Sequencing systems

Abstract

The present disclosure provides flow cell devices, fluidic stations, imaging stations, gantry and grabber systems that facilitate and perform, inter alia, DNA sequencing runs with improved system throughput, reduced system complexity and cost, reduced sequencing reagent consumption, and reduced contamination levels.

Description

Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)FLOW CELL SYSTEMS, DEVICES AND METHOD ASSOCIATED THEREWITHRELATED APPLICATIONS

[0001] This disclosure claims benefit of and priority to U. S. provisional patent application nos.63 / 779,056, filed March 27, 2025, entitled “FLOW CELL DEVICES AND USE THEREOF,” 63 / 809,757, filed May 21, 2025, entitled, “FLOW CELL DEVICES AND USE THEREOF,” 63 / 837,955, filed July 3, 2025, entitled, “FLOW CELL DEVICES AND USE THEREOF,” and 63 / 974,972, filed February 3, 2026, entitled, “FLOW CELL DEVICES AND USE THEREOF.” Each of the foregoing disclosures are incorporated herein by reference in its entirety.BACKGROUND

[0002] Flow cell devices are used in chemistry and biotechnology applications. In nextgeneration sequencing (NGS) systems, flow cell devices are used to immobilize template nucleic acid molecules derived from biological samples and then introduce a repetitive flow of sequencing reagents to attach labeled nucleotides to specific positions in the nucleic acid template molecules. A series of label signals are detected and decoded to reveal the nucleotide sequences of the nucleic acid template molecules, (e.g., immobilized, or amplified, or combinations thereof) attached to a surface of the flow cell.

[0003] Existing NGS flow cell devices are multi-layered structures fabricated from planar surface substrates and other flow cell components, which are then bonded to form fluid flow channels. Such flow cell devices may require costly, multi-step precision fabrication techniques to achieve the required design specifications. On the other hand, inexpensive and off-the-shelf, single channel capillaries are available in a variety of sizes and shapes but are generally not suited for ease of handling and compatibility with the repetitive switching between reagents required for applications such as NGS.SUMMARY

[0004] Described herein are flow cell devices and systems, fluidic dispensing devices, fluidicAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)stations, and other parts of NGS sequencing systems for sequencing nucleic acids. The devices, systems, and methods described herein can advantageously achieve efficient delivery' and usage of reagents to significantly lower consumable costs and reduce delivery' time of reagents in sequencing analysis. The devices, systems, and methods described herein can advantageously achieve more efficient and effective cleaning and alleviate contamination caused by reagent residuals, thereby increasing accuracy and reliability of sequencing analysis. The devices, systems, and methods herein can advantageously allow or cause delivery or purging of a bolus of air (e.g., an amount of air, a bolus of air, quantum of air, or a flow of air or otherwise gaseous flow) between administration of two liquid reagents without impairing chemical functioning of the flow cell device (also referred to herein as “flow cells”) and its sequencing coating(s), which may not be feasible with existing flow cells and their coatings. Such bolus of air or gas may greatly facilitate cleaning and thus reduces contamination by left-over or residual reagents in subsequent reactions on the flow cell. The bolus of air between administration of reagents may improve a homogeneity of the reagents across a channel of the flow cell device, thereby reducing concentration gradients of the reagent and improving accuracy of sequencing.

[0005] The devices, systems, and methods herein can advantageously eliminate series of tubing (e.g., a common line for different reagents) for reagent administration such that the flow cell devices can be robust against fluidics errors and adaptable to different fluidic control and administration. The devices, systems, and methods herein can reduce dead volume or residuals that may exist in existing flow cell and fluidic dispensing devices, thus, saving reagent cost for various sequencing applications. For example, the flow cell devices herein may not include locked-in tubing, and therefore, errors resulting from malfunction of the tubing (e.g., a clogged tube) can be easily resolved in comparison to existing flow cell systems. As another example, the flow cell devices herein can be conveniently adapted for the addition / removal of nozzles or dispensing tips for a new sequencing application. As yet another example, the fluidic connection between the dispensing tips and the flow cell device is made reversible, making dispensing of different fluids using different tips flexible with minimal cross contamination. Furthermore, the flow cell devices and systems herein can include an open landing area in connection with a funnel shape, which advantageously achieves convenient distribution of reagents on the flow cell and with less waste or residuals or reagents in comparison to existing devices. The flow cell devices and system herein also may allow accurate and reliable fluidic dispensing with less actuation mechanisms in theAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)system, e.g., using only actuator(s) for the dispensing tips. The flow cell devices and systems described herein advantageously separate the fluidic station(s) and the imaging station, thereby reduce possible fluidic contamination, thermal interference, or mechanical disturbance to the samples during imaging, and advantageously increase sequencing throughput by enabling using the fluidic stations and imaging station in parallel. The flow cell devices and systems described herein advantageously allow hybrid fluidic communication (e.g., closed communication via manifold or open communication via dispensing tip(s)) at the fluidic station that can be repeated multiple times during a sequencing cycle thereby provide compatibility with various sequencing protocols and allow saving of reagents. The fluidic stations described herein advantageously allow the flow cell device to be in multiple positions to enable hybrid fluidic communication and conveniently allow coupling by the flow cell device to an automated grabber for transportation between the fluidic and imaging station. The flow cell devices and systems described herein are suitable for rapid DNA sequencing and can help realize more efficient use of expensive reagents and reduce the amount of time for sample pre-treatment and replication compared to other DNA sequencing techniques. Therefore, flow cell devices and systems described herein can result in a faster and more cost-effective sequencing method than other systems known in the art.

[0006] In some embodiments, a sequencing system is provided that includes a flow cell device comprising one or more channels defined by one or more substrates, where the one or more channels are configured to allow one or more types of fluids to flow therethrough, one or more inlets in the one or more substrates and in fluidic communication with the one or more channels, and one or more outlets in the one or more substrates and in fluidic communication with the one or more channels. The system further includes a fluidic station including a manifold including one or more fluidic pathways and one or more openings, one or more reagent reservoirs, and an actuation mechanism configured to move the flow cell device to: a closed position, at least along a z direction, where the one or more inlets of the flow cell device and the one or more openings of the manifold are sealingly coupled to each other for fluidic communication from the one or more reagent reservoirs to the flow cell device, and an open position, where the one or more inlets are accessible by a dispensing tip for fluidic communication from the dispensing tip to the flow cell device. The system further includes an imaging station including: a sample stage for positioning the flow cell device thereon, and a sample stage actuator that moves the sample stage and the flow cell device at least alone the z direction for focusing the flow cell device. The system further yetAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)includes a grabber and gantry system configured to: grab the flow cell device from one of the fluidic station and the imaging station, sense coupling of the flow cell device to the grabber and gantry system, and move the flow cell device between the fluidic station and the imaging station such that the flow cell device is positioned for imaging or for fluidic communication with the one or more reagent reservoirs. The grabber and gantry system is configured to move the flow cell device to one of the fluidic station and the imaging station within a single sequencing cycle of a sequencing run and move a second flow cell device to the other one of the fluidic station and the imaging station within the single sequencing cycle,

[0007] In some embodiments, a sequencing system is provided and includes a flow cell device including one or more channels defined by one or more substrates, where the one or more channels are configured to allow one or more types of fluids to flow therethrough, one or more inlets in the one or more substrates and in fluidic connection with the one or more channels, and one or more outlets in the one or more substrates and in fluidic connection with the one or more channels. The system also includes a fluidic station including a manifold including one or more fluidic pathways, and one or more openings. The system further includes one or more reagent reservoirs, and an actuation mechanism comprising an actuator that moves at least in a direction orthogonal to a z direction or rotates about the direction orthogonal to the z direction to move the flow cell device to: a closed position, along the z direction, where the one or more inlets of the flow cell device and the one or more openings of the manifold are sealingly coupled to each other for fluidic communication from the one or more reagent reservoirs to the flow cell device, and an open position, where the one or more inlets are accessible by a dispensing tip for fluidic communication from the dispensing tip to the flow cell device.

[0008] In some embodiments, a sequencing system is provided which includes a flow cell device including: one or more channels defined by one or more substrates, where the one or more channels are configured to allow one or more types of fluids to flow therethrough, one or more inlets in the one or more substrates and in fluidic connection with the one or more channels, and one or more outlets in the one or more substrates and in fluidic connection with the one or more channels. The system also includes an imaging station including: a sample stage for positioning the flow cell device thereon, a sample stage actuator that generates a movement that is not along a z direction, and a movable member operatively coupled to the sample stage actuator and transforms the movement thereof to move the sample stage and the flow cell device at least along the z direction.Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)|0009] In some embodiments, a sequencing system is provided which includes: a flow cell device comprising one or more channels defined by one or more substrates, where the one or more channels are configured to allow one or more types of fluids to flow therethrough, one or more inlets in the one or more substrates and in fluidic connection with the one or more channels, and one or more outlets in the one or more substrates and in fluidic connection with the one or more channels. The system further includes a fluidic station including: a manifold including one or more fluidic pathways, and one or more openings. The system further yet includes an imaging station including a sample stage for positioning the flow cell device thereon, and a grabber and gantry system configured to: grab the flow cell device from one of the fluidic station and the imaging station, sense coupling of the flow cell device to the grabber and gantry system, thereby generating sensing data, and in response to determining the sensing data satisfying a predetermined criterion moving the flow cell device between the fluidic station and the imaging station, such that the flow cell device is positioned for imaging or for fluidic communication with one or more reagent reservoirs. Also, in response to determining the sensing data failing the predetermined criterion, positioning the flow cell device back to one of the fluidic station and the imaging station, where the grabber and gantry system is configured to move the flow cell device to one of the fluidic station and the imaging station within a single sequencing cycle of a sequencing run and move a second flow cell device to the other one of the fluidic station and the imaging station within the single sequencing cycle.

[0010] In some embodiments, a sequencing system is provided which includes a flow cell device comprising: one or more channels defined by one or more substrates, where the one or more channels are configured to allow one or more types of fluids to flow therethrough, one or more inlets in the one or more substrates and in fluidic connection with the one or more channels, and one or more outlets in the one or more substrates and in fluidic connection with the one or more channels. The system also includes a manifold, including one or more fluidic pathways and one or more openings, and a fluidic station including one or more reagent reservoirs. The system further includes an actuation mechanism configured to move the flow cell device to: a closed position, at least along a z direction, where the one or more inlets of the flow cell device and the one or more openings of the manifold are coupled to each other for fluidic communication from the one or more reagent reservoirs to the flow cell device, one or more open positions, where at least one of the one or more inlets is accessible by a dispensing tip for fluidic communication from theAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)dispensing tip to the flow cell device, a grabber position, where the flow cell device is decoupled from the fluidic station and is configured to be accessible by a grabber for moving the flow cell device away from the fluidic station, a loading or unloading position, where the flow cell device is accessible by a user, and a decoupled position that is optional, where the flow cell device is decoupled from the manifold and at a same location in a plane orthogonal to the z direction as the closed position. The system further yet includes an imaging station, and a grabber and gantry system including the grabber and configured to: grab the flow cell device from one of the fluidic station and the imaging station, sense coupling of the flow cell device to the grabber, and move the flow cell device between the fluidic station and the imaging station so as to position the flow cell device in one of the imaging station for imaging or for fluid communication with one or more reagent reservoirs of the flow cell system.

