlet channel (662) may have a portion (4667) having a rounded cross-sectional profile and an adjacent portion (4669) having a rectangular cross-sectional profile. In some embodiments, the rounded cross-sectional profile of portion (4667) may have a radius of curvature ranging from approximately 500 pm to approximately 1000 pm. Portion (4667) may form part of a valve (4690), which may receive pneumatic pressure via a pneumatic channel (4322a). Pneumatic channel (4322a) may be like pneumatic channel (322a). Portion (4669) may extend downstream of portion (4667).

[0333] It should be understood from FIG. 63 and the above description that pneumatic channel (4322b) may be positioned over, and thus overlap, portion (4663) along the z- dimension; but pneumatic channel (4322b) may not be positioned over, and thus may not overlap, portion (4665) along the z-dimension. Similarly, pneumatic channel (4322a) may be positioned over, and thus overlap, portion (4667) along the z-dimension; but pneumatic channel (4322a) may not be positioned over, and thus may not overlap, portion (4669) along the z-dimension.

[0334] FIGS. 64A-64B show an example of operation of valve (4690), though it should be understood that valve (4692) may operate in a similar fashion. As shown, pneumatic channel (4322a), which is in the form of a recess on the bottom surface of layer (), may be positioned over portion (4667), which may be in the form of a recess on the bottom surface of layer (4400). Portion (4667) may have a rounded cross-sectional profile along the y-z plane. In FIG. 64A, pneumatic channel (4322a) may be in a non-pressurized state, such that valve (4690) may be in an open state. Fluid may thus flow freely through valve (4690) and thereby reach fluidic components via the remainder of second outlet channel (4664) downstream of valve (4690), including portion (4669). In FIG. 64B, pneumatic channel (4322a) may be in a pressurized state. This pressurization in channel (4322a) may deform the region of layer (4400) defining portion (4667) downwardly against the underlying surface (4502), thereby transitioning valve (4690) to a closed state. When pneumatic pressure is relieved in channel(4322a), the region of layer (4400) defining portion (4667) may resiliently return back to the state shown in FIG. 64 A, thereby transitioning valve (4690) back to the closed state.

[0335] In some embodiments, the entire remainder of second outlet channel (4664) downstream of valve (4690) has a rectangular cross-sectional profile like portion (4669) described above. Also in some embodiments, the portion (4665) of first outlet channel (4662) having a rectangular cross-sectional profile may persist until reaching a secondary sorting region like secondary sorting region (204). Portions of fluidic channels along valves within such a secondary sorting region may also have a rounded cross-sectional profile like portions (4663, 4667) described above, with the remaining portions of such fluidic portions (e.g., portions that are not along valves) having rectangular cross-sectional profiles.

[0336] VI. Example of Another Cartridge

[0337] FIG. 31 shows an example of another cartridge (3000) that may be used with system (100) in place of cartridge (200). Except as otherwise noted below, cartridge (3000) of this example may be structurally configured and operable like cartridge (200). Cartridge (3000) of this example may include a sample fluid receiving region (3002) and a flow control fluid receiving region (3004). A flow channel (3006) may lead from sample fluid receiving region (3002) to a junction (3006). A pair of flow channels (3008) may lead from flow control fluid receiving region (3004) to junction (3006). A sampling channel (3012) may extend from junction (3006) to a bend (3014), which may lead to a sample output region (3018) via an outlet channel (3016).

[0338] A cell containing fluid may be communicated through sample fluid receiving region (3002), and a flow control fluid may be communicated through flow control fluid receiving region (3004). These two fluids may meet at junction (3010), which may provide a flow focusing feature, with the merged fluids being conveyed along sampling channel (3012). Light source (130) and optical assembly (132) may illuminate imaging region (3020); while objective lens assembly (140) and camera (142) may capture images of cells within imaging region (3020). The fluid may continue around bend (3014), through outlet channel (3016), and exit cartridge (3000) at sample output region (3018). The fluid that exits cartridge (3000) at sample output region (3018) may be further conveyed to a reservoir that is either integrated into the instrument of system (100) or is external to the instrument.

[0339] Cartridge (3000) may thus be similar to cartridge (200) except that cartridge (3000) may lack the sorting capabilities of cartridge (200). Nevertheless, the other teachings provided above in the context of cartridge (200) may be readily applied to cartridge (3000).

[0340] VII. Examples of Combinations

[0341] The following examples relate to various non-exhaustive ways in which the teachings herein may be combined or applied. The following examples are not intended to restrict the coverage of any claims that may be presented at any time in this application or in subsequent filings of this application. No disclaimer is intended. The following examples are being provided for nothing more than merely illustrative purposes. It is contemplated that the various teachings herein may be arranged and applied in numerous other ways. It is also contemplated that some variations may omit certain features referred to in the below examples. Therefore, none of the aspects or features referred to below should be deemed critical unless otherwise explicitly indicated as such at a later date by the inventors or by a successor in interest to the inventors. If any claims are presented in this application or in subsequent filings related to this application that include additional features beyond those referred to below, those additional features shall not be presumed to have been added for any reason relating to patentability.

[0342] Example 1

[0343] An apparatus comprising: a cartridge including: a first layer, a first fluid input port to receive fluid to flow through the cartridge, the first fluid input port including a first opening in the first layer, a first fluid output port to convey fluid from the cartridge, the first fluid output port including a second opening in the first layer, and a first pneumatic p ort to convey pneumatic pressure to the cartridge, the first pneumatic port including a third opening in the first layer; a first fluid conduit to removably insert into the first fluid input port via the first opening, the first fluid conduit including a first flexible tube; a second fluid conduit to removably insert into the first fluid output port via the second opening, the second fluid conduit including a second flexible tube; and a first pneumatic conduit to removably insert into the first pneumatic port via the third opening, the first pneumatic conduit including a third flexile tube.

[0344] Example 2

[0345] The apparatus of Example 1, the first fluid input port to provide a friction fit with the first fluid conduit; the first fluid output port to provide a friction fit with the second fluid conduit; and the first pneumatic port to provide a friction fit with the first pneumatic conduit.

[0346] Example 3

[0347] The apparatus of any of Examples 1 through 2, further comprising a cartridge support assembly to removably receive the cartridge.

[0348] Example 4

[0349] The apparatus of Example 3, further comprising a stage assembly supporting the cartridge support assembly, and the stage assembly to move the cartridge support assembly along one or more dimensions and thereby move the cartridge along the one or more dimensions.

[0350] Example 5

[0351] The apparatus of Example 4, the cartridge support assembly including a fluid conduit guide to receive and guide one or both of the first fluid conduit or the second fluid conduit.

[0352] Example 6

[0353] The apparatus of Example 5, the fluid conduit guide including a head, and the one or both of the first fluid conduit or the second fluid conduit passing through the head.

[0354] Example 7

[0355] The apparatus of Example 6, the head including a channel having a tapered passageway, and the one or both of the first fluid conduit or the second fluid conduit passing through the tapered passageway.

[0356] Example 8

[0357] The apparatus of any of Examples 6 through 7, the fluid conduit to allow the one or both of the first fluid conduit or the second fluid conduit to enter the head along one dimension and exit the head along another dimension.

[0358] Example 9

[0359] The apparatus of any of Examples 6 through 8, the head to rotate about an axis with the one or both of the first fluid conduit or the second fluid conduit disposed in the head.

[0360] Example 10

[0361] The apparatus of Example 9, further comprising a first resilient member to resiliently bias the head toward a neutral angular position.

[0362] Example 11

[0363] The apparatus of Example 10, the first resilient member including a torsion spring.

[0364] Example 12

[0365] The apparatus of any of Examples 10 through 11, the first resilient member to resiliently bias the head in a first angular direction toward the neutral angular position, and the apparatus further comprising a second resilient member to resiliently bias the head in a second angular direction toward the neutral angular position.

[0366] Example 13

[0367] The apparatus of any of Examples 4 through 12, the cartridge support assembly including a pneumatic conduit guide to receive and guide the first pneumatic conduit.

[0368] Example 14

[0369] The apparatus of Example 13, the pneumatic conduit guide including a head, and the first pneumatic conduit passing through the head.

[0370] Example 15

[0371] The apparatus of Example 14, the head to rotate about an axis with the first pneumatic conduit disposed in the head.

[0372] Example 16

[0373] The apparatus of Example 15, further comprising a first resilient member to resiliently bias the head toward a neutral angular position.

[0374] Example 17

[0375] The apparatus of Example 16, the first resilient member including a torsion spring.

[0376] Example 18

[0377] The apparatus of any of Examples 16 through 17, the first resilient member to resiliently bias the head in a first angular direction toward the neutral angular position, and the apparatus further comprising a second resilient member to resiliently bias the head in a second angular direction toward the neutral angular position.

[0378] Example 19

[0379] The apparatus of any of Examples 3 through 18, the cartridge support assembly including: a platform, the cartridge to fit on the platform, and a plurality of retainers, the plurality of retainers to retain the cartridge on the platform.

[0380] Example 20

[0381] The apparatus of Example 19, the platform including an optically transmissive material to allow a camera to image a region of the cartridge through the platform.

[0382] Example 22

[0383] The apparatus of any of Examples 19 through 20, at least one retainer of the plurality of retainers being movable relative to the platform to selectively engage the cartridge.

[0384] Example 23

[0385] The apparatus of Example 22, the cartridge support assembly further including a resilient member to resiliently urge the at least one retainer of the plurality of retainers into engagement with the cartridge.

[0386] Example 24

[0387] The apparatus of any of Examples 1 through 23, the first fluid conduit having an open free end and a grip spaced away from the open free end, the open free end to fit in the first fluid input port.

[0388] Example 25

[0389] The apparatus of Example 24, the grip to restrict a dept of insertion of the first fluid conduit into the first fluid input port.

[0390] Example 26

[0391] The apparatus of any of Examples 24 through 25, the grip including a magnetic coupling element to magnetically couple with a complementary magnetic coupling element.

[0392] Example 27

[0393] The apparatus of Example 26, further comprising a cartridge support assembly to removably receive the cartridge, and the cartridge support assembly including the complementary magnetic coupling element.

[0394] Example 28

[0395] The apparatus of any of Examples 1 through 27, the cartridge further including a fluidic channel defining at least part of a fluid path between the first fluid input port and the first fluid output port.

[0396] Example 29

[0397] The apparatus of Example 28, the fluidic channel to receive a fluid containing particles, the apparatus further including a camera to capture one or more images of one or more of the particles in the fluid as the fluid flows through the fluidic channel.

[0398] Example 30

[0399] The apparatus of any of Examples 28 through 29, the cartridge further including a second layer having a recess defining the fluidic channel.

[0400] Example 31

[0401] An apparatus including: a cartridge having a plurality of fluidic ports; a plurality of flexible conduits coupled with the plurality of fluidic ports; a stage assembly to move the cartridge along a plane defined by a first axis and a second axis; and at least one flexible conduit guide having a head, at least one flexible conduit of the plurality of flexible conduits passing through the head, the head to rotate about a third axis while the stage assembly moves the cartridge along the plane.

[0402] Example 32

[0403] An apparatus including: a cartridge having a plurality of fluidic ports; a plurality of flexible conduits to couple with the plurality of fluidic ports, each flexible conduit including a magnetic coupling element; and a cartridge support assembly to removably receive the cartridge, the cartridge support assembly including one or more magnetic coupling elements,the magnetic coupling elements of the plurality of flexile conduits to magnetically couple with the one or more magnetic coupling elements of the cartridge support assembly.

[0404] Example 33

[0405] The apparatus of Example 32, the magnetic coupling elements of a first flexible conduit of the plurality of flexile conduits to magnetically couple with the one or more magnetic coupling elements of the cartridge support assembly when the first flexible conduit is decoupled from the cartridge.

[0406] Example 34

[0407] The apparatus of any of Examples 32 through 33, each flexible conduit including a depth stop feature to restrict a depth of insertion of the flexible conduit into the cartridge.

[0408] Example 35

[0409] A method comprising: moving a cartridge along a plane defined by a first axis and a second axis, the cartridge including a first fluidic conduit extending from the cartridge while the cartridge moves along the plane, the first fluidic conduit passing through a head of a fluidic conduit guide, the head rotating about a third axis while the cartridge moves along the plane and while the first fluidic conduit is disposed in the head.

[0410] Example 36

[0411] The method of Example 36, the cartridge further including a second fluidic conduit extending from the cartridge while the cartridge moves along the plane, the second fluidic conduit passing through the head of a fluidic conduit guide, and the head rotating about the third axis while the cartridge moves along the plane and while the second fluidic conduit is disposed in the head.