[0011] Such embodiments (as well as other embodiments supported by this disclosure) may further include one and / or another of (and, if not mutually exclusive, in some embodiments, a plurality of, in some embodiments, a majority of, in some embodiments, substantially all of, and in some embodiments, all of) the following structures, functions, functionality, steps, elements, and clarifications:the one or more channels include at least 6 channels;a / the grabber and gantry system includes a flow cell carrier configured to hold the flow cell device therein;a / the flow cell carrier is configured to couple to a grabber of the grabber and gantry system when the flow cell device is moved by the grabber;a / the flow cell carrier includes a first coupling element configured to couple to a coupling element of a / the fluidic station;a / the flow cell carrier includes a first or a second coupling element configured to couple to a coupling element of a / the imaging station;the one or more inlets are facing upwards with an opening in a top surface of the flow cell device;the one or more outlets are facing upwards with an opening in a top surface of the flow cell device;a / the flow cell carrier includes a top cover and a flow cell frame that mechanically couples to the one or more substrates of the flow cell device independently;Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)a / the top cover includes: a top anchor element that mechanically couples to the one or more substrates; one or more through holes that allow one or more gaskets to fit through, where the one or more gaskets are configured to contact a top surface of the one or more substrate and sealingly couple to a / the manifold;a / the one or more gaskets include one or more inlet gaskets and one or more outlet gaskets, a / the one or more gaskets are compatible with flow cell devices that are used in flow cell systems with only closed fluidic communication between a / the manifold and the flow cell device via the one or more gaskets;a / the one or more gaskets are configured to enable sealed fluidic communication from a / the manifold to the one or more inlets or from the one or more outlets to a second manifold; a / the one or more gaskets are configured to sealingly couple to the dispensing tip when the flow cell device is in the open position and sealingly couple to a / the manifold when the flow cell device is the closed position;each gasket of a / the one or more gaskets include a cone shaped cavity therewithin; a / the one or more gaskets are configured to sealingly couple to the dispensing tip when the dispensing tip is at least 0.1mm, 0.2mm, 0.3mm, 0.4mm, 0.5mm, 0.6mm, 0.8mm, or 1mm off a predetermined alignment with the one or more inlets of the flow cell device; a / the one or more gaskets are configured to sealingly couple to the dispensing tip when the one or more openings are at least 0.1mm, 0.2mm, 0.3mm, 0.4mm, 0.5mm, 0.6mm, 0.8mm, or 1mm off a predetermined alignment with the one or more inlets of the flow cell device; a / the manifold further includes a manifold barb at each of the one or more openings; a / the manifold barb is tapered at an end thereof, and where the manifold barb is configured to insert at least partly into a corresponding gasket of the one or more inlet gaskets or one or more outlet gaskets;a / the manifold barb is configured to enable face seal of the one or more openings of the manifold and the flow cell device;a / the manifold is movably coupled to a housing of a / the fluidic station;a / the manifold moves at least in a direction orthogonal to the z direction to sealingly couple to the one or more inlets of the flow cell device;a / the flow cell system further includes a second manifold comprising: one or more second fluidic pathways, and one or more second openings, where: the one or more outlets of theAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)flow cell device and the one or more second openings of the manifold are coupled to each other for fluidic communication from the flow cell device to at least a waste reservoir when the flow cell device is in the closed position; or the one or more outlets of the flow cell device and the one or more second openings of the manifold are coupled to each other for fluidic communication from the flow cell device to at least a waste reservoir when the flow cell device is in the open position;a / the second manifold is movably coupled to the housing of the fluidic system;a / the second manifold moves at least in a direction orthogonal to a z direction to sealingly couple to the one or more outlets of the flow cell device;a / the one or more reagent reservoirs include at least one reagent reservoir containing one or more cycling reagents and at least one reagent reservoir containing non-cycling reagents; a / the one or more reagent reservoirs include at least one reagent reservoir containing reagent stored at a temperature lower than ambient temperature;a / the one or more reagent reservoirs include at least one reagent reservoir containing reagent that is thermally controlled;a / the fluidic station further comprising a container for storing one or more dispensing tips; a / the actuation mechanism is configured to move the flow cell device at least in a plane orthogonal to the z direction between the one or more open positions, the grabber position, the loading position, and the decoupled position;a / the actuation mechanism is configured to move the flow cell device from the decoupled position to the closed position and is configured to move the flow cell device from positions that are at least 0.1mm, 0.3 mm, 0.5 mm, 0.8mm or 1mm away from the decoupled position to the closed position;a / the actuation mechanism includes one or more of: a wheel, a roller, a belt, a rail, a slider, a track, a threaded shaft, a lead screw, a rack, and a linear bearing;a / the actuation mechanism include: an actuator that actuates a cam having a cam surface and a follower contacting the cam surface;a / the cam surface includes at least a linear surface or a curved surface;a / the actuator actuates the cam to move linearly or rotate;a / the actuation mechanism includes a first link member and a second link member that is movably connected to the first link member at a pivot point;Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)the flow cell system includes a second fluidic station;a / the imaging station is displaced from the fluidic station along a direction in 3D; a / the sample stage actuator actuates a moving element to move in a direction orthogonal to the z direction and resulting in the sample stage and the flow cell device to move at least along the z direction for focusing the flow cell device;a / the sample stage actuator actuates a moving element to move in a direction orthogonal to the z direction and resulting in the sample stage and the flow cell device to move only along the z direction for focusing the flow cell device;a / the moving element includes an inclined surface or a curved surface;a precision movement of the flow cell device along the z direction is greater than 100 um, 10 um, 2 um, 1 um, 0, 1 um, or 0.05 um;a / the imaging station further includes a x-y stage and a x-y stage actuation mechanism; a / the x-y stage actuation mechanism includes one or more of: a wheel, a roller, a belt, a rail, a slider, a track, a threaded shaft, a lead screw, a rack, and a linear bearing; a / the x-y stage actuation mechanism includes one or more x-y stage actuators that actuate the x-y stage to move along a first direction orthogonal to the z direction, a second direction orthogonal to the z direction, or both;a / the grabber and gantry system include: a gantry assembly configured to move a grabber in 3D relative to a housing of the flow cell system;o the grabber includes at least one of: one or more arms that are configured to contact and engage the flow cell device; one or more engagement features extending from each of the one or more arms; one or more sensors mounted to the one or more arms; and a support body supporting the one or more arms and attaching the one or more arms to the gantry assembly, wherein the one or more arms are configured to move relative to the support body to engage the flow cell device;a / the grabber and gantry’ system is configured to perform one or more operations, within a single sequencing cycle of a sequencing run, including: moving the flow cell device from a / the fluidic station to a / the imaging station; position the flow cell device on the imaging station for imaging; move the flow cell device from the imaging station to the fluidic station; position the flow cell device on the fluidic station; move a second flow cell device from the second fluidic station to the imaging station; position the second flow cell deviceAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)on the imaging station for imaging; move the second flow cell device from the imaging station to the second fluidic station; and position the second flow cell device on the second fluidic station;a / the one or more sensors include one or more of: a reflective optical sensor and an optical emitter; an inductive proximity sensor, a capacitive proximity sensor, a camera and one or more fiducial markers, a contact switch, a distance sensor, and an ultrasonic sensor; a / the gantry assembly is configured to move the one or more arms of the grabber along a z direction to approach the flow cell device and move within an x-y plane to engage the flow cell device;one or more channels including 2, 3, 4,5 6,7, 8, 9, or 10 channels at a same level along a z-axis;each of one or more inlets includes a landing area;each of one or more inlets include a landing area with a diameter of less than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, or 15 mms within an x-y plane;each of one or more landing areas lacks a hydrophobic coating;each of one or more substrates lacks a hydrophobic coating;the flow cell device lacks a hydrophobic coating;each of one or more landing areas lacks a coating that facilitates flowing of fluids from a respective landing area into the one or more channels;a / the manifold further includes a common line that connects at least one of the one or more fluidic pathways to the one or more openings;a / the common line has a volume of less than 1 ul, 10 ul, 20 ul, 40 ul, 60 ul, 80 ul, 100 ul, 200 ul, 300 ul, or 400 ul;a / the common line has a volume of less than 10%, 20%, 40%, 60%, or 80% of a second volume of a channel of the one or more channels of the flow cell device;a / the manifold includes a solid manifold body, and wherein the one or more fluidic pathways and the common line are defined within the solid manifold body;a / the manifold includes a first surface, and the one or more openings are in the first surface; one or more openings are configured to sealingly couple to one or more inlets when the flow cell device is a closed position so that no liquid leakage is detectable by naked eyes when the flow cell device is in the closed position;Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)one or more openings are configured to be at a first distance at least along a z direction relative to the one or more inlets when the flow cell device is in a decoupled position; the flow cell device is in the decoupled position, open access of one or more inlets along a z axis by a fluid dispensing device is blocked by the manifold;the flow cell device is in the open position, open access of at least one of the one or more inlets along a z axis by a fluid dispensing device is not blocked by a / the manifold; upon the flow cell device is in the open position, open access of one or more inlets along a z axis by a fluid dispensing device is not blocked by a / the manifold;a / the manifold is configured to move at least along the z direction bi-directional relative to a housing of the fluidic station;a / the manifold is configured to move at least along the z direction bi-directional relative to a housing of the flow cell system;a / the first distance is greater than 1 mm, 2 mm, 5 mm, 8 mm, or 10 mm;one or more openings are configured to be at a / the first distance at least along a z direction and at a second distance at least along a direction within an x-y plane relative to the one or more inlets when the flow cell device is in an open position;one or more openings are configured to be at a / the second distance at least along a direction within the x-y plane relative to the one or more inlets when the flow cell device is in an open position;a / the second distance is at least 2x, 4x, 6x, 8x, 10x, 15x, 20x, 30x, 40x, or 50x greater than a / the first distance;a / the manifold is configured to move at least along the z axis bi-directional relative to a housing of the fluidic station or a housing of the flow cell system to switch the flow cell device between two positions selected from a / the closed, decoupled, and open positions; a / the manifold is configured to move at least along a direction within the x-y plane bi¬ directional relative to a housing of the fluidic station or a housing of the flow cell system to switch the flow cell device between two positions selected from a / the closed, decoupled, and open positions;the flow cell device is configured to move at least along a / the z axis bi-directional relative to a housing of the fluidic station or a housing of the sequencing system to switch the flow cell device between two positions selected from the open, decoupled, and closed positions;Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)the flow cell device is configured to move at least along a direction within an x-y plane bi¬ directionally relative to a housing of the fluidic station or a housing of the flow cell system to switch the flow cell device between two positions selected from a / the closed, decoupled, and open positions;a / the manifold is configured to move at least along the z axis bi-directional relative to a housing of the fluidic station or a housing of the flow cell system while the flow cell device is fixed relative to the housing of the fluidic station or the housing of the flow cell system to switch the flow cell device between two positions selected from a / the closed, decoupled, and open positions;the flow cell device is configured to move at least along a z axis bi-directionally relative to a housing of the fluidic station or a housing of the flow cell system while a / the manifold is fixed relative to the fluidic station or housing of a sequencing system to switch the flow cell device between two positions selected from a / the closed, decoupled, and open positions;the flow cell system further includes one or more mounting rails configured to allow moveable mounting of the flow cell device thereon;the flow cell system further includes one or more mounting rails configured to allow moveable and reversible mounting of a flow cell carrier along with the flow cell device thereon, and wherein the flow cell device is at least partly within a / the flow cell frame; the flow cell device further includes a motor for driving movement of the flow cell device on one or more mounting rails;the flow cell system further includes a flow cell frame configured to contain the flow cell device at least partly therewithin;a / the flow cell carrier is configured to: hold a flow cell frame or the flow cell device in a fixed position relative to the carrier; and move m 1 dimension, 2 dimensions, or 3 dimensions relative to a housing of the flow cell system;a / the flow cell frame includes one or more alignment holes configured to couple to one or more protrusions on the flow cell carrier;the flow cell device includes one or more alignment holes configured to couple to one or more protrusions on a / the flow cell carrier;andAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)one or more gaskets are at least partly inserted in a / the flow cell frame, a / the flow cell carrier, or both.|0012] In some embodiments, a sequencing system is provided and includes a flow cell device including one or more channels defined by one or more substrates, one or more inlets in the one or more substrates and in fluidic connection with the one or more channels, and one or more outlets in the one or more substrates and in fluidic connection with the one or more channels. The system also includes a manifold including one or more fluidic pathways and one or more openings, a fluidic station including one or more reagent reservoirs, an actuation mechanism configured to move the flow cell device to one or more positions including a closed position at least along a z direction where the one or more inlets of the flow cell device and the one or more openings of the manifold are coupled to each other for fluidic communication from the one or more reagent reservoirs to the flow cell device, one or more open positions where at least one of the one or more inlets is accessible by a dispensing tip for fluidic communication from the dispensing tip to the flow cell device, a grabber position, where the flow cell device is decoupled from the fluidic station and is configured to be accessible by a grabber for moving the flow cell device away from the fluidic station, a loading or unloading position, where the flow cell device is accessible by a user, and a decoupled position, where the flow cell device is decoupled from the manifold and at a same location in a plane orthogonal to the z direction as the closed position. The system further includes an imaging station configured to image one or more samples immobilized on the flow cell device, and a grabber and gantry system configured to grab the flow cell device from one of the fluidic station and the imaging station, move the flow cell device between the fluidic station and the imaging station, and position the flow cell device on the other one of the fluidic station and the imaging station for imaging the one or more samples or fluidic communication with the one or more reagent reservoirs. Positioning of the flow cell device is based on a first calibrated position of the fluidic station or a second calibrated position of the imaging station, where the first calibrated position and the second calibrated position are determined during an automatic calibration using at least part of the grabber as a sensor.

[0013] In some embodiments, a sequencing system is provided and includes a flow cell device having one or more samples immobilized thereon, a fluidic station, an imaging station, and a grabber and gantry system for positioning the flow cell device on the fluidic station or the imaging station, which includes a grabber configured to engage the flow cell device, a gantry assemblyAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)configured to move the grabber along one or more axis or rotate about one or more axis, a sensing system configured to detect one or more changes in an electrical signal when the grabber approaches and touches the fluidic station or the imaging station with movement along one or more axis or rotation about one or more axis, where at least part of the grabber or at least part of the fluid ic station or imaging station forms an electrode of the sensing system. The sequencing system also includes a hardware processor configured to determine a first calibrated position of the fluidic station or a second calibrated position of the imaging station based on the detected one or more changes in the electrical signal.

[0014] Such embodiments (as well as other embodiments supported by this disclosure) may further include one and / or another of (and, if not mutually exclusive, in some embodiments, a plurality of, in some embodiments, a majority of, in some embodiments, substantially all of, and in some embodiments, all of) the following structures, functions, functionality, steps, elements, and clarifications:a / the first calibrated position of the fluidic station and a / the second calibrated position of the imaging station are determined during an automatic calibration using at least part of the grabber and gantry system as a sensor or as an electrode of the sensor;a / the sensor comprises a capacitive sensor;a / the at least part of the grabber as a / the electrode includes metal or is conductive; the grabber is mechanically connected via a connector to a gantry assembly of the grabber and gantry system, and / or a / the connector is electrically insulating thereby electrically isolating the grabber from a / the gantry assembly;the imaging station includes one or more first pins that are electrically conductive; the fluidic station includes one or more second pins that are electrically conductive; the grabber is configured to contact at least some of the one or more first pins and a first non- conductive location of the fluidic station sequentially for determining the first calibrated position of the fluidic station;the grabber is configured to contact at least some of the one or more second pins and a second non-conductive location of the imaging station sequentially for determining the second calibrated position of the imaging station;a / the first non-conductive location is comprised at a surface of the fluidic station; a / the second non-conductive location is comprised at a surface of the imaging station;Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)a / the connector is configured to prevent electrical conduction between the grabber and a / the gantry assembly;a / the sensor detects a first change in an electrical signal corresponding to a non-conductive contact between the grabber and the first non-conductive location of the fluidic station; a / the sensor detects a second change in an electrical signal corresponding to a conductive contact between the grabber and the one or more second pins;the grabber is configured to sequentially move toward the fluidic station along a plurality of directions and contact the fluidic station a plurality of times to determine the first calibrated position of the fluidic station;contacting the fluidic station a / the plurality of times includes at least a non-conductive contact and a conductive contact;contacting the fluidic station a / the plurality of times includes at least a non-conductive contact with the first non-conductive location and a conductive contact with at least some of one or more first pins;a / the plurality of directions comprise an X direction, a Y direction, and a Z direction; a / the automatic calibration determines a rotational alignment of the grabber relative to the fluidic station or the imaging station;a / the rotational alignment includes at least a theta rotation about a z axis;the grabber includes one or more alignment features configured to contact the fluidic station and the imaging station during the automatic calibration;a / the alignment features include one or more of: a first tip at a first arm, a second tip at a second arm, the first arm, and the second arm of the grabber;a / the automatic calibration includes determining a first coarse position of the fluidic station or a second coarse position of the imaging station, and / or determining the first calibrated position or the second calibrated position based on the first coarse position or the second coarse position;determining a / the first or second coarse position includes sensing a change in an electrical signal as the grabber approaches a first non-conductive location of the fluidic station or second non-conductive location of the imaging station;determining a / the first or a / the second calibrated position includes detecting a change in an electrical signal as the grabber makes a conductive contact with one or more first pins ofAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)the fluidic station or one or more second pins of the imaging station;a second fluidic station, the grabber and gantry system being configured to grab the flow cell device from one of the fluidic station, a / the second fluidic station, and the imaging station, moving the flow cell device between the fluidic station, the second fluidic station, and the imaging station, and / or positioning the flow cell device on another one of the fluidic station, the second fluidic station, and the imaging station for fluidic communication with one or more reagent reservoirs or the imaging station, where positioning of the flow cell device is based on a first calibrated position of the fluidic station, a second calibrated position of the imaging station, or a third calibrated position of the second fluidic station; an / the automatic calibration occurs before, during, or after a sequencing run (in some embodiments, at least two thereof, and in some embodiments, all three);an / the automatic calibration includes at least one: determining the first or second calibrated positions during a set-up of the system, and recalibrating the first or second calibrated positions after a disturbance occurs after the set-up of the flow cell system;anda / the electrical signal includes a capacitance signal(s) over time.

[0015] In some embodiments, a method for automatic calibration of positions of a fluidic station and an imaging station in a sequencing system is provided and includes a grabber and gantry system configured to move a flow cell device between the fluidic station and imaging station. The method includes moving a grabber of the grabber and gantry system toward the fluidic station or imaging station, sensing, using a sensor comprising at least part of the grabber, a change in an electrical signal as the grabber moves, detecting a touch event between the grabber and fluidic station or the imaging station based on the sensed change in the electrical signal, recording a position of the grabber corresponding to the touch event, and determining, at least along a first axis or about a first rotational axis, a first calibrated position of the fluidic station or a second calibrated position of the imaging station based on the recorded position.

[0016] Such embodiments (as well as other embodiments supported by this disclosure) may further include one and / or another of (and, if not mutually exclusive, in some embodiments, a plurality' of, in some embodiments, a majority of, in some embodiments, substantially all of, and in some embodiments, all of) the following structures, functions, functionality, steps, elements, and clarifications:Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)moving the grabber toward the fluidic station or imaging station includes sequentially moving the grabber toward the fluidic station or the imaging station along a plurality of directions and contacting the fluidic station or imaging station a plurality of times; moving the grabber toward the fluidic station or imaging station is at least along the first axis, a second axis, or a third axis;sensing, using the sensor comprising at least part of the grabber, the change in the electrical signal as the grabber moves includes sampling the electrical signal at a sampling rate determined based on a speed of movement of the grabber, and determining the change in the electrical signal from a baseline electrical signal;a / the sampling rate is greater than 100 Hz, 200 Hz, 300 Hz, 400 Hz, or 500 Hz; a / the electrical signal is sampled using a capacitance-to-digital converter coupled to the grabber;detecting a / the touch event includes determining that the change is above a first threshold, a second threshold, or both, and / or m response to determining that the change is above the first threshold but not above the second threshold, determining the touch event as a non-conductive touch or as at least along the first axis, and / or m response to determining that the change is above the second threshold, determining the touch event as a conductive touch as at least along the second axis;recording the position of the grabber corresponding to the touch event includes recording a first position corresponding to a location at least along the first axis when the grabber contacts a surface of the fluidic station or imaging station during a first movement of the grabber along at least the first axis;recording the position of the grabber corresponding to the touch event includes recording second and third positions corresponding to a location along at least a second axis when the grabber contacts one or more first pins of the fluidic station or one or more second pins of the imaging station during movement of the grabber along the second axis; recording the position of the grabber corresponding to the touch event includes recording fourth and fifth positions corresponding to a location along a third axis when the grabber contacts the one or more first pins of the fluidic station or the one or more second pins of the imaging station during movement of the grabber along the third axis;recording the position of the grabber corresponding to the touch event includes recordingAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)the first position corresponding to a coarse location along a first axis when the grabber contacts a surface of the fluidic station or imaging station during a first movement of the grabber along the first axis, recording second and third positions corresponding to a coarse location along a second axis and a coarse rotational alignment about a rotational axis when the grabber contacts one or more first pins of the fluidic station or one or more second pins of the imaging station using two different spots on the grabber during movement of the grabber along the second axis, recording fourth and fifth positions corresponding to a refined location along a third axis and a refined rotational alignment about the rotational axis when the grabber contacts one or more first pins of the fluidic station or one or more second pins of the imaging station during movement of the grabber along the third axis and optionally based on the coarse rotational alignment, recording sixth and seventh positions corresponding to a refined location along the second axis when the grabber contacts one or more first pins of the fluidic station or one or more second pins of the imaging station using another two different spots on the grabber during movement of the grabber along the second axis and based on the coarse location along the second axis, and recording eighth and ninth positions corresponding to a refined location along the first axis when the grabber contacts one or more first pins of the fluidic station or one or more second pins of the imaging station during movement of the grabber along the first axis and based on the coarse location along the first axis;a / the first axis is a z axis, and a / the second and a / the third axis are within an x-y plane; determining the change in the electrical signal from a baseline electrical signal includes determining a magnitude change in the electrical signal, determining a shape change in the electrical signal, determining a slope in the electrical signal, or a combination thereof; a / the first threshold is smaller than a / the second threshold;a / the touch event includes at least a non-conductive touch between the grabber and a first non-conductive location of the fluidic station or a second conductive location of the imaging station;a / the touch event includes at least a conductive touch between the grabber and one or more first pins of the fluidic station or one or more second pins of the imaging station; one or more first pins or one or more second pins are electrically conductive;a / the first non-conductive location or a / the second non-conductive location is at a surfaceAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)of the fluidic station or imaging station;a / the sensor is a capacitive sensor;at least part of a / the grabber includes metal, at least part of the grabber is conductive; a / 'tlie sensor is a capacitive sensor, and at least part of the grabber is an electrode of the capacitive sensor;a / the grabber is mechanically connected via a connector to a gantry assembly of the grabber and gantry system, and / or the connector is electrically insulating thereby electrically isolating the grabber from the gantry assembly;a / the imaging station includes one or more first pins that are electrically conductive; the fluidic station includes one or more second pins that are electrically conductive; a / the first non- conductive location is at a surface of the fluidic station;a / the second non-conductive location is at a surface of the imaging station;a / the connector is configured to prevent electrical conduction between the grabber and the gantry assembly;contacting the fluidic station a plurality of times includes at least a non-conductive contact and a conductive contact;contacting the fluidic station a plurality of times includes at least a non-conductive contact with the first non-conductive location and a conductive contact with at least some of a / the one or more first pins;the plurality of directions include at least two of, and preferably three of an X direction, a Y direction, and a Z direction;automatic calibration to determine a rotational alignment of the grabber relative to the fluidic station or the imaging station;rotational alignment includes at least a theta rotation about a z axis;a / the grabber includes one or more alignment features configured to contact the fluidic station and the imaging station during an / the automatic calibration;alignment features include one or more of: a first tip at a first arm, a second tip at a second arm, the first arm, and the second arm of the grabber;a second fluidic station;andautomatic calibration occurs before, during, or after a sequencing run (in someAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)embodiments, at least two thereof, and m some embodiments, all three).