[0412] Example 37

[0413] The method of any of Examples 35 through 36, moving the cartridge along the plane including moving the cartridge from a first position to a second position, the cartridge being located under an illumination head in the second position.

[0414] Example 38

[0415] The method of Example 37, the cartridge being positioned for removal from a cartridge support assembly in the first position.

[0416] Example 39

[0417] The method of any of Examples 37 through 38, further comprising capturing an image of a cell in fluid in the cartridge while the cartridge is in the second position.

[0418] Example 40

[0419] The method of any of Examples 35 through 39, the fluidic conduit engaging another component of an instrument, thereby inducing tension in the fluidic conduit, as the cartridge moves along the plane, the induced tension in the fluidic conduit causing the head to rotate about the third axis.

[0420] Example 41

[0421] An apparatus comprising: a first fluidic path to receive a fluid containing particles; a first sorting region including: a second fluidic path, a third fluidic path, a first junction, the first fluidic path joining the second fluidic path and the third fluidic path at the first junction, a first valve to selectively permit or prevent communication of fluid along the second fluidic path downstream of the first junction, and a second valve to selectively permit or prevent communication of fluid along the third fluidic path downstream of the first junction, a second sorting region including: a fourth fluidic path, a fifth fluidic path, a second junction, the second fluidic path joining the fourth fluidic path and the fifth fluidic path at the second junction, the second junction being downstream of the first valve, a third valve to selectively permit or prevent communication of fluid along the fourth fluidic path downstream of the second junction, and a fourth valve to selectively permit or prevent communication of fluid along the fifth fluidic path downstream of the second junction; an outlet port to extract fluid from the third fluidic path, the outlet port being downstream of the second valve; a first well to receive fluid from the fourth fluidic path, the first well being downstream of the third valve; and a second well to receive fluid from the fifth fluidic path, the second well being downstream of the fourth valve.

[0422] Example 42

[0423] The apparatus of Example 41, the first valve including a pneumatic channel and a deformable layer, and the pneumatic channel to receive pneumatic pressure to deform the deformable layer.

[0424] Example 43

[0425] The apparatus of any of Examples 41 through 42, further comprising a camera to image particles conveyed along the first fluidic path.

[0426] Example 44

[0427] The apparatus of Example 43, further comprising a processor, the processor to classify particles from images captured by the camera.

[0428] Example 45

[0429] The apparatus of Example 44, the processor to control operation of the first valve, the second valve, the third valve, and the fourth valve.

[0430] Example 46

[0431] The apparatus of Example 45, the processor to select one or more valves from the first valve, the second valve, the third valve, and the fourth valve for activation in response to classification of particles.

[0432] Example 47

[0433] The apparatus of any of Examples 41 through 46, further comprising a cartridge, the first fluidic path, the second fluidic path, the third fluidic path, the fourth fluidic path, the fifth fluidic path, the first junction, and the second junction extending along the cartridge.

[0434] Example 48

[0435] The apparatus of Example 47, the first valve, the second valve, the third valve, and the fourth valve being in the cartridge.

[0436] Example 49

[0437] The apparatus of any of Examples 47 through 48, the outlet port providing a path for extraction of fluid from the cartridge via the fluidic path.

[0438] Example 50

[0439] The apparatus of any of Examples 47 through 49, the first well and the second well being in the cartridge.

[0440] Example 51

[0441] An apparatus comprising: a first layer including: a first surface, a second surface, a first fluidic path to receive a fluid containing particles, a second fluidic path, a third fluidic path, and a first junction, the first fluidic path joining the second fluidic path and the third fluidic path at the first junction; a first valve to selectively permit or prevent communication of fluid along the second fluidic path downstream of the first junction; a second valve to selectively permit or prevent communication of fluid along the third fluidic path downstream of the first junction; and a second layer including: a first surface, a second surface overlaying the first surface of the first layer, a first pneumatic channel to pneumatically pressurize the first valve and thereby transition the first valve to a closed state, a second pneumatic channel to pneumatically pressurize the second valve and thereby transition the first valve to a closed state, and a vent passageway, the vent passageway extending from the first surface to the second surface, the vent passageway being open to atmosphere.

[0442] Example 52

[0443] The apparatus of Example 51, the first fluidic path including a first recess in the first surface, the second fluidic path including a second recess in the first surface, and the third fluidic path including a third recess in the first surface.

[0444] Example 53

[0445] The apparatus of any of Examples 51 through 52, the first valve including a region of the second fluidic path adjacent to a corresponding region of the first pneumatic channel, and the second valve including a region of the third fluidic path adjacent to a corresponding region of the second pneumatic channel.

[0446] Example 54

[0447] The apparatus of Example 53, the first layer to deform in the region of the second fluidic path adjacent to the corresponding region of the first pneumatic channel in response to pneumatic pressurization of the first pneumatic channel, and the second layer to deform in the region of the third fluidic path adjacent to the corresponding region of the second pneumatic channel in response to pneumatic pressurization of the second pneumatic channel.

[0448] Example 55

[0449] The apparatus of any of Examples 51 through 54, the second layer further including one or more vent channels extending from the vent passageway along the second surface of the second layer, and the one or more vent channels to provide ventilation via the vent passageway.

[0450] Example 56

[0451] An apparatus comprising: a first layer including: a first surface, a second surface, a first fluidic path to receive a fluid containing particles, a second fluidic path; a first valve to selectively permit or prevent communication of fluid along the second fluidic path downstream of the first junction; and a second layer including: a first surface, a second surface overlaying the first surface of the first layer, a first pneumatic channel to pneumatically pressurize the first valve and thereby transition the first valve to a closed state, a vent passageway, the vent passageway extending from the first surface to the second surface, the vent passageway being open to atmosphere, and a vent channel extending from the vent passageway along the first surface, the vent channel to provide ventilation via the vent passageway.

[0452] Example 57

[0453] The apparatus of Example 56, the first layer further including: a third fluidic path, and a first junction, the first fluidic path joining the second fluidic path and the third fluidic path at the first junction.

[0454] Example 58

[0455] The apparatus of Example 57, further comprising: a second valve to selectively permit or prevent communication of fluid along the third fluidic path downstream of the firstjunction; and the second layer further including: a second pneumatic channel to pneumatically pressurize the second valve and thereby transition the first valve to a closed state.

[0456] Example 59

[0457] The apparatus of Example 58, the vent channel being positioned between the first pneumatic channel and the second pneumatic channel.

[0458] Example 60

[0459] The apparatus of any of clams 56 through 59, the first pneumatic channel including a first recess in the second surface of the second layer, the vent channel including a second recess in the second surface of the second layer, the first surface of the first layer defining a bottom of the first pneumatic channel, and the first surface of the first layer defining a bottom of the second vent channel.

[0460] Example 61

[0461] An apparatus comprising: a first fluidic path to receive a fluid containing particles; a first fluid input port to receive a first conduit to convey fluid containing particles to the first fluidic path; a flow control fluidic path to receive a flow control fluid to focus a flow of the fluid containing particles along the first fluidic path; a second fluid input port to receive a second conduit to convey flow control fluid to the flow control fluidic path; and a flush assembly including: a third fluid input port, a fluid output port, and a fluidic flush channel extending between the third fluid input port and the fluid output port, and the flush assembly to removably receive the first conduit and the second conduit, the flush assembly to permit a flush fluid to be communicated along a fluid path defined by a combination of the first conduit, the second conduit, and the fluidic flush channel, such that the flush fluid enters the flush assembly via the third fluid input port and exits the flush assembly via the fluid output port.

[0462] Example 62

[0463] The apparatus of Example 61 , further comprising a cartridge, the first fluidic path, the flow control fluidic path, and the fluidic flush channel extending along the cartridge.

[0464] Example 63

[0465] The apparatus of Example 62, the first fluid input port, the second fluid input port, the third fluid input port, and the fluid output port extending into the cartridge.

[0466] Example 64

[0467] The apparatus of any of Examples 61 through 63, the first conduit including a first flexible tube, and the second conduit including a second flexible tube.

[0468] Example 65

[0469] A method comprising: inserting a first conduit into a first fluid input port of a cartridge; inserting a second conduit into a second fluid input of the cartridge; conveying a fluid containing particles along a first fluidic path of the cartridge via the first conduit and the first fluid input port; conveying a second fluid along a second fluidic path of the cartridge via the second conduit and the second fluid input port; removing the first conduit from the first fluid input port; removing the second conduit from the second fluid input port; inserting the first conduit into a third port of the cartridge; inserting the second conduit into a fourth port of the cartridge, the third port and the fourth port being coupled via a first fluidic flush channel to form a first flush assembly; and communicating a flushing fluid through the first conduit and the second conduit and further through the first flush assembly.

[0470] Example 66

[0471] The method of Example 65, further comprising capturing images of particles conveyed along the first fluidic path.

[0472] Example 67

[0473] The method of any of Examples 65 through 66, the second fluid providing a focus to flow of the fluid containing particles along the first fluidic path.

[0474] Example 68

[0475] The method of any of Examples 65 through 67, the third port defining an output port of the first flush assembly, the fourth port defining an input port of the first flush assembly, communicating a flushing fluid through the first conduit and the second conduit and further through the first flush assembly including: communicating the flush fluid into the flush assembly via the first conduit, and communicating the flush fluid out of the flush assembly via the second conduit.

[0476] Example 69

[0477] The method of any of Examples 65 through 68, further comprising: inserting a fourth conduit into a fifth fluid input port of the cartridge; inserting a fifth conduit into a sixth fluid input port of the cartridge; conveying the fluid containing particles from the first fluidic path to a receptacle via the fourth conduit and the fifth fluid input port; and conveying a third fluid along a third fluidic path of the cartridge via the fifth conduit and the sixth fluid input port.

[0478] Example 70

[0479] The method of Example 69, further comprising: removingthe fourth conduit from the fifth fluid input port; removing the fifth conduit from the sixth fluid input port; inserting th e fourth conduit into a seventh port of the cartridge; inserting the fifth conduit into a eighth portof the cartridge, the seventh port and the eighth port being coupled via a second fluidic flush channel to form a second first flush assembly; and communicating a flushing fluid through the fourth conduit and the fifth conduit and further through the second flush assembly.

[0480] Example 71

[0481] An apparatus comprising: a cartridge, the cartridge including: a first fluidic path to receive a fluid containing particles, the first fluidic path providing an imaging region to capture images of particles conveyed along the first fluidic path, and an optical fiducial region including a plurality of fiducial elements, each fiducial element of the plurality of fiducial elements having a shape that differs from shapes of the other fiducial elements of the plurality of fiducial elements; and a camera having a field of view, the cartridge being positionable to provide the imaging region and the optical fiducial region simultaneously within the field of view.

[0482] Example 72

[0483] The apparatus of Example 71, the plurality of fiducial elements having elliptical shapes, each elliptical shape having a major axis and a minor axis, major axes and minor axes varying among the plurality of fiducial elements.

[0484] Example 73

[0485] The apparatus of any of Examples 71 through 72, further comprising a processor, the processor to process an image of the optical fiducial region captured by the camera, to thereby determine whether the cartridge is aligned with the camera.

[0486] Example 74

[0487] The apparatus of Example 73, the processor to further process an image of a particle in the fluidic path captured by the camera, to thereby classify the particle.

[0488] Example 75

[0489] The apparatus of any of Examples 73 through 74, the camera to capture images of particles in the fluidic path at different positions along a height of the fluidic path, and the processor to process the images of particles in the fluidic path at different positions along the height of the fluidic path to thereby determine a focus location.

[0490] Example 76

[0491] The apparatus of Example 75, the height of the fluidic path having a vertical center position, the processor to determine the focus location at the vertical center position.

[0492] Example 77

[0493] The apparatus of Example 75, the height of the fluidic path having a vertical center position, the processor to determine the focus location at a vertical position below the vertical center position.

[0494] Example 78

[0495] The apparatus of any of Examples 75 through 77, the particles including beads.

[0496] Example 79

[0497] The apparatus of any of Examples 71 through 78, the cartridge further including a layer having a first surface and a second surface, and the plurality of fiducial elements including recesses in the first surface.

[0498] Example 80

[0499] The apparatus of any of Examples 71 through 79, the cartridge further including a focusing region having a focusing feature, the focusing feature, the cartridge being positionable to provide the imaging region, the optical fiducial region, and the focusing feature simultaneously within the field of view, and the camera having an optical axis extending along a first dimension, the focusing feature having a depth along the first dimension.