[0017] In some embodiments, a sequencing system is provided and includes a flow cell device having one or more samples immobilized thereon, a fluidic station, an imaging station, a fluidic dispensing device configured to releasably engage a dispensing tip via a dispensing head assembly and enable dispensing of fluid from the dispensing tip, and a grabber and gantry system for positioning the dispensing tip for sealed fluidic communication with the flow cell device. The grabber and gantry system includes a gantry assembly mechanically connected to the fluidic dispensing device to move the fluidic dispensing device, and a vision system including a first and second vision sensors facing different directions, a reference structure positioned within fields of view of the first and second vision sensors, and an optical component positioned within the fields of view of the first and second vision sensors for redirecting light. The vision system is configured to determine a reference height of a fluidic interface of the flow cell device based on a seal formed between a reference dispensing tip and the flow cell device and determine a vision-based height of the dispensing tip. The gantry assembly is configured to move the dispensing tip to a cal ibrated dispensing position based on the reference height and the vision-based height of the dispensing tip to enable sealed fluidic communication between the dispensing tip and the flow cell device.

[0018] Such embodiments (as well as other embodiments supported by this disclosure) may further include one and / or another of (and, if not mutually exclusive, in some embodiments, a plurality of, in some embodiments, a majority of, in some embodiments, substantially all of, and in some embodiments, all of) the following structures, functions, functionality, steps, elements, and clarifications:the first and second vision sensors include a first and second camera facing two different directions that are orthogonal to each other;the reference structure includes an aperture with a first light transmission level with a surrounding region of a second light transmission level, and a center of the aperture colocalizes with centers of the two vision sensors;a / the first light transmission level is higher than the second light transmission level; the reference structure includes a center that co-localize with centers of the vision sensors; the reference structure includes an aperture that the reference dispensing tip is configured to go through;Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)the aperture is circular and includes a diameter that is large enough to allow the dispensing tip to go through, and the dispensing tip is skewed relative to a z axis;the optical component includes a mirror placed along a direction that is different from the two different directions that the vision sensors are facing;the optical component is placed diagonally relative to a z axis;the reference height is determined in a first coordinate system, and the vision-based height is determined in a second coordinate system;the vision system is configured to determine a vision-based reference height of the reference dispensing tip when the reference tip is at the reference height; determining the vision-based reference height of the dispensing tip is based on first image data acquired using only the first vision sensor of the vision system;the vision-based reference height of the reference tip is based on a z-offset from a center of a field of view of the first image data acquired using only the first vision sensor of the vision system;determining the vision-based height of the dispensing tip is based on second image data acquired using only the first vision sensor of the vision system;the vision system is configured to determine, using third image data acquired using the first vision sensor of the vision system, a camera offset between the fluidic dispensing device and a center of the second vision sensor of the vision system;a / the camera offset is determined without engaging the reference dispensing tip or dispensing tip by the fluidic dispensing device;the vision system is configured to determine, using fourth image data of the first vision sensor of the vision system, a tip offset between a center of a field of view of the fourth image data and the dispensing tip, wherein the fourth image data is acquired when the dispensing tip is above the reference structure along a z axis;a / the camera offset or the tip offset is within an x-y plane;the vision system is configured to determine a location of an inlet gasket of the flow cell device based on image data of acquired using the second vision sensor;the sealed fluidic communication is between the dispensing tip and a / the inlet gasket of the flow cell device to allow fluidic flow into a corresponding channel of the flow cell device; the calibrated dispensing position includes: a calibrated height along a z axis and calibratedAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)two-dimensional position within an x-y plane;the calibrated height is determined based on the reference height, the vision-based reference height, and the vision-based height of the dispensing tip to enable sealed fluidic communication between the dispensing tip and the flow cell device;a / the calibrated two-dimensional position within the x-y plane is determined based on a / the camera offset, a / the tip offset, and a location of the inlet gasket of the flow cell device to enable sealed fluidic communication between the dispensing tip and the flow cell device; the vision system is configured to determine the calibrated dispensing position of the dispensing tip based on one or more of: the reference height of the reference tip, the vision-based reference height of the reference tip, the vision-based height of the dispensing tip, a / the camera offset, a / the tip offset, and a / the location of a / the inlet gasket of the flow cell device;the reference height of the reference tip, the vision-based reference height of the reference tip, and a / the camera offset are determined before or after a sequencing run and are repeatedly used for a plurality of sequencing runs;a / the tip offset and a / the location of a / the inlet gasket of the flow cell device are determined repeatedly during two or more sequencing cycles of a sequencing run;a / the tip offset and a / the location of a / the inlet gasket of the flow cell device is determined repeatedly within a single cycle of a sequencing run;a / the second vision sensor is fixedly attached to a / the fluidic dispensing device;the second vision sensor faces a z axis, and the first vision sensor faces a direction within an x-y plane;the vision system further includes a light source configure to backlight the dispensing tip when image data is acquired using the first vision sensor, the second vision sensor, or both; a / the reference height and a / the vision-based reference height are along a z axis; one or more of: the first vision sensor, the reference structure, and the optical component of the vision system is fixedly attached to at least part of the fluidic station that is fixed relative to a housing of the system;andthe flow cell device is configured to move relative to one or more of the vision system, the first vision sensor, the second vision sensor, the reference structure, and the opticalAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)component.

[0019] In some embodiments, a method for calibrating a dispensing tip using a vision system for sealed dispensing to a flow cell device is provided and includes moving, by a grabber and gantry system, a reference dispensing tip engaged by a fluidic dispensing device until a seal is formed between the reference dispensing tip and the flow cell device, determining a reference height of a fluidic interface of the flow cell device based on the seal, determining a vision-based reference height of the reference dispensing tip using first image data from two vision sensors of the vision system, engaging a dispensing tip by the fluidic dispensing device, determining a vision-based height of the dispensing tip using second image data from the two vision sensors, and determining a calibrated dispensing position at least along a first direction of the dispensing tip for sealed dispensing to the flow cell device based on the reference height, the vision-based reference height, and the vision-based height.

[0020] Such embodiments (as well as other embodiments supported by this disclosure) may further include one and / or another of (and, if not mutually exclusive, in some embodiments, a plurality of, in some embodiments, a majority of, in some embodiments, substantially all of, and in some embodiments, all of) the following structures, functions, functionality, steps, elements, and clarifications:moving the reference dispensing tip until a seal is formed between the reference dispensing tip and the flow cell device includes moving the reference dispensing tip through an aperture of a reference structure of the vision system;determining the reference height of the fluidic interface of the flow cell device based on the seal does not rely on image data acquired using the vision system;determining the reference height of the fluidic interface of the flow cell device based on the seal is in a first coordinate system, and determining the vision-based reference height of the reference dispensing tip using the first image data from two vision sensors of the vision system is in a second coordinate system;determining the reference height of a fluidic interface of the flow cell device based on the seal is based on a height of the fluidic dispensing device when the seal is formed; the first direction is along z axis;determining the vision-based reference height of the reference dispensing tip using firstAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)image data from two vision sensors of the vision system includes determining a first distance from the reference tip to a center of a field of view of the first image data; determining the vision-based reference height of the reference dispensing tip using first image data from two vision sensors of the vision system includes determining a first distance from the reference tip to a center of the aperture of the reference structure in the first image data;determining the vision-based height of the dispensing tip using second image data from two vision sensors of the vision system includes determining a second distance from the dispensing tip to the center of the field of view of the second image data; determining the vision-based height of the dispensing tip using second image data from two vision sensors of the vision system includes determining a second distance from the dispensing tip to the center of the aperture of the reference structure in the second image data;determining the calibrated dispensing position at least along the first direction of the dispensing tip for sealed dispensing to the flow cell device is based on the first distance and the second distance;determining the calibrated dispensing position at least along the first direction of the dispensing tip for sealed dispensing to the flow cell device is based on an offset corresponding to the first and second coordinate system;a / the offset corresponding to the first and second coordinate system is determined based on a difference between the reference height of the fluidic interface of the flow cell device based on the seal and the vision- based reference height of the reference dispensing tip using the first image data;moving, by a gantry assembly of the grabber and gantry system, the fluidic dispensing device relative to a reference structure of the vision system, generating, by the vision system, third image data of the fluidic dispensing device and the reference structure from only the second vision sensor of the vision system, and / or determining, based on the third image data and the reference structure, a spatial relationship between the vision system and the fluidic dispensing device;moving by the gantry assembly of the grabber and gantry system, the fluidic dispensing device relative to a reference structure of the vision system includes moving the fluidicAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)dispensing device to a reference location so that a dispensing head assembly of the fluidic dispensing device is at a center of a field of view of the third image data, and / or moving the fluidic dispensing device away from the reference location so that a center of the second vision sensor is at the center of the field of view of the third image data;a / the reference location is within an / the x-y plane and is relative to the reference structure; a / the spatial relationship between the vision system and the fluidic dispensing device includes a distance from the dispensing head assembly to a center of the second vision sensor within an / the x-y plane;moving the fluidic dispensing device to the reference location, the fluidic dispensing device engages the dispensing tip via the dispensing head assembly, and / or determining an offset of the dispensing tip relative to a reference based on fourth image data obtained from only a / the first vision sensor of the vision system;a / the reference includes a center of field of view of a / the fourth image data;the reference includes a center of a / the first vision sensor in a / the fourth image data; moving the second vision sensor and the fluidic dispensing device so that a center of the second vision sensor aligns with an inlet gasket of the flow cell device;determining a location of a / the inlet gasket of the flow cell device based on image data of acquired using a / the second vision sensor;determining a / the calibrated dispensing position of a / the dispensing tip at least within a plane orthogonal to a / the first direction for sealed dispensing to the flow cell device based on a / the spatial relationship between a / the vision system and a / the fluidic dispensing device, the offset of the dispensing tip relative to the reference, and the location of a / the inlet gasket;moving the dispensing tip to the calibrated dispensing tip by a grabber and gantry assembly to form a sealed fluidic connection between the dispensing tip and the inlet gasket of the flow cell device;sealingly dispensing from the dispensing tip one or more reagents to a channel of the flow cell device via the inlet gasket;andmoving the dispensing tip to the calibrated dispensing tip by the grabber and gantry assembly includes moving the dispensing head assembly to a position determined based onAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)the spatial relationship between the vision system and the fluidic dispensing device and the location of the inlet gasket so that the dispensing tip is moved to the calibrated position. |0021] While many of the embodiments disclosed herein are directed at sequencing systems, it will be appreciated that such structure and methods can be applicable outside of sequencing, and encompass, for example, flow cell systems in general. For the avoidance of doubt, claims directed to sequencing systems can be drafted as flow cell systems in general.

[0022] These and other embodiments, as well as objects and advantages thereof, will become even clearer with reference to the figures, a brief description of this is provided below, and following detailed description.INCORPORATION BY REFERENCE

[0023] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference in their entirety to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference in its entirety. In the event of a conflict between a term herein and a term in an incorporated reference, the term herein controls.BRIEF DESCRIPTION OF THE DRAWINGS

[0024] The novel features of the inventive concepts are set forth with particularity' in the appended claims. A better understanding of the features and advantages of the present inventive concepts will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the inventive concepts are utilized, and the accompanying drawings of which:

[0025] FIG. 1 illustrates a block diagram of a computer-implemented system for performing operations in DNA sequencing and sequencing analysis, according to some embodiments.

[0026] FIGS. 2A-2E show schematics of a flow cell device, according to some embodiments.

[0027] FIGS. 2F-2J show schematics of a flow cell device, according to some embodiments,

[0028] FIGS. 3A -3B show schematics of a flow cell system including the flow cell device, theAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)dispensing tips, and waste collecting mechanism, according to some embodiments.

[0029] FIG. 3C shows a schematic of a flow cell system including the flow cell device, the dispensing tips, and waste collecting mechanism, according to some embodiments.

[0030] FIG. 3D shows a schematic of a flow cell system including the flow cell device and wasting collecting mechanism, according to some embodiments.

[0031] FIGS. 4A -4E show schematics of the flow cell device at different positions relative to the manifold, and the pumps and the fluid dispensing device, according to some embodiments.

[0032] FIGS. 4F-4I show schematics of exemplary embodiments of the manifold and the flow cell device, according to some embodiments.

[0033] FIGS. 5A -5E show schematics of the flow cell device at different positions relative to the manifold, the pumps and the fluid dispensing device, according to some embodiments.

[0034] FIG. 5F shows a schematic of the flow cell device, the manifold, and the fluid dispensing device, according to some embodiments.

[0035] FIGS. 6A -6C show schematics of the valve and the manifold, according to some embodiments.

[0036] FIG. 7 shows a flow chart of an exemplary embodiment of the methods of using the flow cell system for a sequencing application.

[0037] FIG. 8 shows an exemplary embodiment of a flow cell system (e.g., a flow cell system within a sequencing system), according to some embodiments.

[0038] FIGS. 9A-9E shows an exemplary embodiment of a fluidic station of a flow cell (e.g., sequencing) system, according to some embodiments, with FIGS. 9A-9D showing components thereof, and FIG. 9E illustrating a portion of an assembled station.

[0039] FIG. 10 shows an exemplary embodiment of the fluidic station in FIG. 9E in relation to a first manifold (corresponding to inlets of a flow cell device) and a second manifold (corresponding to outlets of the flow cell device) and a rotary valve for controlling fluidic communication through the manifold, according to some embodiments.

[0040] FIGS. 11A-11B show an exemplary embodiment of a first part of an actuation mechanism of the fluidic station that moves the flow cell device at least along a z direction,Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)according to some embodiments.

[0041] FIGS. 12A-12B show an exemplary embodiment of the first part of the actuation mechanism of the fluidic station that moves the flow cell device at least along a z direction, according to some embodiments.

[0042] FIGS. 13A-13B show an exemplary embodiment of the first part of the actuation mechanism of the fluidic station that moves the flow cell device at least along a z direction, according to some embodiments.

[0043] FIGS. 14A-14B show an exemplary embodiment of the first manifold, according to some embodiments.

[0044] FIGS. 15A-15E show exemplary embodiments of the first manifold with a manifold barb that can sealingly couple to a dispensing tip (FIGS. 15A, 15D) and sealingly couple to an inlet gasket of the flow cell device (FIGS. 15B-15E), according to some embodiments.

[0045] FIGS. 16A-16B show exemplary embodiments of the imaging station of the flow cell system configured with a sample actuator that can move the flow cell device thereon at least along a z direction, according to some embodiments.

[0046] FIG. 16C shows an exemplary’ embodiment of the flow cell device and flow cell frame for holding the flow cell device at least partly therein, according to some embodiments.

[0047] FIG. 17A-17B show an exemplary’ embodiment of the gantry and grabber system and the coupling of the grabber to the flow cell device (FIG. 17A), according to some embodiments. FIG. 17B is a close-up view of the grabber,

[0048] FIG. 18 shows an exemplary embodiment of the fluidic dispensing device and the vision system for aligning the dispensing tip for fluidic communication with the flow cell device, according to some embodiments.

[0049] FIGS. 19A-19G show various top view illustrations of an exemplary' embodiment of the operation of sequentially moving the grabber toward the fluidic station along a plurality of directions and contact the fluidic station a plurality of times, according to some embodiments.

[0050] FIG. 20 shows an exemplary embodiment of a change in electrical signal over time, e g., a capacitance change over time relative to a baseline capacitance caused by movements and touchAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)events of the grabber, according to some embodiments.

[0051] FIGs. 21A-21H show various side-views of a reference structure having first area (e.g., a rectangular or square surrounding area) that is opaque (does not transmit light) and a second area (e.g., a circular aperture) which allows light to travel therethrough.

[0052] FIGs. 22A-22E show various images of first image data or second image data which include images acquired by the first camera (e.g., cam 1) of a vision system according to some embodiments.DETAILED DESCRIPTION

[0053] Described herein are inventions and corresponding embodiments for systems and devices (as well as methods associated therewith) to analyze nucleic acid sequences, e.g., from amplified nucleic acid arrays in flow cells or from an array of immobilized nucleic acids. The systems, devices, and methods described herein can also be useful in, e.g., sequencing for comparative genomics, tracking gene expression, microRNA sequence analysis, epigenomics, and aptamer and phage display library characterization, as well as other sequencing applications. The systems, devices, and methods disclosed herein comprise various combinations of optical, mechanical, fluidic, thermal, electrical, and computing devices / aspects. The systems, devices, and methods described herein can also be useful for imaging applications that use sequencing systems to image target analytes such as proteins or nucleic acid in cells or tissues disposed within flow cell devices. See, e.g,, published PCT application no. W02024040068, the contents of which are incorporated by reference in their entireties herein.

[0054] Although the flow cell devices and systems disclosed herein are with respect to DNA sequencing applications, it is worth noting that such flow cell devices and systems, in some embodiments, can be used in other biological or chemical analysis applications, e.g., immunostaining, that uses a microfluidic device like the flow cell devices and systems disclosed herein.

[0055] The advantages of the disclosed flow cell devices, fluidic control devices, and systems include, but are not limited to: significantly lower consumable costs (e.g., as compared to those for currently available nucleic acid sequencing systems); efficient and effective cleaning of flowAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)cell devices, thereby reducing contamination of sequencing processes by residual reagent(s); reduced delivery' time of reagents, reduced washing time, and increased homogeneity of reagents on the flow cells; reduced device and system manufacturing / maintenance complexity and cost; and flexible system throughput and flexible adaptation of the systems to different sequencing applications.Sequencing systems

[0056] Disclosed herein, in some embodiments, are flow cell devices and systems (and methods associated therewith) that can be employed for performing or facilitating DNA sequencing analysis using sequencing systems (the phrases “flow cell system” and “sequencing system” can be used interchangeably throughout the present disclosure). Such sequencing systems may utilize various sequencing techniques including but not limited to the sequencing techniques disclosed herein.

[0057] FIG. 1 illustrates a block diagram of a sequencing system 100 for performing sequencing and sequencing analysis, according to one or more embodiments disclosed herein. The sequencing system 100, according to some embodiments, includes a flow cell device 200, a sequencer 114, an imager 116, a data storage device 122, and a user interface 124. The sequencing system 100 may optionally be connected to a cloud 130 (e.g., a network which may include the internet, for ultimately coupling with a server, a computing device, database, and the like). The sequencing system 100 may include one or more of dedicated processors 118, an integrated circuit (e.g., Field- Programmable Gate Array(s) (FPGAs)) 120, other circuitry, and / or a computer system 126.

[0058] In some embodiments, a flow cell device 200, 300, 4000, 5000 is configured to capture DNA fragments and form DNA sequences for base-calling on the flow cell device. The flow cell device 200, 300, 4000, 5000 can include a support as described herein. The support can be a solid support. The support can include a surface coating thereon as disclosed herein. The surface coating can be a polymer coating as disclosed herein. The surface coating can be disposed on a surface of the one or more channels of the flow cell device. A different or identical surface can be placed on a surface of an inlet of the flow cell device.

[0059] In some embodiments, the flow cell device 200, 300, 4000, 5000 can include a plurality of tiles (e.g., portions, locations, areas, sections, etc.) thereon configured to be imaged by theAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)imager 116, and each tile may be separated into a plurality of sub-tiles. In some embodiments, the sub-tiles may be organized in a grid. Each sub-tile can include a plurality' of clusters or polonies (e.g., a collection of DNA molecules such as the concatemer template molecules disclosed herein) thereon. In some embodiments, the flow cell device 200, 300, 4000, 5000 may include a number of tiles in a range of about 1 tile to about 2000 tiles, about 100 tile to about 1500 tiles, or about 200 tiles to about 500 tiles, inclusive of all ranges and subranges therebetween. In some embodiments, each tile may be divided into a number of sub-tiles in a range of about 2 sub-tiles to about 200 sub-tiles, about 10 sub-tiles to about 100 sub-tiles, or about 20 sub-tiles to about 50 subtiles, inclusive of all ranges and subranges therebetween. In some embodiments, the sub-tiles may be organized in a grid that may have M by N sub-tiles. As a nonlimiting example, a flow cell can have 424 tiles, and each tile can be divided into a 6 x 9 grid, therefore 54 sub-tiles. In some embodiments, the imager 116 may be configured to obtain one or more images (hereinafter, “flow cell image(s)” of the plurality of tiles, a subset of the plurality of tiles, and / or a subset of the plurality of sub-tiles. The flow cell image(s) as disclosed herein can include an image including signals (e.g., fluorescence levels) of the plurality of clusters or polonies. The flow cell image can include one or more tiles of signals or one or more sub-tiles of signals. In some embodiments, a flow cell image can be an image that includes all the tiles and approximately all signals thereon. The flow cell image can be acquired from a channel during (i) an imaging cycle or (ii) a sequencing cycle using the imager 116. In some embodiments, each tile may include millions of polonies or clusters. As a nonlimiting example, a tile can include about 1 to 10 million clusters or polonies. Each polony can be a collection of many copies of DNA molecules.|0060] More details of the flow cell device 200, 300, 4000, 5000 and its functional and structural elements are disclosed herein in relation to figures, e.g., FIGS.2A-2D, 3A-3D, 4A-4I, 5A-5F, 6A- 6C, and 7A-7B.

[0061] The sequencer 114 may be configured to flow one or more or mixtures of reagents onto the flow cell. Such mixtures of reagents include nucleotide mixtures, polymerases, reagents to add or cleave chain terminating moieties from the nucleotides in between nucleotide addition steps and perform other steps for the formation of the DNA molecules suitable for sequencing applications on the flow cell device 200, 300, 4000, 5000. The nucleotides may have fluorescent elements (also referred to as “labels” or “moieties”) attached that emit light or energy at a wavelength that indicates the type of nucleotide. Each type of fluorescent element may correspond to a particularAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)nucleotide base (e.g., A, G, C, T). The fluorescent elements may emit light in visible wavelengths. In some embodiments, the sequencer 114 and the flow cell device 200, 300, 4000, 5000 may be configured to perform various sequencing methods disclosed herein or known in the art, for example, sequencing-by-avidity, sequencing by binding or sequencing by synthesis.

[0062] For example, each nucleotide base may be assigned a color. Different types of nucleotides can have different colors. Adenine (A) may be red, cytosine (C) may be blue, guanine (G) may be green, and thymine (T) may be yellow, for example. The color or wavelength of the fluorescent element for each nucleotide may be selected so that the nucleotides are distinguishable from one another based on the wavelengths of light emitted by the fluorescent elements.

[0063] The imager 116 may be configured to capture images of the flow cell device 200, 300, 4000, 5000 after each flowing step. In some embodiments, the imager 116 may include a camera configured to capture digital images, such as a CMOS or a CCD camera. The camera may be configured to capture images at the wavelengths of the fluorescent elements bound to the nucleotides. The images can be called flow cell images,

[0064] In some embodiments, the imager 116 can include one or more optical systems disclosed herein. The optical system(s) can be configured to capture optical signals from the flow cell and generate corresponding digital images thereof. The digital images can then be used for base calling.

[0065] In an embodiment, the images of the flow cell may be captured in groups, where each image in the group is taken at a wavelength or in a spectrum that matches or includes one of the fluorescent elements. In another embodiment, the images may be captured as single images that captures all of the wavelengths of the fluorescent elements.

[0066] The resolution of the imager 116, in some embodiments, controls the level of detail in the flow cell images, including, for example, pixel size. In existing systems, resolution is important as it controls the accuracy with which a spot-finding algorithm identifies the polony centers. In some embodiments, the image resolution of flow cell images disclosed herein can be about 10 nanometers (nm) to 900 nm, inclusive of all ranges or subranges therebetween. In some embodiments, the image resolution of the flow cell images can be between about 10 nm to about 900 nm, about 10 nm to about 500 nm, about 10 nm to about 200 nm, about 20 nm to about 500 nm, about 20 nm to about 200 nm, or any range or subrange therebetween. One way to increase the accuracy of spot finding is to improve the resolution of the imager 116, or improve theAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)processing performed on images taken by imager 116. Detecting polony centers in pixels other than those detected by a spot-finding algorithm can be performed. Suitable spot- finding algorithms will be known to persons of ordinary' skill in the art. These methods can allow for improved accuracy in detection of polony centers without increasing the resolution of the imager 116. The resolution of the imager 116 may be less than existing systems with comparable performance, which may reduce the cost of the sequencing system 100.

[0067] The image quality of flow cell images can control base calling accuracy. The imager 116 disclosed herein can increase the accuracy of base calling Alternatively, processing performed on images taken by imager 116 can result in a better image quality.

[0068] After base calling is performed, a processor (e.g., dedicated processors 118, FPGA(s) 120, computer system 126, or a combination thereof) may optionally perform additional processing and / or analysis of base calling results. In some embodiments, after base calling is performed, the sequencing read(s) (processed and / or raw) can be output from the system to an external device (e.g,, the cloud 130 and / or to a computer system 126). The sequencing read(s) herein can include a forward read (Rl), a reverse read(R2), or both. The sequencing reads herein can be any orderly sequence of bases of A, T, C, and G.

[0069] In some embodiments, the sequencing read(s) can be communicated (e g., directly or indirectly) to computer system 126 for subsequent analysis such as adaptor trimming, or phasing, for example.

[0070] Such sequencing analysis methods, including primary analysis, or secondary analysis, or combinations thereof, can be advantageously performed in parallel in the computer system 126, without interference with or delay of existing sequencing workflow of the system 100. Results of sequencing analysis can be made available for generating sequencing results for users. Some or all operations of the sequencing process can be advantageously performed by the FPGA(s) and data can be communicated between the CPU(s) and FPGA(s) to reduce the total operational time from methods operating without the FPGA(s).

[0071] The operations or actions disclosed herein may be performed by the dedicated processors 118, the FPGA(s) 120, the computer system 126, or a combination thereof. One or more operations or actions in methods disclosed herein may be performed by the dedicated processors 118, the FPGA(s) 120, the computer system 126, or a combination thereof. In some embodiments, whichAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)operations or actions are to be performed by the dedicated processors 118, the FPGA(s) 120, the computer system 126, or their combinations can be determined based on one or more of: a computation time for the specific operation(s), the complexity of computation in the specific operation(s), the need for data transmission between the hardware devices, or combinations thereof.

[0072] The computer system 126 can include one or more general purpose computers that provide interfaces to run a variety of programs in an operating system, such as Windows™ or Linux™. Such an operating system may provide great flexibility to a user.

[0073] In some embodiments, the dedicated processors 118 may be custom processors with specific hardware or instructions for performing method steps (e.g., rather than general purpose computers). Dedicated processors 118 can directly run specific software without an operating system. The lack of an operating system reduces overhead, at the cost of the flexibility in what the dedicated processors 118 may perform. A dedicated processor may make use of a custom programming language, which may be designed to operate more efficiently than the software run on general -purpose computers. This may increase the speed at which the steps are performed and allow for real time processing.

[0074] In some embodiments, the FPGA(s) 120 may be configured to perform operations of the sequencing analysis methods described herein. An FPGA is programmed as hardware that may perform a specific task. A special programming language may be used to transform software steps into hardware componentry. Once an FPGA is programmed, the hardware directly processes digital data that is provided to it without running software. The FPGA instead uses logic gates and registers to process the digital data. Because there is no overhead required for an operating system, an FPGA may process data faster than a general-purpose computer. Similar to dedicated processors 118, this is at the cost of flexibility.

[0075] The lack of software overhead may also allow an FPGA to operate faster than a dedicated processor 118, although this can depend on the exact processing to be performed and the specific FPGA 120 and dedicated processor 118.

[0076] A group of FPGA(s) 120 may be configured to perform processing steps in parallel. For example, a number of FPGA(s) 120 may be configured to perform a processing step for an image, a set of images, a sub-tile, or a select region in one or more images. In some embodiments, eachAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)FPGA 120 may perform a respective step or sub-step of the processing steps at the same time, reducing the time needed to process data. This may allow the processing steps to be completed in real time or near real-time. Further discussion of the use of FPGAs is provided below.

[0077] Performing the processing steps in real time may allow the system 100 to use less memory, as the data may be processed as it is received rather than stored for subsequent analysis. This provides advantages over conventional systems, which may store the data before the data is processed, which may require more memory and / or accessing and communication with a computer system located in the cloud 130.

[0078] In some embodiments, the data storage device 122 is used to store information used in or obtained from sequencing analysis. For example, the DNA sequences determined after adaptor trimming may be stored in the data storage device 122, Compressed, or uncompressed, or combinations thereof, sequencing data may be stored in the data storage device 122. The FASTQ file may also be stored in the data storage device 122.

[0079] The user interface 124 may be used by a user to operate the sequencing system or access data stored in the data storage device 122 or the computer system 126.

[0080] The computer system 126 may control the general operation of the sequencing system and may be coupled to the user interface 124. In some embodiments, the computer system 126 may perform one or more steps in sequencing analysis, such as base calling, adaptor trimming, demultiplexing, phasing etc.. The computer system 126 may include a memory configured to store information regarding the operation of the sequencing system 100, such as, for example, configuration information, instructions for operating the sequencing system 100, or user information. The computer system 126 may be configured to pass information between the sequencing system 100 and the cloud 130. For example, the computer system 126 may be configured to receive base calling results from the dedicated processors 118 and / or FPGA(s) and send the base calling results to the cloud 130 for storage and / or further analysis.

[0081] As discussed above, the sequencing system 100 may have dedicated processors 118, FPGA(s) 120, or the computer system 126. The sequencing system 100 may use one, two, or all of these elements to accomplish the processing described above. In some embodiments, when these elements are present together, the processing tasks are split between them. For example, the FPGA(s) 120 may be used to perform some portion or all of sequencing analysis operations, whileAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)the computer system 126 may perform other processing functions for the sequencing system 100. The distribution of processing across the dedicated processor(s) 118, the FPGA(s) 120, and / or general-purpose processors (e.g., in the computer system 126) can enable parallel processing and / or increase efficiency of processing steps. For example, complex processing steps may be allocated to the dedicated processor(s) 118 and / or FPGA(s) 120 while processing for general operation of the system 100 is carried out by the computer system 126.

[0082] Various combinations of these elements may allow various system embodiments that balance efficiency and speed of processing with cost of processing elements.

[0083] The cloud 130 may be a network, server, remote storage, or some other remote computing system separate from the sequencing system 100. The connection to cloud 130 may allow access to data stored externally to the sequencing system 100 or allow for updating of software in the sequencing system 100.Flow cell devices

[0084] Disclosed herein, in some embodiments, are flow cell devices, systems, and methods associated therewith, that can be employed for performing or facilitating DNA sequencing analysis. Flow cell devices herein can be used to immobilize template nucleic acid molecules derived from biological samples and introduce a repetitive flow of sequencing reagents (e.g., sequencing-by-binding, sequencing-by-synthesis, or sequencmg-by-avidity, or combinations thereof) to attach labeled nucleotides or labeled multivalent molecules to specific positions in the template sequences. A series of labeled signals are detected and decoded to reveal the nucleotide sequences of the template molecules, e.g., immobilized, or amplified, or combinations thereof, nucleic acid template molecules attached to a surface of the flow cell.

[0085] In some embodiments, flow cell devices, e.g., 200, 300, disclosed herein can comprise one or more substrates, one or more channels, one or more inlets, and one or more outlets. The inlet(s), channel(s), and outlet(s) are formed in the one or more substrates and are in fluidic communication. FIGS. 2A - 3D show exemplary embodiments of flow cell devices 200, 300. In some embodiments, a flow cell system 1000 herein may include a flow cell device 200, 300 and a fluidic dispensing device 280 configured to administer fluids and / or air to channels of the flow cellAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)devices, e.g., during sequencing analysis of one or more samples.

[0086] In some embodiments, a flow cell device includes: one or more channels defined by one or more substrates, where the one or more channels are configured to allow fluids to flow therethrough; an inlet formed in the one or more substrates, the inlet in fluidic connection with the one or more channels, where the inlet includes a landing area with a diameter of less than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, or 15 mms within an x-y plane, where the inlet is coupled with a dispensing guide that extends along an axis orthogonal to the x-y plane beyond the one or more substrates; an outlet in the one or more substrates and in fluidic connection with the one or more channels; and a cleaning outlet in the one or more substrates and in fluidic connection with the inlet; and a fluidic dispensing device configured to dispense the fluids via the inlet to the one or more channels.

[0087] FIGS. 2A-2E show an embodiment of the flow cell device 200 with the dispensing guide 4210. FIG. 2A shows a top view of the flow cell device 200 with two channels. FIG. 2B is a perspective view of the flow cell device with a cross-section of one of the channels, FIG. 2C shows the close-up of the cross-section in FIG. 2B. FIG.2D shows a close-up view of the area in the dotted line in FIG.2C. FIG.2E shows a close-up cross-sectional view of the dispensing guide open landing area in correspondence with a fluidic channel in FIG. 2B, In this particular embodiment, a cleaning outlet 270 extends from a bottom surface 222 of a top substrate 220 of the flow cell device to a bottom surface 231 of a bottom substrate 230 of the flow cell device 200 (FIGS. 2C).

[0088] FIGS. 2F-2J show another embodiment of the flow cell device 200 with the dispensing guide 4210. The flow cell device 200 in FIGS. 2F-2J is similar to the flow cell device 200 in FIGS. 2A-2E except the location of the cleaning outlet 270 and / or the fluidic pathway 271 leading from the landing area 241 to the cleaning outlet 270. FIG. 2F shows a top view of the flow cell device 200 with two channels. FIG. 2I is a perspective view of the flow cell device with transparency to show the open landing area 241, the cleaning outlet 270, and the fluidic pathway connecting them in between.

[0089] FIG. 2G shows the close-up of the cross-section in FIG. 2F. FIG.2H shows a close-up view of the area in the dotted line in FIG. 2G. In this particular embodiment, the possible air bubbles at the landing area may rise up toward the top surface of the top substrate and the cleaning outlet may be configured to facilitate removal of the possible air bubbles when the fluidic pathwayAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)connecting the cleaning outlet is in between the top surface of the top substrate and the dispensing guide 4210.|0090] In some embodiments, the location of the cleaning outlet and its relative location with respect to the landing area may advantageously allow efficient cleaning of the residuals on the landing area via the cleaning outlet. In some embodiments, the distance between a center of the landing area and the center of the cleaning outlet within the same x-y plane is at most 1 mm, 2 mm, 3 mm, 4 mm, 5 mm, 6 mm, 7 mm, 8 mm, 9 mm, 10 mm, 12 mm, 15 mm, 18 mm, 20 mm, 22 mm, 25 mm, or 30 mm. The distance between the landing area and the cleaning outlet is to facilitate short and efficient fluidic transfer between the landing area and the cleaning outlet.