[0500] Example 81

[0501] The apparatus of Example 80, the cartridge further including a layer having a first surface and a second surface, and the focusing feature including a recess in the first surface.

[0502] Example 82

[0503] The apparatus of Example 81, the focusing feature having a curved wall, the curved wall providing a cross-sectional area along a first plane that varies along the first dimension, and the first plane being perpendicular to the first dimension.

[0504] Example 83

[0505] The apparatus of any of Examples 71 through 82, further comprising a processor, the camera to capture images of the focusing feature at different positions along a height of the focusing feature, and the processor to process the images of the focusing feature at different positions along the height of the focusing feature to thereby determine a focus location.

[0506] Example 84

[0507] An apparatus comprising: a first layer; a second layer positioned over the first layer, the second layer including: a first fluidic channel, the first fluidic channel including a first portion and a second portion adjacent to the first portion, the first portion having a rectangular cross-section, the second portion having a rounded cross-section; and a third layer positioned over the second layer, the third layer including a first pneumatic channel, the firstpneumatic channel to apply pneumatic pressure against the second portion of the first fluidic channel to thereby deform the second portion against the first layer and thereby prevent communication of fluid through the first fluidic channel.

[0508] Example 85

[0509] The apparatus of Example 84, the second layer including resilient material to return the second portion to a non -deformed state in response to removal of pneumatic pressure in the first pneumatic channel.

[0510] Example 86

[0511] The apparatus of any of Examples 84 through 85, the first fluidic channel to convey a fluid containing particles.

[0512] Example 87

[0513] The apparatus of any of Examples 84 through 86, the second layer having a first surface adjacent to the first layer and a second surface adjacent to the third layer, and the first fluidic channel including a recess in the first surface of the second layer.

[0514] Example 88

[0515] The apparatus of any of Examples 84 through 87, the third layer having a first surface adj acent to the second layer and a second surface, and the first pneumatic channel including a recess in the first surface of the third layer.

[0516] Example 89

[0517] The apparatus of any of Examples 84 through 88, the first pneumatic channel being positioned over the second portion such that the first pneumatic channel overlaps the second portion.

[0518] Example 90

[0519] The apparatus of any of Examples 84 through 89, the first portion being positioned such that the first pneumatic channel does not overlap the first portion.

[0520] Example 91

[0521] The apparatus of any of Examples 84 through 90, the first layer further including: a junction upstream of the first fluidic channel, a second fluidic channel upstream of the junction, and a third fluidic channel downstream of the junction.

[0522] Example 92

[0523] The apparatus of Example 91 , the third fluidic channel including a third portion and a fourth portion adjacent to the third portion, the third portion having a rectangular crosssection, and the fourth portion having a rounded cross -section.

[0524] Example 93

[0525] The apparatus of Example 92, the third layer further including a second pneumatic channel, the second pneumatic channel to apply pneumatic pressure against the fourth portion of the third fluidic channel to thereby deform the fourth portion against the first layer and thereby prevent communication of fluid through the third fluidic channel.

[0526] VII. Miscellaneous

[0527] While the examples provided above include cells or beads as particles, the teachings herein may be readily applied to other contexts where other kinds of particles are used in addition to or in lieu of cells or beads.

[0528] The foregoing description is provided to enable a person skilled in the art to practice the various configurations described herein. While the subject technology has been particularly described with reference to the various figures and configurations, it should be understood that these are for illustration purposes only and should not be taken as limiting the scope of the subject technology. The subject matter described herein is not limited in its application to the details of construction and the arrangement of components set forth in the description herein or illustrated in the drawings hereof. The subject matter described herein is capable of other implementations and of being practiced or of being carried out in various ways.

[0529] It is to be understood that the above description is intended to be illustrative, and not restrictive. For example, the above-described examples (and / or aspects thereof) may be used in combination with each other. In addition, many modifications may be made to adapt a particular situation or material to the teachings of the presently described subject matter without departing from its scope. While the dimensions, types of materials and coatings described herein are intended to define the parameters of the disclosed subject matter, they are by no means limiting and instead illustrations. Many further examples will be apparent to those of skill in the art upon reviewing the above description. The scope of the disclosed subject matter should, therefore, be determined with reference to the appended claims, along with the full scope of equivalents to which such claims are entitled. Further, the limitations of the following claims are not written in means — plus-function format and are not intended to be interpreted based on 35 U.S. C. §112(f), unless and until such claim limitations expressly use the phrase “means for” followed by a statement of function void of further structure.

[0530] The following claims recite aspects of certain examples of the disclosed subject matter and are considered to be part of the above disclosure. These aspects may be combined with one another.

Claims

CLAIMSWhat is claimed is:

1. An apparatus comprising: a cartridge including: a first layer, a first fluid input port to receive fluid to flowthrough the cartridge, the first fluid input port including a first opening in the first layer, a first fluid output port to convey fluid from the cartridge, the first fluid output port including a second opening in the first layer, and a first pneumatic port to convey pneumatic pressure to the cartridge, the first pneumatic port including a third opening in the first layer; a first fluid conduit to removably insert into the first fluid input port via the first opening, the first fluid conduit including a first flexible tube; a second fluid conduit to removably insert into the first fluid output port via the second opening, the second fluid conduit including a second flexible tube; and a first pneumatic conduit to removably insert into the first pneumatic port via the third opening, the first pneumatic conduit including a third flexile tube.

2. The apparatus of claim 1 , the first fluid input port to provide a friction fit with the first fluid conduit; the first fluid output port to provide a friction fit with the second fluid conduit; and the first pneumatic port to provide a friction fit with the first pneumatic conduit.

3. The apparatus of any of claims 1 through 2, further comprising a cartridge support assembly to removably receive the cartridge.

4. The apparatus of claim 3, further comprising a stage assembly supporting the cartridge support assembly, and the stage assembly to move the cartridge support assembly along one or more dimensions and thereby move the cartridge along the one or more dimensions.

5. The apparatus of claim 4, the cartridge support assembly including a fluid conduit guide to receive and guide one or both of the first fluid conduit or the second fluid conduit.

6. The apparatus of claim 5, the fluid conduit guide including a head, and the one or both of the first fluid conduit or the second fluid conduit passing through the head.

7. The apparatus of claim 6, the head including a channel having a tapered passageway, and the one or both of the first fluid conduit or the second fluid conduit passing through the tapered passageway.

8. The apparatus of any of claims 6 through 7, the fluid conduit to allow the one or both of the first fluid conduit or the second fluid conduit to enter the head along one dimension and exit the head along another dimension.

9. The apparatus of any of claims 6 through 8, the head to rotate about an axis with the one or both of the first fluid conduit or the second fluid conduit disposed in the head.

10. The apparatus of claim 9, further comprising a first resilient member to resiliently bias the head toward a neutral angular position.

11. The apparatus of claim 10, the first resilient member including a torsion spring.

12. The apparatus of any of claims 10 through 11, the first resilient member to resiliently bias the head in a first angular direction toward the neutral angular position, and the apparatus further comprising a second resilient member to resiliently bias the head in a second angular direction toward the neutral angular position.

13. The apparatus of any of claims 4 through 12, the cartridge support assembly including a pneumatic conduit guide to receive and guide the first pneumatic conduit.

14. The apparatus of claim 13 , the pneumatic conduit guide including a head, and the first pneumatic conduit passing through the head.

15. The apparatus of claim 14, the head to rotate about an axis with the first pneumatic conduit disposed in the head.

16. The apparatus of claim 15, further comprising a first resilient member to resiliently bias the head toward a neutral angular position.

17. The apparatus of claim 16, the first resilient member including a torsion spring.

18. The apparatus of any of claims 16 through 17, the first resilient member to resiliently bias the head in a first angular direction toward the neutral angular position, and the apparatus further comprising a second resilient member to resiliently bias the head in a second angular direction toward the neutral angular position.

19. The apparatus of any of claims 3 through 18, the cartridge support assembly including: a platform, the cartridge to fit on the platform, and a plurality of retainers, the plurality of retainers to retain the cartridge on the platform.

20. The apparatus of claim 19, the platform including an optically transmissive material to allow a camera to image a region of the cartridge through the platform.

22. The apparatus of any of claims 19 through 20, at least one retainer of the plurality of retainers being movable relative to the platform to selectively engage the cartridge.

23. The apparatus of claim 22, the cartridge support assembly further including a resilient member to resiliently urge the at least one retainer of the plurality of retainers into engagement with the cartridge.

24. The apparatus of any of claims 1 through 23, the first fluid conduit having an open free end and a grip spaced away from the open free end, the open free end to fit in the first fluid input port.

25. The apparatus of claim 24, the grip to restrict a dept of insertion of the first fluid conduit into the first fluid input port.

26. The apparatus of any of claims 24 through 25, the grip including a magnetic coupling element to magnetically couple with a complementary magnetic coupling element.

27. The apparatus of claim 26, further comprising a cartridge support assembly to removably receive the cartridge, and the cartridge support assembly including the complementary magnetic coupling element.

28. The apparatus of any of claims 1 through 27, the cartridge further including a fluidic channel defining at least part of a fluid path between the first fluid input port and the first fluid output port.

29. The apparatus of claim 28, the fluidic channel to receive a fluid containing particles, the apparatus further including a camera to capture one or more images of one or more of the particles in the fluid as the fluid flows through the fluidic channel.

30. The apparatus of any of claims 28 through 29, the cartridge further including a second layer having a recess defining the fluidic channel.

31. An apparatus including: a cartridge having a plurality of fluidic ports; a plurality of flexible conduits coupled with the plurality of fluidic ports; a stage assembly to move the cartridge along a plane defined by a first axis and a second axis; and at least one flexible conduit guide having a head, at least one flexible conduit of the plurality of flexible conduits passing through the head, the head to rotate about a third axis while the stage assembly moves the cartridge along the plane.

32. An apparatus including: a cartridge having a plurality of fluidic ports;a plurality of flexible conduits to couple with the plurality of fluidic ports, each flexible conduit including a magnetic coupling element; and a cartridge support assembly to removably receive the cartridge, the cartridge support assembly including one or more magnetic coupling elements, the magnetic coupling elements of the plurality of flexile conduits to magnetically couple with the one or more magnetic coupling elements of the cartridge support assembly.

33. The apparatus of claim 32, the magnetic coupling elements of a first flexible conduit of the plurality of flexile conduits to magnetically couple with the one or more magnetic coupling elements of the cartridge support assembly when the first flexible conduit is decoupled from the cartridge.

34. The apparatus of any of claims 32 through 33, each flexible conduit including a depth stop feature to restrict a depth of insertion of the flexible conduit into the cartridge.

35. A method comprising: moving a cartridge along a plane defined by a first axis and a second axis, the cartridge including a first fluidic conduit extending from the cartridge while the cartridge moves along the plane, the first fluidic conduit passing through a head of a fluidic conduit guide, the head rotating about a third axis while the cartridge moves along the plane and while the first fluidic conduit is disposed in the head.

36. The method of claim 35, the cartridge further including a second fluidic conduit extending from the cartridge while the cartridge moves along the plane, the second fluidic conduit passing through the head of a fluidic conduit guide, and the head rotating about the third axis while the cartridge moves along the plane and while the second fluidic conduit is disposed in the head.

37. The method of any of claims 35 through 36, moving the cartridge along the plane including moving the cartridge from a first position to a second position, the cartridge being located under an illumination head in the second position.

38. The method of claim 37, the cartridge being positioned for removal from a cartridge support assembly in the first position.

39. The method of any of claims 37 through 38, further comprising capturing an image of a cell in fluid in the cartridge while the cartridge is in the second position.

40. The method of any of claims 35 through 39, the fluidic conduit engaging another component of an instrument, thereby inducing tension in the fluidic conduit, as the cartridge moves along the plane, the induced tension in the fluidic conduit causing the head to rotate about the third axis.

41. An apparatus comprising: a first fluidic path to receive a fluid containing particles; a first sorting region including: a second fluidic path, a third fluidic path, a first junction, the first fluidic path joining the second fluidic path and the third fluidic path at the first junction, a first valve to selectively permit or prevent communication of fluid alongthe second fluidic path downstream of the first junction, and a second valve to selectively permit or prevent communication of fluid along the third fluidic path downstream of the first junction, a second sorting region including: a fourth fluidic path, a fifth fluidic path, a second junction, the second fluidic path joining the fourth fluidic path and the fifth fluidic path at the second junction, the second junction being downstream of the first valve, a third valve to selectively permit or prevent communication of fluid along the fourth fluidic path downstream of the second junction, and a fourth valve to selectively permit or prevent communication of fluid alongthe fifth fluidic path downstream of the second junction;an outlet port to extract fluid from the third fluidic path, the outlet port being downstream of the second valve; a first well to receive fluid from the fourth fluidic path, the first well being downstream of the third valve; and a second well to receive fluid from the fifth fluidic path, the second well being downstream of the fourth valve.