[0091] In some embodiments, the distance between the landing area and the cleaning outlet is configured to reduce the bubbles that may occur in the cleaning outlet from traveling to the open landing area.

[0092] In some embodiments, the one or more substrates include a top substrate, e.g., 220, and a bottom substrate e.g., 230, In some embodiments, the one or more substrates may comprise a middle substrate (not shown). The one or more substate may be fixedly attached to each other, via the middle substrate or an interface, for example, the middle substrate or interface may include pressure sensitive adhesive (PSA), gasket, overmolding, or UV adhesive,

[0093] In some embodiments, the flow cell device may include a coating that may facilitate administration of fluids via the inlet into the one or more channels, e.g., a hydrophobic coating. The coating may reduce residuals that may be left at or near the inlet that may require washing or otherwise may contaminate the subsequent administration of different reagent(s). The top substrate may comprise a top surface 221. In some embodiments, the top surface 221 of the top substrate 220 may be least partly coated with a coating 249, e.g., in the area around the inlet. The coating 249 may be optional. In some embodiments, the top substrate 220 includes a bottom surface 222 that lacks any coating, e.g., hydrophobic coating. In some embodiments, the bottom substrate 230 lacks any coating.

[0094] In some embodiments, the inlet includes a landing area 241 at a top surface of a bottom substrate 230 of the one or more substrates where the landing area is at least partly coated with the coating. In some embodiments, the inlet includes a landing area at a top surface of a bottom substrate of the one or more substrates, and the landing area lacks the coating.Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)|0095] In some embodiments, the inlet 240 may be a void or cavity formed in the one or more substrates and in fluidic communication with the channel(s) 250. The inlet may have various 3D geometrical shapes such as, e.g., a cylinder shape. In some embodiments, the inlet includes a wall 242 defining a height thereof and a landing area 241 at the bottom substrate 230 defining a diameter thereof. In some embodiments, the landing area 241 is at the bottom of the inlet. In some embodiments, the wall 242 of the inlet is at least partly coating with the coating, e.g., hydrophobic coating. Coating on the wall may facilitate fluid administered by the dispensing tips to not adhere or stay on or near the wall but to go to the landing area and into the one or more channels. In some embodiments, the wall 242 lacks any hydrophobic coating. In some embodiments, the height of the inlet is at least 0,1, 0,2, 0.3, 0.4, 0,5, 0.6, 0.8, 0.9, 1, 1.2, 1,5, or 2 mm. The landing area may be of a circular shape, e.g., 241 in FIG. 2D, In some embodiments, the inlet includes a landing area with a diameter of less than 0.5, 1, 2, 3, 4, 5, 6, 8, or 10 mms within an x-y plane. In some embodiments, it is advantageous to keep the landing area small, e.g., with a diameter of less than 2, 3, or 4 mms to reduce residual build-up at the inlet, therefore reducing dead volumes of the reagents during sequencing. However, reducing the size of the landing area may require, in some embodiments, increased precision in administering fluids onto the landing area. Further, reducing the size of the landing area may require the inlet to have a thickness at least enough to allow a delivery volume that is no smaller than a volume of the one or more channels. However, the height of the top substrate (i.e., thickness of the inlet) may be limited for transmitting and receiving optical signals of the samples immobilized on the one or more substrate. As such, the thickness of the inlet (e.g., 0.6 mm) with the small landing area (e.g., diameter of 1 mm ) may not be sufficient to accommodate a volume that is greater than the volume of a channel of the flow cell device (e.g., 70 ul).

[0096] In some embodiments, the flow cell device advantageously includes a dispensing guide 4210 that may be configured to guide reagent dispensing from the dispensing tips to the landing area. The dispensing guide may be removably or permanently coupled to a top surface of the top substrate of the flow cell device. For example, the dispensing guide may be permanently attached to the flow cell device using pressure sensitive adhesive or UV adhesive, so it is unremovable part of the flow cell device. The dispensing guide may be sealed coupled to the flow cell device to avoid reagent leakage. The dispensing guide may be sealed coupled to a top surface of the top substrate of the flow cell d evice. The dispensing guide may be made of various geometrical shapes.Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)|0097] In some embodiments, the dispensing guide may work with the inlet with a small landing area (e.g., with a diameter of 1 mm) with a limited height (e.g., 0.5 mm).

[0098] As shown in FIG. 2A, each channel 250 may be coupled with a dispensing guide 4210. The dispensing guide of the first channel (top channel) is made transparent to show the cleaning outlet 270 in fluidic communication with the inlet.

[0099] In some embodiments, the dispensing guide includes a tip portion 4012 and a base portion 4011, where the tip portion 4212 includes a tip diameter that is 2x, 4x, 6x, 8x, 10x, 12, 15x, 20x, or smaller than a base diameter of the base portion 4011 (e.g., the diameter at the widest at the base portion). In some embodiments, the tip diameter and base diameter are inner diameters of the cavity of the dispensing guide. In some embodiments, the tip diameter is smaller than the diameter of landing area for sealingly coupling to the inlet, e.g., as shown in FIG, 2E. In some embodiments, the tip diameter is less than 1, 2, 3, 4, 5, 6, 8, 10, or 12 mms. In some embodiments, the base portion 4011 of the dispensing guide includes a funnel shape. In some embodiments, the base portion 4011 of the dispensing guide includes a cylindrical shape with a funnel-shaped inner surface, e.g., shown in FIGS.2A-2C. The funnel may have various angles with the x-y plane, e.g., angle a in FIG, 2C. In some embodiments, the angle may be in the range from 20 degrees to 80 degrees. In some embodiments, the angle may be in the range from 30 degrees to 70 degrees. In some embodiments, the angle may be in the range from 35 degrees to 65 degrees. In some embodiments, the tip portion 4012 of the dispensing guide includes a cylindrical shape. In some embodiments, the dispensing guide includes a gasket that facilitates sealingly coupling to the one or more substrate. In some embodiments, the dispensing guide is permanently fixed at least to a top substrate of the one or more substrates. In some embodiments, the dispensing guide is configured to guide open dispensing of the fluids from a dispensing tip of a fluidic dispensing device 280 into the inlet of the flow cell device. In some embodiments, the dispensing guide is configured to guide open dispensing of the fluids from a dispensing tip of the fluidic dispensing device 280 at various heights or various positions within the x-y plane into the inlet of the flow cell device, e.g., FIG. 2E.

[0100] In some embodiments, the dispensing guide is at least partly coated with the coating, e.g., hydrophobic coating. In some embodiments, the tip portion 4012 of the dispensing guide is at least partly coated with the coating. In some embodiments, the tip portion 4012 of the dispensingAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)guide is completely coated with the coating on the inner surface surrounding the cavity at the tip portion. In some embodiments, the base portion 4011 of the dispensing guide is at least partly coated with the coating, e.g., on the inner surface surrounding the cavity at the base portion.

[0101] In some embodiments, the dispensing guide herein, e.g., 4210 or 4310, may comprise glass, plastic, or other materials.

[0102] In some embodiments, the tip portion of the dispensing guide includes a height along an axis orthogonal to the x-y plane, e.g., z axis, and the height is greater or equal to the height of the inlet. In some embodiments, the height of the tip portion is at least 0.5 mm, 0.8 mm, 0.9 mm, 1 mm, 1.2 mm, 1.4 mm, 1.6 mm, 2 mm, or more. In some embodiments, the base portion of the dispensing guide includes a height along the z axis, and the height is at least 2, 3, 4, 5, 6, 7, 8, 9, 10 mm or more,

[0103] In some embodiments, the dispensing guide includes a cavity, e.g., 4013 in FIG. 2E, configured to contain a first volume of liquids therewithin, where the first volume is 10%, 20%, 30%, 40%, 50%, or 60% more than a second volume of a channel of the one or more channels. For example, if one channel of the flow cell device has a volume of 50 ul, the cavity of the dispensing guide may be 30% more of that volume, and the volume may be 65 ul. In some embodiments, the first volume is in a range from 20 ul to 500 ul. In some embodiments, the first volume is in a range from 50 ul to 300 ul. In some embodiments, the first volume is in a range from 80 ul to 200 ul. In some embodiments, the first volume is in a range from 100 ul to 160 ul.

[0104] In some embodiments, the flow cell device may be configured to receive reagents dispensed from the dispensing tips without any dispensing guide disclosed herein. In such embodiments, the landing area of the flow cell device, e.g., 241, may be openly exposed in the area, and the dispensing tip may dispense reagents from above the open landing area. In some embodiments, the dispensing tip may dispense reagents after contacting at least part of the landing area. For example, the dispensing tip may be flexible and may deform slightly after contacting the open landing area before any dispensing of reagents occurs.

[0105] Air bubbles introduced during and / or after dispensing the reagents to the open landing area, and such air bubbles at the landing area may travel into the channels sometimes cause sequencing errors. For example, air bubble may generate inaccurate image intensity and / or may cause unreliable sequencing reactions of sample(s). The air bubble may be caused by variousAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)reasons including a pressure difference across different channels and / or different landing pads. Such pressure differences may be caused by, for example, fluidic connection(s) across different landing pads.

[0106] Accordingly, m some embodiments, such pressure differences (which may cause generation of air bubbles) may be reduced or eliminated by connecting each cleaning outlet independently to the shared waste fluidic pathway while blocking connections from other cleaning outlet(s). In some embodiments, each cleaning outlet may be connected to a multiple-way valve, e.g., a rotary shear valve, and the valve opens fluidic connection from the waste fluidic pathway to one or more cleaning outlet(s) while keeping fluidic connection to other cleaning outlet(s) closed. In some embodiments, the valve may have a short common line to minimize possible waste of reagents.

[0107] In some embodiments, the flow cell device may have a “mega” channel having a volume that is equivalent to a combination of multiple channels, e.g., 2 channels. Such a “mega” channel may have a single open landing area as a channel that was combined. In some embodiments, the “mega” channel may have multiple open landing area(s). In some embodiments, dispensing to the “mega” channel may occur at different times at different landing areas. In some embodiments, reagents may flow simultaneously from the landing area toward the “mega” channel. In some embodiments, air bubbles in the “mega” channel may be reduced or eliminated using the multiple- way valves as the channels disclosed herein. Embodiments of preparing samples of “mega” channels are disclosed in detail in provisional application Nos. 63 / 706,241 and 63 / 707,675 and are incorporated herein by reference in their entireties.

[0108] In some embodiments, the dispensing tip is configured to dispense a predetermined volume of reagent(s) to the landing area, e.g., 241, either with or without the dispensing guide. In some embodiments, the predetermined volume of reagent(s) is greater than a bubble free volume which flows into the corresponding channel of the landing area. The bubble free volume is greater than or equal to a minimal volume needed for the sequencing reaction(s). The bubble free volume can vary based on factors including but not limited to: channel size, channel volume, sample density, sequencing chemistry, temperature, reagent flow rate, and reagent concentration. For example, the bubble free volume may be 80 ul, which is 20%, 30%, or 40% greater than the minimal reagent volume needed for a first sequencing reaction in a first channel. TheAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)predetermined volume of reagent is greater than the minimal reagent volume, e.g., ¼ greater. The air bubbles may have a tendency to stay at or near a top portion of the reagent volume at the landing area, thus, after the bubble free volume exit the open landing area from the bottom of the reagent volume and flow into the channel, the top portion of the reagent volume and the bubbles may still stay at the open landing area.

[0109] In some embodiments, the bubble free volume may be in a range from 10 ul to 800 ul. In some embodiments, the bubble free volume may be in a range from 20 ul to 500 ul. In some embodiments, the bubble free volume may be in a range from 30 ul to 400 ul. In some embodiments, the bubble free volume may be in a range from 30 ul to 200 ul. In some embodiments, the bubble free volume may be in a range from 40 ul to 200 ul. In some embodiments, the bubble free volume may be in a range from 50 ul to 120 ul.

[0110] In some embodiments, the bubble free volume may be in a range from 10 ul to 800 ul. In some embodiments, the bubble free volume may be in a range from 20 ul to 500 ul. In some embodiments, the bubble free volume may be in a range from 30 ul to 400 ul. In some embodiments, the bubble free volume may be in a range from 30 ul to 200 ul. In some embodiments, the bubble free volume may be in a range from 40 ul to 200 ul. In some embodiments, the bubble free volume may be in a range from 50 ul to 120 ul.

[0111] In some embodiments, the predetermined volume of reagent(s) may be 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% greater than the corresponding bubble free volume.

[0112] In some embodiments, a dead volume or residual (e.g., a residual left in the inlet and / or other parts of the flow cell system but did not reach the one or more channels after a complete dispense) is no more than 0.5%, 1%, 1.5%, 2%, 3%, 4%, 5%, 6%, or 8% of the volume of a channel, e.g., the second volume. FIG. 2E shows residual may remain at the corners where the inlet wall and the landing area meets. Such residual may cause waste of reagent as it does not go into the one or more channels additional actuation after dispensing. Such residual may also cause contamination if it stays in the inlet and mix with a different reagent that is administered. Thus, minimizing the residual or dead volume is advantageous to reduce reagent consumption and avoid cross contamination and consequent sequencing errors. For example, when a channel has a volume of 70 ul, the residual volume can be reduced to 2 to 3 ul using the flow cell system disclosed herein.

[0113] In some embodiments, the flow cell system herein reduces reagents consumption byAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)2%, 5%, 8%, 10%, 15%, 18%, 20% or more for identical sequencing applications using existing flow cell systems. In some embodiments, the flow cell system herein reduces dead volume or residual volume by 2x, 4x, 5x, 6x, 8x, 9x, 10x or more for identical sequencing applications using existing flow cell systems.

[0114] In some embodiments, a dispensing volume to each individual channel is 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50% or more than the volume of the individual channel. For example, for a channel volume of 80 ul, the dispensing volume of 20% more is 96 ul using the flow cell system herein. The dispensing volume of the flow cell system herein for a single dispense is 2%, 5%, 8%, 10%, 15%, 20%, or less than the dispensing volume required by an existing flow cell system in a single dispense. For example, for an existing flow cell system, a single dispense of a first reagent of 100 ul is needed for an individual channel of 60 ul to remove bubbles and / or account for dead volumes in the fluidic pathways. Using the flow cell system herein, a single dispense of the first reagent of 70 ul is needed for the same channel of 60 ul m the same sequencing application to avoid undesired bubbles in the channel(s) and / or to account for dead volume or residuals in the fluidic pathways leading to the flow cell device, thus the dispensing volume of 70 ul is 30% less than 100 ul required in existing flow cell systems.

[0115] In some embodiments, the fluidic dispensing device may be actuated to dispense the fluids, e.g., reagent, buffer, a bolus (e.g., of air) etc. through the one or more dispensing tips. The fluidic dispensing device may apply positive pressure on the fluids for dispensing them to the flow cell device. In some embodiments, additional pressure, e.g., negative pressure, may be applied via the outlet to facilitate fluid communication to the flow cell device, e.g., to facilitate fast and homogenous delivery of reagents to the samples within the one or more channels. In some embodiments, the flow cell systems herein may only require the positive pressure on the fluids for dispensing fluids to the inlet, to the one or more channels, and to the outlet of the flow cell device. In some embodiments, the flow cell systems herein remove the need to apply any negative pressure via the inlet, outlet, and / or the cleaning outlet on the fluids for flowing the fluids in or out from the flow cell device.

[0116] In some embodiments, the flow cell systems utilizing only positive pressure includes a simpler yet still efficient dispensing scheme with flow cell devices with an open landing area. Such flow cell systems advantageously simplifies the design of fluidic pathways leading in and out ofAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)the flow cell device, reduces number of valves requires, reduces length of tubes required, and also reduces the number of actuation mechanisms required, e.g., no vacuum needed via the inlet during dispensing.

[0117] In some embodiments, the positive pressure is in a range from 1 kilopascal (kPa) to 800 kPa. In some embodiments, the positive pressure is in a range from 1 kPa to 500 kPa. In some embodiments, the positive pressure is in a range from 1 kPa to 300 kPa. In some embodiments, the positive pressure is in a range from 1 kPa to 200 kPa. In some embodiments, the positive pressure is in a range from 1 kPa to 120 kPa.

[0118] In some embodiments, the negative pressure is in a range from -1 kPa to -800 kPa. In some embodiments, the negative pressure is in a range from -1 kPa to -500 kPa. In some embodiments, the negative pressure is in a range from -1 kPa to -300 kPa. In some embodiments, the negative pressure is in a range from -1 kPa to -200 kPa. In some embodiments, the negative pressure is m a range from -1 kPa to -120 kPa.

[0119] In some embodiments, additional pressure, e.g., negative pressure, may be applied via the outlet and / or the cleaning outlet, e.g., 270, for cleaning fluids from the one or more channels and from the inlet.

[0120] In some embodiments, the flow cell system includes: a flow cell device comprising: one or more channels defined by one or more substrates, where the one or more channels are configured to allow fluids to flow therethrough and to allow a bolus of gas to flow therethrough between one or more of the fluids; an inlet formed in the one or more substrates, the inlet in fluidic connection with the one or more channels; a dispensing guide positioned above the inlet; and an outlet in the one or more substrates and in fluidic connection with the one or more channels; and a fluidic dispensing device comprising one or more dispensing tips, where each of the one or more dispensing tips is configured to dispense the fluids and the bolus of gas to inlet by first coupling to the dispensing guide. FIGS. 3A-3D show embodiments of the flow cell device 300 and the one or more dispensing tips 380 of the fluid dispensing device herein.

[0121] In some embodiments, the one or more substrates, one or more channels, the inlet, and outlet of the flow cell device 300 comprise similar features as their corresponding counterparts of the flow cell device 200 disclosed above and are not repeated below.Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)

[0122] In some embodiments, each of the one or more dispensing tips 380 is configured to dispense the fluids via a positive pressure (e.g., pushing the fluids into the flow cell device and / or out of the flow cell device) applied on the fluids. In some embodiments, each of the one or more dispensing tips is configured to dispense the fluids without using any negative pressure on the fluids (e.g., suction or vacuum of the fluids via the outlet). Comparing with existing flow cell systems, usage of only the positive pressure removes the need of using a vacuum or pump for exerting negative pressure(s), thus simplifies the flow cell system and advantageously reduces the cost, size, and complexity of the system, and make the flow cell system more reliable and less prone to malfunctions.

[0123] In some embodiments, one or more pumps or other actuation mechanisms may be used to apply positive pressure on the fluids and to drive fluidic flow through the one or more dispensing tips.

[0124] In some embodiments, the dispensing guide 4310 is configured to facilitate coupling of the dispensing tip(s) to the inlet 340 of flow cell device 300 for accurate and safe dispensing of the fluids. In some embodiments, the dispensing guide 4310 includes a guide body 4314 defining a guide hole 4311. The guide body may be flexible or deformable to allow coupling to the dispensing tip(s) going through the guide hole 4311. The guide body in some embodiments may be rigid and not deformable. The guide hole may be a through hole extending at least along the z axis. In some embodiments, the dispensing guide 4310 includes a guide hole 4311 with a position fixed relative to the inlet, e.g., FIGS. 3A-3B The guide body 4314 of the dispensing guide may have various height along the z axis. FIGS. 3A and 3B show guide bodies 4314 with different heights. The guide body may or may not be coupled with the gasket 4313, e.g., FIGS. 3A-3B.

[0125] In some embodiments, the dispensing guide 4310 is fixedly attached to the flow cell device, e.g., adhered to the top substrate 320 of the flow cell device. In some embodiments, the dispensing guide 4310 includes a gasket 4313 that is attached to the flow cell device, e.g., the top substrate of the flow cell device. In some embodiments, the gasket is fixedly and sealingly attached to the one or more substrates. In some embodiments, the attachment of the gasket may prevent fluid leakage when the dispensing tip is at least partly inserted in the gasket or in the inlet for fluid dispensing. In some embodiments, the gasket may have various shapes to facilitate insertion of the dispensing tips through its cavity. For example, the gasket may have a funnel shape (not shown)Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)to guide insertion of the dispensing tip at its top portion. In some embodiments, the gasket includes a cavity 4315 therewithin where the gasket is configured to allow a dispensing tip to insert at least partly through the cavity. In some embodiments, the cavity 4315 includes an elongated shape along z axis and the gasket is configured to allow a dispensing tip to insert completely through the cavity to be in contact with the inlet. In other words, the dispensing guide 4310 may allow removable and leakage proof coupling to different dispensing tips, e.g., dispensing tips with different sizes or shapes, to ensure accurate and safe dispensing of fluids to the inlet of the flow cell devices. As an example, the dispensing guide may allow a removable and leakage proof coupling to a first dispensing tip so that it is at a first distance above the top substrate for accurate and safe dispensing, and after removing the first dispensing tip, the dispensing guide may allow a second removable and leakage proof coupling to a second dispensing tip so that it is at a second distance above the top substrate for accurate and safe dispensing to the same inlet,

[0126] In some embodiments, the guide hole may be of various geometrical shapes to guide the dispensing tips, although it is shown as a cylindrical shape in FIGS, 3A-3B. In some embodiments, the dispensing guide advantageously remove the need to have a large inlet (e.g., diameter of greater than 3mm, 4mm, 5mm, or more). In existing flow cell devices, such a large inlet with a large landing area may be required in order to hold a fluidic volume that is comparable to the volume of a channel of the flow cell device. In some embodiments, the inlet 340 may have a diameter in the x-y plane that is no greater than 0.5 mm, 1 mm, 1.5 mm, 2 mm, 2.5 mm, 3 mm, 3.5 mm, 4 mm, 5 mm, or 6 mm. In some embodiments, the cavity of the gasket may have a diameter that is identical to the diameter of the inlet in the x-y plane. In some embodiments, the inlet 340 may have a diameter in the x-y plane that is greater than the diameter of the dispensing tip to allow the dispensing tip to insert at least partly into the inlet. In some embodiments, the inlet 340 may have a diameter in the x-y plane that is greater than the diameter of the dispensing tip to allow the dispensing tip to insert and at least partly in contact with a landing area 341 of the inlet at the bottom substrate of the flow cell device (not shown).

[0127] In some embodiments, the dispensing guide 4310 is configured to be removably and fixedly couple to a dispensing tip 380 inserting through the guide hole 4311. After a dispense is completed, the dispensing guide 4310 is configured to allow decoupling of the dispensing tip from the flow cell device and the dispensing guide, at least via a force or pressure that pulls the dispensing tip upward and away from the dispensing guide.Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)

[0128] In some embodiments, a projection of the guide hole to an x-y plane overlaps at least partly with the projection of the inlet to the x-y plane to ensure that dispensing tip going through the guide hole may accurately contact the inlet for fluid dispensing.

[0129] In some embodiments, the flow cell device is configured to allow formation of a leakage proof coupling of a dispensing tip with the inlet, and where the leakage proof coupling is reversible. In some embodiments, the flow cell device is configured to allow formation of a coupling of a dispensing tip with the inlet, where a leakage of less than 0.001 ul, 0.01 ul, 0.1 ul, or 1 ul occurs at the coupling when the dispensing tip dispenses a volume of more than 50, 60, 70, 80, or 100 ul. In some embodiments, the flow cell device is configured to allow formation of a coupling of a dispensing tip with the inlet, where a leakage of less than 0.01%, 0.05%, 0.1%, 0.5%, 1%, 2%, 3%, or 5% of the dispensing volume. In some embodiments, a dispensing volume for a single dispense is in a range from 1 ul to 500 ul. In some embodiments, a dispensing volume for a single dispense is m a range from 10 ul to 200 ul. In some embodiments, a dispensing volume for a single dispense is in a range from 10 ul to 100 ul.

[0130] In some embodiments, the inlet includes a wall 342 defining a height thereof and a landing area 341 defining a diameter thereof. In some embodiments, the wall of the inlet is at least partly coated with the coating, e.g., a hydrophobic coating. In some embodiments, the wall 242 lacks any hydrophobic coating. In some embodiments, the inlet includes a landing area at a top surface of a bottom substrate 330 of the one or more substrates where the landing area is at least partly coated with the coating to facilitate fluid communication into the channels.

[0131] In some embodiments, the surfaces of the one or more substrates may be at least partly coated with the coating, e.g., the top surface of the top substrate or the top surface of the bottom substrate (349 in FIG. 3B). In some embodiments, the surfaces of the one or more substrates may lack any coating, e.g., hydrophobic coating.

[0132] In some embodiments, the wall of the inlet is at least partly coated with the coating, e.g., a hydrophobic coating, and the landing area lacks the coating to reduces residuals build-up at the landing area or other areas of the inlet.

[0133] In some embodiments, the flow cell device 300 lacks a cleaning outlet m fluidic connection with the inlet. In some embodiments, the flow cell systems with a flow cell device 300 lack an actuator that applies negative pressure to the fluids through the outlet 360 of the flow cellAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)device 300. In some embodiments, the flow cell systems with a flow cell device 300 lack an actuator that applies negative pressure to the fluids through the cleaning outlet in fluidic communication with the inlet (not shown) of the flow cell device 300.

[0134] In some embodiments, the flow cell system includes a dispensing manifold 381 (which can be moved along arrow 383) and dispensing guide 4310 to facilitate dispensing of the fluids to the flow cell device 300, e.g., FIG. 3C. The dispensing guide 4310 may comprise a gasket 4313 (to facilitate sealing) similar to that disclosed in relation to FIGS. 3A-3B In some embodiments, the manifold may be coupled with the dispensing guide sealingly and reversibly for dispensing of the fluids. The manifold may form a face seal with the gasket of the dispensing guide, for example, via a pressure or force applied on the manifold toward the gasket. In some embodiments, the dispensing manifold may be configured to hold the one or more dispensing tips in fixed position relative to each other. The dispensing manifold may be actuated by an actuator to move in 3D to position the dispensing tip relative to the inlet of the flow cell device. In some embodiments, the pressure or force on the manifold to form a seal with the gasket may be applied in response to determining that the dispensing tip is aligned with the inlet of the flow cell device in the x-y plane. The seal may prevent or minimize leakage of fluids from the seal during dispensing of the fluids to the inlet via the positive pressure. The seal is removed once the pressure or force on the manifold is removed, thereby allowing retrieval of the dispensing tip after a dispense of the fluid(s) is completed.

[0135] In some embodiments, the flow cell system herein may further include a waste container 391 or waste collection well. Waste or otherwise fluids exiting from the outlet 260, 360 of the flow cell device 200, 300 may be collected into the waste container. Such fluids exiting from the outlet 260, 360 of the flow cell device 200, 300 may be actuated by a positive pressure applied via a / the dispensing tip 392. Waste or otherwise fluids exiting from the outlet 260, 360 of the flow cell device 200, 300 may not need to be actuated by any negative pressure, e.g., vacuuming pressure applied via an outlet 393, but only utilize the positive pressure for driving the fluids to exit the outlet(s). In some embodiments, the flow cell system herein may include an actuator for collecting waste or fluids in the waste container. The actuator may include but is not limited to a vacuum or a pump. In some embodiments, different tubing may be used to facilitate collection of the waste with only application of the positive pressure. For example, tubing below the height of the inlet may be used to facilitate waste flowing out from the inlet and into the waste container,Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)e.g., FIG. 3D. This may also be referred to as a trap 394.

[0136] In some embodiments, the flow cell device, e.g., 200, 300, is configured to hold one or more samples immobilized thereon for sequencing. In some embodiments, the one or more samples include in situ cells or tissue.

[0137] Although only two channels are shown m the flow cell devices, e.g., 200, 300, disclosed herein, various number of channels can be implemented in the flow cell device as the structure elements of the flow cell device and the fluidic dispensing device are scalable. As an example, each channel may have its own corresponding inlet and outlet, and optionally a corresponding cleaning outlet. Each channel may correspond to its dispensing guide attached on the flow cell device. One or more dispensing tips may dispense, via the dispensing guide, into each individual channel of the flow cell device.

[0138] In some embodiments, the alignment and movement of the one or more dispensing tips, the dispensing manifold, and / or the flow cell device can be automatically controlled by the computer system 126 without any manual adjustment by the user.Sequencing systems for hybrid fluidic communication

[0139] In some embodiments, the sequencing systems may be configured to allow hybrid fluidic communication from reagent reservoirs, buffers, and / or other chemical solutions to the flow cell device thereby advantageously improving sequencing throughput, reduce dead volumes thus saving reagent costs, reduce cross contamination by reagents, and improved flexibility and compatibility with various sequencing protocols, thereby enabling sequencing of different samples (e.g., multi-omic samples, in situ samples, etc.)

[0140] In some embodiments, disclosed herein is the sequencing system (e.g., system 100 in FIG. 1) comprising: an optical system (e.g., imager 116 in FIG. 1); a flow cell system 1000 disclosed herein (comprising the flow cell device); an imaging station configured to allow positioning of a flow cell device of the flow cell system thereon for imaging using the optical system; one or more fluidic station or a nest bank configured for positioning of the flow cell device thereon for fluidic communication with a fluid storage device, e.g., via closed fluidic communication through a manifold or via open fluidic communication via dispensing tips, and for thermal control of one or more samples immobilized on the flow cell device; and a movable armAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)configured to move the flow cell device and at least a second flow cell device between the imaging station and the fluidic station within a same sequencing cycle of a sequence run. The sequencing system may further comprise a housing configured to enclose the optical system, the flow cell system, the fluid storage device, the imaging station and the fluidic station therewithin. Embodiments of the imaging station, fluidic station / nest bank, the flow cell device, and moveable arm are disclosed in detail in PCT Application No. PCT / US2024 / 0039563 and is incorporated by reference herein in its entirety.

[0141] In some embodiments, the flow cell devices and systems disclosed herein are configured for hybrid fluidic communication which include: closed fluidic communication (e.g., via a closed coupling of the flow cell device and the manifold (e.g., at the inlets), and a close coupling of the manifold or a second manifold or fluidic chip to the fluid storage system (e.g., e.g., at the reagent reservoirs); and also open fluidic communication (e.g., via dispensing tips to the flow cell device). Flow cell devices and systems capable of such hybrid fluidic communication advantageously alleviate problems in existing fluidic communication in sequencing systems including but not limited to: bubbles in microfluidic channels of the flow cell device, dead volumes (e.g., greater than 60 ul, 80 ul, or more), leakage of reagents in open dispensing to the flow cell device, low reagent flow speed or efficiency (e.g., a flow rate of less than 10 ul or 20 ul per second), waste of reagents due to dead volume and reagent contamination, system scalability to use flow cell devices with wider or longer channels, scalability to flow cells with a large number of channels (e.g., 6 lanes, 8 lanes, 12 lanes or more), and kinking in tubing between the flow cell device and the fluid storage device. Flow cell devices and systems utilizes hybrid fluidic communication to advantageously allow different fluids to be delivered to the flow cell device via the closed and / or open fluidic communication at the same or different flow rates, with the same or different volume(s), with the same or different precision of fluidic communication, without leakage, and with small dead volume(s) (e.g., less than 80 ul) to improve sequencing efficiency and throughput and reduce sequencing time and cost. The flow cell devices and systems disclosed herein may be compatible with separated fluidic station and imaging station to further improve system efficiency and throughput and minimize system damages caused by leakage or other fluidic or thermal problems.

[0142] An exemplary flow cell (e.g., sequencing) system 100 disclosed herein is shown in FIG. 8. In this particular embodiment, the sequencing system includes a housing 8005 that remainsAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)static relative to the environment it is positioned in, e.g., relative to a table or benchtop. The housing may enclose structural and functional elements disclosed herein of the sequencing system therewithin. FIG. 8 is a front view of the sequencing system. The sequencing system 100 may comprise one or more fluidic stations (e.g., two fluidic stations 8010 with flow cell devices coupled thereon), one or more imaging stations 8015, one or more imagers 116, and a gantry’ and grabber system 8020 that moves the flow cell device among the fluidic and imaging stations. The one or more flow cell devices (e.g., 200, 300, 4000, 5000, 16000,) that may be positioned on the imaging station during imaging, on the fluidic stations for sequencing reactions. Such movement of the flow cell device may occur within a single sequencing cycle, repeat within the single sequencing cycle or across multiple sequencing cycles in a sequencing run.

[0143] In some embodiments, the sequencing system 100 includes a flow cell system disclosed herein. In some embodiments, the sequencing system 100 includes a flow cell device disclosed herein.

[0144] In some embodiments, the sequencing system 100 includes one or more fluidic stations herein. Each fluidic station may be configured to couple a flow cell device thereon for fluidic communications between the flow cell device and the reagent reservoirs or other sequencing solutions, e.g., buffers.

[0145] In some embodiments, the fluidic station may comprise one or more manifold for fluidic communication to the flow cell device (e.g., manifold, 4500, 5500, 1400, 1500). The manifold may comprise one or more fluidic pathways; and one or more openings.

[0146] The fluidic station may comprise one or more reagent reservoirs. The fluidic station may comprise an actuation mechanism configured to move the flow cell device to a couple of different positions during a sequencing cycle of a sequencing run. In some embodiments, the different positions of the flow cell device may include a closed position, at least along a z direction, where the one or more inlets of the flow cell device and the one or more openings of the manifold are sealingly coupled to each other for fluidic communication from the one or more reagent reservoirs to the flow cell device; and an open position, where the one or more inlets are accessible by a dispensing tip for fluidic communication from the dispensing tip to the flow cell device.

[0147] In some embodiments, the sequencing system 100 may include one or more imaging stations. The imaging station may comprise the imager disclosed herein for imaging the samplesAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)immobilized on the flow cell device. The imaging station may include a sample stage for positioning the flow cell device thereon; and a sample stage actuator that moves the sample stage and the flow cell device at least along the z direction for focusing the flow cell device.

[0148] In some embodiments, the sequencing system 100 may include a grabber and gantry system configured to control movement of the flow cell among the fluidic stations and the imaging station. In some embodiments, the grabber and gantry system 8020 is configured to: grab the flow cell device from one of the fluidic station and the imaging station; sense coupling of the flow cell device to the grabber; move the flow cell device between the fluidic station and the imaging station; and position the flow cell device on the other one of the fluidic station for imaging or for fluidic communication with the one or more reagent reservoirs of the sequencing system, where the grabber and gantry system is configured to move the flow cell device to one of the fluidic station and the imaging station within a single sequencing cycle of a sequencing run and move a second flow cell device to the other one of the fluidic station and the imaging station within the single sequencing cycle.