42. The apparatus of claim 41 , the first valve including a pneumatic channel and a deformable layer, and the pneumatic channel to receive pneumatic pressure to deform the deformable layer.

43. The apparatus of any of claims 41 through 42, further comprising a camera to image particles conveyed along the first fluidic path.

44. The apparatus of claim 43, further comprising a processor, the processor to classify particles from images captured by the camera.

45. The apparatus of claim 44, the processor to control operation of the first valve, the second valve, the third valve, and the fourth valve.

46. The apparatus of claim 45, the processor to select one or more valves from the first valve, the second valve, the third valve, and the fourth valve for activation in response to classification of particles.

47. The apparatus of any of claims 41 through 46, further comprising a cartridge, the first fluidic path, the second fluidic path, the third fluidic path, the fourth fluidic path, the fifth fluidic path, the first junction, and the second junction extending along the cartridge.

48. The apparatus of claim 47, the first valve, the second valve, the third valve, and the fourth valve being in the cartridge.

49. The apparatus of any of claims 47 through 48, the outlet port providing a path for extraction of fluid from the cartridge via the fluidic path.

50. The apparatus of any of claims 47 through 49, the first well and the second well being in the cartridge.

51. An apparatus comprising: a first layer including: a first surface, a second surface, a first fluidic path to receive a fluid containing particles, a second fluidic path, a third fluidic path, and a first junction, the first fluidic path joining the second fluidic path and the third fluidic path at the first junction; a first valve to selectively permit or prevent communication of fluid along the second fluidic path downstream of the first junction; a second valve to selectively permit or prevent communication of fluid along the third fluidic path downstream of the first junction; and a second layer including: a first surface, a second surface overlaying the first surface of the first layer, a first pneumatic channel to pneumatically pressurize the first valve and thereby transition the first valve to a closed state, a second pneumatic channel to pneumatically pressurize the second valve and thereby transition the first valve to a closed state, and a vent passageway, the vent passageway extending from the first surface to the second surface, the vent passageway being open to atmosphere.

52. The apparatus of claim 51, the first fluidic path including a first recess in the first surface, the second fluidic path including a second recess in the first surface, and the third fluidic path including a third recess in the first surface.

53. The apparatus of any of claims 51 through 52, the first valve including a region of the second fluidic path adjacent to a corresponding region of the first pneumaticchannel, and the second valve including a region of the third fluidic path adjacent to a corresponding region of the second pneumatic channel.

54. The apparatus of claim 53, the first layer to deform in the region of the second fluidic path adjacent to the corresponding region of the first pneumatic channel in response to pneumatic pressurization of the first pneumatic channel, and the second layer to deform in the region of the third fluidic path adjacent to the corresponding region of the second pneumatic channel in response to pneumatic pressurization of the second pneumatic channel.

55. The apparatus of any of claims 51 through 54, the second layer further including one or more vent channels extending from the vent passageway along the second surface of the second layer, and the one or more vent channels to provide ventilation via the vent passageway.

56. An apparatus comprising: a first layer including: a first surface, a second surface, a first fluidic path to receive a fluid containing particles, and a second fluidic path; a first valve to selectively permit or prevent communication of fluid along the second fluidic path downstream of the first junction; and a second layer including: a first surface, a second surface overlaying the first surface of the first layer, a first pneumatic channel to pneumatically pressurize the first valve and thereby transition the first valve to a closed state, a vent passageway, the vent passageway extending from the first surface to the second surface, the vent passageway being open to atmosphere, and a vent channel extending from the vent passageway along the first surface, the vent channel to provide ventilation via the vent passageway.

57. The apparatus of claim 56, the first layer further including: a third fluidic path, and a first junction, the first fluidic path joining the second fluidic path and the third fluidic path at the first junction.

58. The apparatus of claim 57, further comprising: a second valve to selectively permit or prevent communication of fluid along the third fluidic path downstream of the first junction; and the second layer further including: a second pneumatic channel to pneumatically pressurize the second valve and thereby transition the first valve to a closed state.

59. The apparatus of claim 58, the vent channel being positioned between the first pneumatic channel and the second pneumatic channel.

60. The apparatus of any of clams 56 through 59, the first pneumatic channel including a first recess in the second surface of the second layer, the vent channel including a second recess in the second surface of the second layer, the first surface of the first layer defining a bottom of the first pneumatic channel, and the first surface of the first layer defining a bottom of the second vent channel.

61. An apparatus comprising: a first fluidic path to receive a fluid containing particles; a first fluid input port to receive a first conduit to convey fluid containing particles to the first fluidic path; a flow control fluidic path to receive a flow control fluid to focus a flow of the fluid containing particles along the first fluidic path; a second fluid input port to receive a second conduit to convey flow control fluid to the flow control fluidic path; and a flush assembly including: a third fluid input port, a fluid output port, and a fluidic flush channel extending between the third fluid input port and the fluid output port,the flush assembly to removably receive the first conduit and the second conduit, and the flush assembly to permit a flush fluid to be communicated along a fluid path defined by a combination of the first conduit, the second conduit, and the fluidic flush channel, such that the flush fluid enters the flush assembly via the third fluid input port and exits the flush assembly via the fluid output port.

62. The apparatus of claim 61 , further comprising a cartridge, the first fluidic path, the flow control fluidic path, and the fluidic flush channel extending along the cartridge.

63. The apparatus of claim 62, the first fluid input port, the second fluid input port, the third fluid input port, and the fluid output port extending into the cartridge.

64. The apparatus of any of claims 61 through 63, the first conduit including a first flexible tube, and the second conduit including a second flexible tube.

65. A method comprising: inserting a first conduit into a first fluid input port of a cartridge; inserting a second conduit into a second fluid input of the cartridge; conveying a fluid containing particles along a first fluidic path of the cartridge via the first conduit and the first fluid input port; conveying a second fluid along a second fluidic path of the cartridge via the second conduit and the second fluid input port; removing the first conduit from the first fluid input port; removing the second conduit from the second fluid input port; inserting the first conduit into a third port of the cartridge; inserting the second conduit into a fourth port of the cartridge, the third port and the fourth port being coupled via a first fluidic flush channel to form a first flush assembly; and communicating a flushing fluid through the first conduit and the second conduit and further through the first flush assembly.