[0149] In some embodiments, the sequencing system 100 may include one or more fluidic stations. In some embodiments, each fluidic station (e.g., 8010) herein includes an actuation mechanism that is configured to move the flow cell device, relative to the manifold, to a plurality of positions either within a single sequencing cycle of a sequencing run, across multiple sequencing cycles, and / or after a sequencing run has been completed.

[0150] The actuation mechanism may include a first part that moves the flow cell device at least along z direction from or to the closed position. The actuation mechanism may include a second part that moves the flow cell device relative to the manifold along an axis orthogonal to the z direction among different positions, e.g., the open position, the grabber position, the loading position, etc.

[0151] In some embodiments, the actuation mechanism may (1) enable sealed fluidic communication therebetween when they are coupled to each other (in the closed position); (2) decouple the flow cell device from the manifold (in a decoupled position); (3) allow access of the flow cell device by dispensing tips (in the open position) to allow open fluidic communication to the flow cell device; (4) allow access of the flow cell device by the grabber and gantry system in a grabber position; and (5) allow access of the flow cell device by the user for loading or unloadingAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)the flow cell device relative to the fluidic station.

[0152] In some embodiments, the first part of the actuation mechanism includes an actuator that moves linearly, e.g., at least in a direction orthogonal to a z direction, or rotates, e.g., about the direction orthogonal to the z direction which results in the movement of the flow cell device. In some embodiments, the actuator moves in a direction that is not along the z direction but results in movement of the flow cell device in the z direction.

[0153] In some embodiments, the first part of the actuation mechanism includes a drive member that contacts the actuator and moves as a result of the actuation. In some embodiments, the actuation mechanism includes an optional movement member or output member that transfers the movement from the drive member to the flow cell device.

[0154] In some embodiments, the precision of movement of the flow cell device by the first part of the actuation mechanism may be within ± 5 mm, ± 4 mm, ± 3 mm, ± 1 mm, ± 1 mm, ± 0.8 mm, ± 0.6 mm, ± 0.5 mm, ± 0,4 mm, ± 0.2 mm, ± 0.1 mm, or ± 0.05 mm.

[0155] FIGS. 11A-11B, FIGS. 12A-12B, and FIGS. 13A-B show’ exemplary embodiments of the first part of the actuation mechanism of the fluidic station disclosed herein.

[0156] FIGS. 11A-11B shows an exemplary embodiment of the first part of the actuation mechanism 1111 of the fluidic station 8010 in a side view. FIGS. 11A-11B show two end points of the flow cell device with movement along z direction by the actuation mechanism. In some embodiments, the first part of the actuation mechanism 1111 includes an actuator 1112 mounted to a static base 1113 of the fluidic station. The actuator 1112 may be configured to generate controlled motion, e.g., linear motion along an axis within the x-y plane. Exemplary actuator includes but is not limited to: a rotary motor, a lead screw or ball screw, a pneumatic or hydraulic cylinder, and a solenoid.

[0157] The output of the actuator 1112 may be operatively coupled to a drive member 1114. The drive member may have a first end coupled to the actuator and a second end coupled to a movement member 1115. The movement member 1115 may convert motion by the drive member 1114 into vertical displacement, thereby raising or lowering the flow cell device 5000 along z direction relative to the static base of the fluidic station. In this embodiment, the drive member is a cam (e.g., a ramp cam) and the movement member includes an arm which has a portion thatAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)travels along the inclined surface of the drive member to move the flow cell device along the z direction.

[0158] In some embodiments, the first part of the actuation mechanism converts motion generated by the actuator into controlled vertical movement of the flow cell device. Reverse actuation correspondingly may lower the flow cell device. In some embodiments, the actuation mechanism may enable precise, repeatable vertical positioning while allowing the actuator to be positioned laterally relative to the flow cell device to save space and reduce size of the fluidic station.

[0159] In some embodiments, the first part of the actuation mechanism includes: an actuator that actuates a cam having a cam surface and a follower contacting the cam surface. The cam surface may comprise at least a linear surface or a curved surface. In some embodiments, the actuator actuates the cam to move linearly or rotate.

[0160] In some embodiments, the first part of the actuation mechanism includes a first link member and a second link member that is movably connected to the first link member at a pivot point,

[0161] FIGS. 12A-12B shows an exemplary embodiment of the first part of the actuation mechanism having the first and second link member.

[0162] In some embodiments, the first and second link member are mechanically coupled at a mid-pivot point 1215 and can be actuated by the actuator 1211 to produce scissor-like movement to move the sample stage and the flow cell device along the z direction.

[0163] In some embodiments, the actuator 1211 is mounted to the base and is mechanically coupled to the lower end of the first link member 1212. As the actuator 1211 moves, it may apply a force to the first link member 1212 thereby causing the first link member 1212 to rotate about its lower pivot point 1213 relative to the base. Rotation of the first link member 1212 may result in a corresponding rotation of the second link member 1216 about the mid pivot point 1215. The upper end of the second link member 1216 is pivotably connected to the sample stage at an upper pivot point 1214. Rotation of the second link member 1216 about the mid pivot point 1215 causes the upper pivot point 1214 to translate vertically resulting in movement of the sample stage and the flow cell device along the z direction.Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)

[0164] FIGS. 13A-13B show an exemplary embodiment of the first part of the actuation mechanism 1311 having a rotatory cam 1314. In some embodiments, there may multiple rotary cams installed below the sample stage and the flow cell device at different locations, e.g., at 4 corners. Rotation of the actuator causes the rotary cam(s) to rotate and depending on the cam surface of the rotatory cam, the flow cell device may be moved along the z direction. The cam surface may include features that provides stop(s) for the motion of the flow cell device, e.g., at a lowest point along z direction and / or at a highest point along z direction. As shown in FIGS. 13A-13B, in this particular embodiment, the cam surface is curved with a protrusion that provides hard stops (1315) at two ends of z movement of the flow cell device.

[0165] In some embodiments, the first part of the actuation mechanism is configured to move the flow cell device from the decoupled position to the closed position. In some embodiments, the first part of the actuation mechanism is configured to move the flow cell device from positions that are at least 0.1 mm, 0,2 mm, 0,3 mm, 0.4 mm, 0.5 mm, 0,6 mm, 0,7 mm, 0.8 mm, or 1 mm away from the decoupled position to the closed position. In some embodiments, the first part of the actuation mechanism is configured to move the flow cell device from positions that are at least 0.5 mm, 0.8 mm, 1 mm, 1.2 mm, 1.5 mm, 1.8 mm, 2 mm, 3 mm, 4 mm, or 5 mm away from the decoupled position to the closed position.

[0166] In some embodiments, the second part of the actuation mechanism of the fluidic station is configured to move the flow cell device at least in the x-y plane. In some embodiments, the second part of the actuation mechanism is configured to move the flow cell device: at least in a plane orthogonal to the z direction between one or more positions. Such part of the actuation mechanism may include one or more of: a wheel, a roller, a belt, a rail, a slider, a track, a threaded shaft, a lead screw, a rack, and a linear bearing. FIGS. 9A-9E and FIG. 10 show an exemplary embodiment of the second part of actuation mechanism that is configured to move the flow cell devices among different positions. Such positions may include: the one or more open positions, the grabber position, the loading position, and the decoupled position.

[0167] In this embodiment, the second part of the actuation mechanism includes a drawer tray that is configured to be moved by an actuator of the part of the actuation mechanism and is configured to hold the flow cell device thereon. In this embodiment, the second part of the actuation mechanism includes one or more rails, and the drawer tray may be movably mountedAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)thereon, so that the drawer may automatically move along the rails. The drawer may also be manually moved along the rails (e.g., for loading the flow cell device by a user). In some embodiments, the drawer tray 8016 is configured to hold flow cell device, flow cell frame, and flow cell carrier thereon, optionally fixed to a wall of the drawer 8019. The wall of the drawer may be fixed to the drawer tray 8016 but moveable relative to the one or more rails 8021. In some embodiments, the drawer tray may also be configured to hold other parts of the fluidic station 8010 thereon, including but not limited to a thermal stack of the flow cell device 8017, a thermal stack of the reagent reservoirs 8018, and a docking structure 8019 for holding at least some of the reagent reservoirs, the flow cell device, and the dispensing tips.

[0168] In some embodiments, the second part of the actuation mechanism is configured to move one or more structural elements of the fluidic station along with the flow cell device. Such structural elements include: the thermal stack of the flow cell, one or more reagent reservoirs, the thermal stack for at least some of the reagent reservoirs, a container for storing dispensing tips (e.g., clean and / or used dispensing tips), and the docking structure of the fluidic station.

[0169] In some embodiments, the first part of the actuation mechanism is configured to move one or more structural elements (e.g., of the fluidic station or of the flow cell system) along with the flow cell device. Such structural elements include: the thermal stack of the flow cell, the frame of the flow cell device, and the flow cell carrier. In some embodiments, the first part of the actuation mechanism is configured to move the second manifold (e.g., 1550) corresponding to the outlets of the flow cell device when moving the flow cell device so that the second manifold stay sealingly coupled to the outlet(s) when the flow cell device moves among different positions (e.g., among decoupled position and one or more open positions).

[0170] In some embodiments, the second part of the actuation mechanism is configured to not move the manifold (e.g., 1500), the valve (e.g., 7000) connecting to the manifold along with moving the flow cell device. In some embodiments, the manifold is decoupled from the flow cell device when the flow cell device moves away from the closed position. In some embodiments, the second part of the actuation mechanism is configured to not move the second manifold (e.g., 1550) with moving the flow cell device. In some embodiments, the second manifold is decoupled from the flow cell device when the flow cell device moves away from the closed position. In some embodiments, the second part of actuation mechanism is configured to not move one or moreAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)reagent reservoirs connecting to the valve when moving the flow cell device.

[0171] In some embodiments, some structural elements are fixedly attached to a housing 8030 of the fluidic station that is static. Such structural element may include the manifold and / or the rotary valve. FIG. 10 shows an exemplary embodiment in which the manifold corresponding to inlet(s) of the flow cell device 1500 is fixedly attached to the housing 8030 of the fluidic station 8010. The valve 7001 (e.g., rotary’ valve) for controlling fluidic communication via the manifold may also be fixedly attached to the housing of the fluidic station.

[0172] In some embodiments, the first part of the actuation mechanism, the second part of the actuation mechanism, or both is configured to move the flow cell device to: a closed position, at least along a z direction, where the one or more inlets of the flow cell device and the one or more openings of the manifold are coupled to each other for fluidic communication from the one or more reagent reservoirs to the flow cell device; one or more open positions, where at least one of the one or more inlets are accessible by a dispensing tip for fluidic communication from the dispensing tip to the flow cell device; a grabber position, where the flow cell device is decoupled from the fluidic station and is configured to be accessible by a grabber for moving the flow cell device away from the fluidic station; a loading or unloading position, where the flow cell device is accessible by a user; and a decoupled position that is optional, where the flow cell device is decoupled from the manifold and at the same location in the plane orthogonal to the z direction as the closed position.

[0173] FIGS.4A- 4H show an exemplary embodiment of the first manifold, and the flow cell device in different positions disclosed herein. The different positions may include a loading / unloading position for a user to load or unload a flow cell device; a decouple position in which the flow cell device is at the corresponding x, y location of the first manifold, but has not be moved closed to the first manifold for sealed coupling; a closed position in which the inlets of the flow cell device are sealmgly coupled to the openings of the first manifold; one or more open positions in which one or more inlet are accessible from above by dispensing tips (e.g., the first manifold is not blocking access from above one or more inlet(s) by the dispensing tip (s); and a grabber position in which the flow cell device can be accessed by the grabber. As a nonlinnting example, FIG. 4B shows the closed position; FIG. 4A shows the decoupled position; FIG. 4C shows one position in which all the inlets are accessible by the dispensing tip; flow direction mayAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)be according to arrow 4001.

[0174] In some embodiments, the loading / unloading position and the grabber position may be at the opposite ends along a direction in the x-y plane. For example, for the sequencing system 100 in FIG. 8, front access of the fluidic station is provided, and the loading / unloading position may be close to the front side of the sequencing system, and the closed or open positions are further away from the front side of the sequencing system than the loading / unloading position. The grabber position may be toward the back of the sequencing system, closer to the back side of the sequencing system than the closed and open positions, thus facilitating and reducing moving distance of the grabber and other structural elements of the gantry assembly since the gantry and grabber system is located toward the back side of the sequencing system. In some embodiments, the loading / unloading position and / or grabber position does not overlap with the other positions to allow clear access to the flow cell device and avoid blockage and / contact of other structural elements in adjacent areas of the flow cell device.

[0175] In some embodiments, the fluidic station may include one or more reagent reservoirs. The reservoirs may include at least one reagent reservoir containing one or more cycling reagents and at least one reagent reservoir containing non-cycling reagents. In some embodiments, the one or more reservoirs include at least two reagent reservoirs that are independently thermally controlled. The one or more reagent reservoirs may comprise at least one reagent reservoir containing reagent stored at a temperature lower than ambient temperature and at least one reagent reservoir containing reagent at ambient temperature. In some embodiments, the one or more reagent reservoirs includes at least one reagent reservoir containing reagent that is thermally controlled. In some embodiments, the fluidic station further comprising a container 8041 for storing one or more dispensing tips.

[0176] In some embodiments, the manifold herein, either the first or second manifold (e.g., 1500, 4500, 5500, 5590), includes a manifold barb (e.g., 1555, 1555 2, 1555 3, 1555 4) at each of the one or more openings. In some embodiments, the manifold barb is tapered at an end thereof (e.g., the distal end inserting into a gasket of the flow cell device). In some embodiments, the manifold barb is configured to insert at least partly into a corresponding gasket of the inlet or outlet of the flow cell device (e.g., 100, 4000, 5000, 16000). In embodiments where the flow cell device may not have any corresponding inlet or outlet gaskets or any build-in features in the inlet or outletAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)that are functionally or structurally similar to a separate gasket, the manifold barb is configured to insert at least partly into the inlet(s) or outlet(s) of the flow cell device directly.

[0177] In some embodiments, the manifold barb (e.g., 1555, 1555 2, 1555 3, 1555 4) is configured to allow sealed coupling of the manifold to the flow cell device when it is inserted into the gasket(s) of the flow cell device or the flow cell device directly. In some embodiments, the manifold barb (e.g., 1555, 1555_2, 1555_3, 1555_4) is configured to enable face seal of the one or more openings of the manifold and the flow cell device. FIGS. 14A-14B shows a manifold 1400 and its barbs 1555 in a perspective view (FIG. 14A) and in a perspective view when it is sealingly coupled to inlet gaskets (e.g., 5313, 5313’) of the flow cell device 5000.

[0178] In some embodiments, the inlet gaskets may have various shapes. As a nonlimiting example, the inlet gaskets may include a conical shape, a cylindrical shape, or their combinations (e.g., 5313’, 5313’_1, 5313 ’_2 in FIGS. 15B -15E). In some embodiments, the inlet gaskets may include a portion that is identical or sufficiently identical (e.g., m shape and size) to an existing gasket of a flow cell device that only uses closed fluidic communication via traditional manifol ds. As shown in FIG. 15E, the inlet gasket 5313’_2 may include a button portion of a shape of an existing gasket of a flow cell device that can be used in traditional closed-fluidic communication-only sequencing systems. A top portion of the inlet gasket 5313’__2 may include a conical shape. Utilization of such inlet gaskets may allow compatibility to existing flow cell devices and extension of existing fluidic systems of a sequencing system to hybrid fluidic communication as disclosed herein via the manifold and the dispensing tips. Utilization of such inlet gaskets may allow removal of the existing inlet gaskets of existing flow cells and extension of existing fluidic systems to hybrid fluidic communication disclosed herein. Alternative, the inlet gasket may only have the top conical portion of the inlet gasket 5313’ 2 as shown in FIG. 15E and enable sealed coupling of the manifold and the flow cell device by using the combination of the inlet gasket with the existing gasket.

[0179] In some embodiments, the manifold is movably coupled to a housing of the fluidic system. Coupling of the manifold and the flow cell device may include moving the manifold relative to the housing of the fluidic station while keeping the flow cell device relatively static to the housing of the fluidic station. In some embodiments, the manifold moves at least in a direction orthogonal to the z direction to sealingly couple to the one or more inlets of the flow cell device.Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)In some embodiments, the second manifold is movably coupled to the housing of the fluidic station. In some embodiments, the second manifold moves at least in a direction orthogonal to the z direction to sealingly couple to the one or more outlets of the flow cell device.

[0180] In some embodiments, the manifold (e.g., 1400, 1500, 1550) may be fixedly coupled to the housing of the fluidic station, e.g., 8030, while the flow cell device may move relative to the housing to enable sealed coupling of the flow cell device to the manifold.

[0181] In some embodiments, the housing of the fluidic station does not move when the flow cell device or other parts within the drawer tray 8016 moves along the rail(s) of the fluidic station. In other words, the housing of the fluidic station is static relative to the housing of the sequencing system.