66. The method of claim 65, further comprising capturing images of particles conveyed along the first fluidic path.

67. The method of any of claims 65 through 66, the second fluid providing a focus to flow of the fluid containing particles along the first fluidic path.

68. The method of any of claims 65 through 67, the third port defining an output port of the first flush assembly, the fourth port defining an input port of the first flush assembly, communicating a flushing fluid through the first conduit and the second conduit and further through the first flush assembly including: communicating the flush fluid into the flush assembly via the first conduit, and communicating the flush fluid out of the flush assembly via the second conduit.

69. The method of any of claims 65 through 68, further comprising: inserting a fourth conduit into a fifth fluid input port of the cartridge; inserting a fifth conduit into a sixth fluid input port of the cartridge; conveying the fluid containing particles from the first fluidic path to a receptacle via the fourth conduit and the fifth fluid input port; and conveying a third fluid along a third fluidic path of the cartridge via the fifth conduit and the sixth fluid input port.

70. The method of claim 69, further comprising: removing the fourth conduit from the fifth fluid input port; removing the fifth conduit from the sixth fluid input port; inserting the fourth conduit into a seventh port of the cartridge; inserting the fifth conduit into a eighth port of the cartridge, the seventh port and the eighth port being coupled via a second fluidic flush channel to form a second first flush assembly; and communicating a flushing fluid through the fourth conduit and the fifth conduit and further through the second flush assembly.

71. An apparatus comprising: a cartridge, the cartridge including: a first fluidic path to receive a fluid containing particles, the first fluidic path providing an imaging region to capture images of particles conveyed along the first fluidic path, and an optical fiducial region including a plurality of fiducial elements, each fiducial element of the plurality of fiducial elements having a shape that differs from shapes of the other fiducial elements of the plurality of fiducial elements; and a camera having a field of view, the cartridge being positionable to provide the imaging region and the optical fiducial region simultaneously within the field of view.

72. The apparatus of claim 71, the plurality of fiducial elements having elliptical shapes, each elliptical shape having a major axis and a minor axis, major axes and minor axes varying among the plurality of fiducial elements.

73. The apparatus of any of claims 71 through 72, further comprising a processor, the processor to process an image of the optical fiducial region captured by the camera, to thereby determine whether the cartridge is aligned with the camera.

74. The apparatus of claim 73, the processor to further process an image of a particle in the fluidic path captured by the camera, to thereby classify the particle.

75. The apparatus of any of claims 73 through 74, the camera to capture images of particles in the fluidic path at different positions along a height of the fluidic path, and the processor to process the images of particles in the fluidic path at different positions along the height of the fluidic path to thereby determine a focus location.

76. The apparatus of claim 75, the height of the fluidic path having a vertical center position, the processor to determine the focus location at the vertical center position.

77. The apparatus of claim 75, the height of the fluidic path having a vertical center position, the processor to determine the focus location at a vertical position below the vertical center position.

78. The apparatus of any of claims 75 through 77, the particles including beads.

79. The apparatus of any of claims 71 through 78, the cartridge further including a layer having a first surface and a second surface, and the plurality of fiducial elements including recesses in the first surface.

80. The apparatus of any of claims 71 through 79, the cartridge further including a focusing region having a focusing feature, the focusing feature, the cartridge being positionable to provide the imaging region, the optical fiducial region, and the focusing feature simultaneously within the field of view, and the camera having an optical axis extending along a first dimension, the focusing feature having a depth along the first dimension.81 . The apparatus of claim 80, the cartridge further including a layer having a first surface and a second surface, and the focusing feature including a recess in the first surface.

82. The apparatus of claim 81, the focusing feature having a curved wall, the curved wall providing a cross-sectional area along a first plane that varies along the first dimension, and the first plane being perpendicular to the first dimension.

83. The apparatus of any of claims 71 through 82, further comprising a processor, the camerato capture images of the focusing feature at different positions along a height of the focusing feature, and the processor to process the images of the focusing feature at different positions along the height of the focusing feature to thereby determine a focus location.

84. An apparatus comprising: a first layer; a second layer positioned over the first layer, the second layer including:a first fluidic channel, the first fluidic channel including a first portion and a second portion adjacent to the first portion, the first portion having a rectangular cross-section, the second portion having a rounded cross-section; and a third layer positioned over the second layer, the third layer including a first pneumatic channel, the first pneumatic channel to apply pneumatic pressure against the second portion of the first fluidic channel to thereby deform the second portion against the first layer and thereby prevent communication of fluid through the first fluidic channel.

85. The apparatus of claim 84, the second layer including resilient material to return the second portion to a non-deformed state in response to removal of pneumatic pressure in the first pneumatic channel.

86. The apparatus of any of claims 84 through 85, the first fluidic channel to convey a fluid containing particles.

87. The apparatus of any of claims 84 through 86, the second layer having a first surface adjacent to the first layer and a second surface adjacent to the third layer, and the first fluidic channel including a recess in the first surface of the second layer.

88. The apparatus of any of claims 84 through 87, the third layer having a first surface adjacent to the second layer and a second surface, and the first pneumatic channel including a recess in the first surface of the third layer.

89. The apparatus of any of claims 84 through 88, the first pneumatic channel being positioned over the second portion such that the first pneumatic channel overlaps the second portion.

90. The apparatus of any of claims 84 through 89, the first portion being positioned such that the first pneumatic channel does not overlap the first portion.91 . The apparatus of any of claims 84 through 90, the first layer further including: a junction upstream of the first fluidic channel,a second fluidic channel upstream of the junction, and a third fluidic channel downstream of the junction.

92. The apparatus of claim 91, the third fluidic channel including a third portion and a fourth portion adjacent to the third portion, the third portion having a rectangular crosssection, and the fourth portion having a rounded cross -section.

93. The apparatus of claim 92, the third layer further including a second pneumatic channel, the second pneumatic channel to apply pneumatic pressure against the fourth portion of the third fluidic channel to thereby deform the fourth portion against the first layer and thereby prevent communication of fluid through the third fluidic channel.

Images