[0182] In some embodiments, the fluidic station 8010 may further comprise a second manifold comprising: one or more second fluidic pathways; and one or more second openings. The second openings may be identical or substantially identical to the first openings of the first manifold. The second fluidic pathways may be identical or different in distribution, shape, and / or size from the first fluidic pathways of the manifold. For example, the second fluidic pathways may not need to have a size, shape, and distribution that may reduce dead volumes. In some embodiments, the manifold may correspond to the inlets of the flow cell device, and the second manifold may correspond to the outlets of the flow cell device,

[0183] In some embodiments, the one or more outlets of the flow cell device and the one or more second openings of the second manifold are coupled to each other for fluidic communication from the flow cell device to at least a waste reservoir when the flow cell device is in the closed position. In some embodiments, the one or more outlets of the flow cell device and the one or more second openings of the second manifold are coupled to each other for fluidic communication from the flow cell device to at least a reservoir for reusable reagents when the flow cell device is in the closed position. In some embodiments, the one or more outlets of the flow cell device and the one or more second openings of the second manifold remain coupled to each other for fluidic communication from the flow cell device to at least a waste reservoir or reagent reservoir for reuse when the flow cell device is in the open position and / or in the decoupled position.

[0184] In some embodiments, the one or more outlets of the flow cell device and the one or more second openings of the second manifold disconnect from each other when the flow cellAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)device is in the grabber position or loading / unloading position.

[0185] In embodiments where the second manifold is fixed relative to the housing of the fluidic station (e.g., 8030), the one or more outlets of the flow cell device and the one or more second openings of the second manifold disconnect from each other when the flow cell device is in the decoupled position and / or one or more open positions.

[0186] In some embodiments, the one or more channels of the flow cell device includ es at least 6 channels. In some embodiments, the one or more channels comprise 2, 3, 4, 5 6,7, 8, 9, or 10 channels at a same level along the z direction. In some embodiments, the one or more channels includes at least two channels that are at two different levels along the z direction.

[0187] In some embodiments, the flow cell system further comprising a flow cell carrier configured to hold the flow cell device therein. In some embodiments, the flow cell carrier is configured to couple to the grabber of the grabber and gantry system when the flow cell device is moved by the grabber (e.g., 5 10).

[0188] In some embodiments, the flow cell carrier includes a first coupling element configured to couple to a coupling element of the fluidic station. In some embodiments, the flow cell carrier includes the first or a second coupling element configured to couple to a coupling element of the imaging station. Nonlimiting examples of the coupling element of the flow cell carrier include alignment holes (e.g., 5112), and the coupling element of the fluidic station may include matching pins or protrusion. Another example of the coupling element include magnetic pins or studs.

[0189] In some embodiments, the one or more inlets of the flow cell device are facing upwards with an opening in a top surface of the flow cell device. In some embodiments, the one or more outlets of the flow cell device are facing upwards with an opening in a top surface of the flow cell device.

[0190] In some embodiments, the flow cell system herein may advantageously include a flow cell frame that independently aligns with the one or more substrates of the flow cell device to facilitate hybrid fluidic communication through the flow cell frame to the one or more substrate. Such hybrid fluidic communication may include closed fluidic communication via the manifold and open fluidic communication via the dispensing tip(s) disclosed herein.

[0191] FIG. 16C shows an exemplary flow cell frame of the flow cell system disclosed hereinAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)in a top view, side view, and an expand view of the side view. In some embodiments, the flow cell frame 16100 includes a top cover 16105 and a bottom frame 16110 that mechanically aligns and / or couples to the one or more substrates of the flow cell device independently. In some embodiments, the top cover includes: a top anchor element 16106 that mechanically couples to the one or more substrates 16020; one or more through holes that allow inlet gaskets and / or outlet gaskets 16313 to fit through, where the gaskets 16313 are configured to contact a top surface of the one or more substrates and sealingly couple to the manifold or the dispensing tips for hybrid fluidic communication,

[0192] In some embodiments, the gaskets of the flow cell device includes one or more inlet gaskets and / or one or more outlet gaskets. In some embodiments, the gaskets are compatible not only with the flow cell devices disclosed herein, but also the existing flow cell devices (either directly or with the existing gaskets therein) that are used in sequencing systems with only closed fluidic communication between the manifold and the flow cell device via the gaskets.

[0193] In some embodiments, the gaskets are configured to reversibly and sealingly couple to the manifold (e.g., via variously-shaped manifold barbs) to enable sealed fluidic communication from the first manifold to the one or more inlets or from the one or more outlets to the second manifold. In some embodiments, the gaskets are configured to reversibly and sealingly couple to the dispensing tip(s) when the flow cell device is in the open position and reversibly and sealingly couple to the first manifold when the flow cell device is the closed position.

[0194] In some embodiments, the gaskets are configured to enable repeated coupling and decoupling to the first manifold and to the dispensing tips respectively in any order that is required in a single cycle or across different cycles in a sequencing run. In some embodiments, the gaskets are configured to enable repeated coupling and decoupling to the second manifold in a single cycle or across different cycles in a sequencing run.

[0195] In some embodiments, at least some gaskets comprise a cone shaped cavity therewithin, e.g., 5313’, 5313 1, 5313’ 2 in FIGS. 15A-15E. In some embodiments, at least some of the gasket includes a cylindrical shaped cavity therewithin, e.g., 5313 1, 5313’ 2 in FIGS. 15D-15E. In some embodiments, at least some gaskets comprise a cavity with at least two geometrical shapes, e.g., cone and cylinder as shown in FIG. 15D.

[0196] In some embodiments, the gaskets are configured to sealingly couple to the dispensingAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)tip when the dispensing tip is at least 0.1mm, 0.2 mm, 0.3 mm, 0.4 mm, 0.5 mm, 0.6 mm, 0.8 mm, 1 mm, 1.2 mm, 1.5 mm, or 2 mm off a predetermined alignment with the one or more inlets of the flow cell device. In some embodiments, the gaskets are configured to sealingly couple to the dispensing tip when the one or more openings are at least 00.1mm, 0.2 mm, 0.3 mm, 0.4 mm, 0.5 mm, 0.6 mm, 0.8 mm, 1 mm, 1.2 mm, 1.5 mm, or 2 mm off a predetermined alignment with the one or more outlets of the flow cell device. As shown in FIG. 15A, the dispensing tip is configured to insert at least partly into the gasket to allow sealed coupling between the dispensing tip and the gasket. Depending on the different offsets from a perfect alignment of the gasket and the dispensing tip, the insertion depths of the dispensing tip to enable sealingly coupling may vary. In some embodiments, the depth along z direction and the shape of the gasket are configured to allow sealed coupling when the dispensing tip is at least 00.1mm, 0,2 mm, 0,3 mm, 0.4 mm, 0.5 mm, 0.6 mm, 0.8 mm, 1 mm, 1.2 mm, 1.5 mm, or 2 mm off a predetermined alignment with the one or more outlets of the flow cell device.

[0197] Similarly, as shown in the rightmost panel of FIG. 15B and FIGS. 15C-15E, Depending on the different offsets from a perfect alignment of the gasket and the manifold (e.g., at the manifold barb), the insertion depths of the manifold barb to enable sealingly coupling may vary. In some embodiments, the depth along z direction and the shape of the gasket are configured to allow sealed coupling when the manifold barb is at least 0.1mm, 0.2 mm, 0.3 mm, 0.4 mm, 0.5 mm, 0.6 mm, 0.8 mm, 1 mm, 1.2 mm, 1.5 mm, or 2 mm off a predetermined alignment with the one or more outlets of the flow cell device.

[0198] In some embodiments, the gaskets are configured to sealingly couple to the one or more openings of the first or second manifold when the one or more openings of the manifold (e.g., at the distal end of the manifold barb) is at least 0.1 mm, 0.2 mm, 0.3 mm, 0.4 mm, 0.5 mm, 0.6 mm, 0.8 mm, 1 mm, 1.2 mm, 1.5 mm, or 2 mm off a predetermined alignment with the one or more inlets or outlets of the flow cell device.

[0199] In some embodiments, the gaskets herein are made with deformable or non-stiff materials. Non-limiting examples of the materials include rubber, plastic, polymer, etc.

[0200] In some embodiments, the sequencing system herein includes one or more imaging stations. In some embodiments, the imaging station is spatially displaced from the fluidic station along a direction in 3D, e.g., 8015 and 8010 as shown in FIG. 8. The spatial separation of theAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)fluidic station and imaging station may advantageously reduce possible contaminations that may be caused by reagents and other liquids to the imaging station, reduce possible impact of the thermal control of the fluidic station to imaging quality; and reduce possible mechanical interferences to the sample caused by various structural elements of the fluidic station. The spatial separation may also advantageously reduce idling of the fluidic or imaging part of a sequencing cycle by allowing different sequencing processes (e.g., two flow cells with two different sequencing protocols and / or sequencing chemistry) to be performed in parallel on the fluidic and imaging stations.

[0201] FIGS. 16A and 16B show embodiments of the imaging station disclosed herein.

[0202] In some embodiments, the imaging station 8015 may comprise a sample stage 8055 (which can move along a z-axis, e.g., “z” stage) for positioning the flow cell device (e.g., 200, 300, 4000, 5000) thereon for imaging and a sample stage actuator (e.g,, a motor, not shown) that generates a movement (e.g., not along a z direction) and cause the sample stage (e.g., 8055) to move (e.g. along a z direction). In some embodiments, the imaging station 8015 may comprise a movable member (e.g., 8060) with a base (8065) operatively coupled to the sample stage actuator and transforms the movement thereof to move the sample stage and the flow cell device at least along the z direction.

[0203] As shown in FIGS. 16A-16B, in some embodiments, the sample stage actuator actuates a moving element to move in a direction orthogonal to the z direction and resulting in the sample stage and the flow cell device to move at least along the z direction for focusing the flow cell device (for imaging via an optical system 8029 disclosed herein). In some embodiments, the sample stage actuator actuates a moving element to move in a direction orthogonal to the z direction and resulting in the sample stage and the flow cell device to move only along the z direction for focusing the flow cell device. In some embodiments, the moving element includes an inclined surface or a curved surface. As a nonlimiting example, the moving element includes a wedge 8031. In some embodiments, a precision of the movement of the flow cell device along the z direction is greater than 100 um, 80 um, 60 um, 40 um, 20 um, 10 um, 8 um, 6 um, 4 um, 2 um, 1 um, 0.8 um, 0.6 um, 0.4 um, 0.2 um, 0.1 um, 0.08 um, 0.05 um, 0.02 um, or 0.01 um.

[0204] In some embodiments, the imaging station further includes an x-y stage and a x-y stage actuation mechanism (see, e.g., X stage 8061, Y stage 8063). In some embodiments, the x-y stageAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)actuation mechanism includes one or more of: a wheel, a roller, a belt, a rail, a slider, a track, a threaded shaft, a lead screw, a rack, and a linear bearing. In some embodiments, the x-y stage actuation mechanism includes one or more x-y stage actuators that actuate the x-y stage to move along a first direction orthogonal to the z direction, a second direction orthogonal to the z direction, or both.

[0205] In some embodiments, the x-y stage may include a single stage that may be actuated at least along x and along y direction or any two directions that are orthogonal and within the x-y plane.

[0206] In some embodiments, the x-y stage may include at least two separate stages that each separate stage may be actuated at least along a direction within the x-y plane.

[0207] In some embodiments, the sequencing systems herein includes a gantry and grabber system that moves the flow cell device (e.g., 4000, 5000, 16000) among the fluidic station(s) and the imaging station and position the flow cell device on the fluidic station and / or imaging station for performing sequencing reactions and imaging. In some embodiments, the gantry and grabber system further moves the fluidic dispensing device and the dispensing tip for fluidic communication to the flow cell device at the fluidic station(s), and optionally at the imaging station.

[0208] FIGS. 17A-17B show an exemplary embodiment of the gantry and grabber system herein 17000. FIG. 17A shows the gantry and grabber system 17000 coupled to the flow cell device (e.g., 4000, 5000, 16000) and flow cell carrier (e.g., 5310), and also the fluidic dispensing system with a dispensing head assembly 17900 and the dispensing tip 17080 coupled on the dispensing head assembly in a perspective view. FIG. 17B shows a close-up view of a grabber 17200.

[0209] In some embodiments, the grabber and gantry system (e.g., 17000) includes: a gantry assembly (e.g., 17100) configured to move the grabber (e.g., 17200) in one or more directions in 3D relative to a reference location, e.g., a housing of the sequencing system (e.g., 8005).

[0210] The grabber may comprise: one or more arms (e.g., 17210) that are configured to contact and engage the flow cell carrier; one or more engagement features 17211 (e.g., pins) extending from each of the one or more arms; one or more sensors mounted to the one or moreAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)arms (not shown); and a support body 17220 supporting the one or more arms and attaching the one or more arms to the gantry assembly, where the one or more arms are configured to move relative to the support body 17220 to engage the flow cell device. In some embodiments, the one or more arms are fixedly or movably attached to the support body 17220. The movement of the one or more arms may be at least along x direction, at least along y direction, or at least along z direction. In some embodiments, the one or more arms may move along the x-y plane to ensure coupling to the corresponding engagement features on the flow cell carrier. In some embodiments, the one or more arms may first move along z to arrive at the same z level as the corresponding engagement features and then move within the x-y plane to couple to the corresponding engagement features.

[0211] In some embodiments, the grabber 17200, which may comprise one or more arms, may include a shape that facilitate access of the flow cell device. As a nonlimiting example shown in FIGS. 17A-17B, the one or more arms are shorter at one end further from the support body 17220 than the other end closer to the support body along z direction to facilitate accessing the flow cell device by first descending along z direction to be at about a same level as the flow cell device, and then move within the x-y plane, toward the shorter end of the arm(s) to approach the flow cell device and achieve coupling to the flow cell device. When the one or more arms are properly coupled to the flow cell device, the support body may not be directly above the center of the flow cell device but offset to a side of the flow cell device.

[0212] In some embodiments, the shape of the one or more arms, and their relative position to the support body may advantageously facilitate access to the flow cell even if a portion of the flow cell device’s overhead space is at least blocked or occupied by other structural elements of the fluidic or imaging station. For example, the objective lens of the imaging station may be directly above the flow cell device and blocking at least part of the overhead space of the flow cell device, using the arm(s) with a shorter end as shown in FIG. 17B, and the support body 17220 that is not above the flow cell device or at least only partly above the flow cell device when the flow cell is coupled, the grabber’s motion and movement of the flow cell device does not contact or interfere with the objective lens of the imager.

[0213] In some embodiments, the coupling to the flow cell device by the arms are configured to utilize engagement features thereon. Engagement features on the one or more arms andAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)corresponding engagement features on the flow cell device may be configured to couple mechanically, magnetically, electrically, or electromagnetically to each other. Non-limiting examples of the engagement features and corresponding engagement features includes: a spring, a pin, a protrusion, a hole, a groove, a magnet, and an electromagnet. A nonlimiting example of the engagement feature on the one or more arms include engagement features (e.g., pins) 17211 that are on the inside of the arms, facing the flow cell device and may be coupled to corresponding grooves on the flow cell carrier.

[0214] In some embodiments, the grabber and gantry system 17000 is configured to repeatedly perform one or more operations, within a single sequencing cycle of a sequencing run, or in multiple sequencing cycles of the sequencing run. The one or more operations may comprise: moving the flow cell device from the fluidic station to the imaging station; position the flow cell device on the imaging station for imaging; move the flow cell device from the imaging station to the fluidic station; position the flow cell device on the fluidic station; move a second flow cell device from the second fluidic station to the imaging station; position the second flow cell device on the imaging station for imaging; move the second flow cell device from the imaging station to the second fluidic station; and position the second flow cell device on the second fluidic station. Such operations may occur in the order disclosed herein but may also be performed in various different orders.

[0215] In some embodiments, the gantry assembly is configured to move the one or more arms of the grabber along a z direction to approach the flow cell device and then move within the x-y plane to engage the flow cell device.

[0216] In some embodiments, the gantry assembly is configured to move the one or more arms of the grabber within the x-y plane to approach the flow cell device and then move along the z direction to engage the flow cell device.

[0217] In some embodiments, the grabber may include one or more sensors positioned on the one or more arms. For example, two sensors may be positioned each on an arm of the grabber. In some embodiments, the one or more sensors may include various types of sensors for sensing coupling of the grabber to the flow cell carrier (e.g., yes, they are coupled to each other or no, they are not coupled to each other). In some embodiments, the one or more sensors may include various types of sensors for sensing precision of coupling to the flow cell carrier. For example, aAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)capacitance sensor may return one or more sensed values, e.g., a capacity value or some other values that can be derived therefrom, and comparing, by a processor of the sequencing system, the sensed value(s) to a predetermined value or range may determine whether the coupling is satisfactory or not. A predetermined criterion may include that the sensed value(s) is required to be greater than a predetermined capacitance value, within a capacitance range, or within a preset offset to one or more values or ranges. The predetermined values or ranges may be customized based on designs of the electrodes, the electrical field applied, and other settings of the grabber and the flow cell. If the sensed values satisfies the predetermined criterion, a secured coupling is formed between the grabber and the flow cell, the grabber may lift up the flow cell from one of the fluidic station and the imaging station and move between the fluidic station and the imaging station, such that the flow cell device is positioned for imaging or for fluidic communication with one or more reagent reservoirs. In response to determining the sensing data failing the predetermined criterion, the grabber may position the flow cell device back to one of the fluidic station and the imaging station or retry coupling with the flow cell device. Non-limiting examples of the one or more sensors may include one or more of: a reflective optical sensor and an optical emitter; an inductive proximity sensor, a capacitive proximity sensor, a camera and one or more fiducial markers, a contact switch, a distance sensor, and an ultrasonic sensor.

[0218] In some embodiments, the gantry and grabber system herein may include a vision system. The vision system may include one or more cameras. Nonlimiting examples of the cameras may utilize different wavelengths of the light not limited to the visible light. The vision system may include at least two cameras for alignment of the dispensing tip to the flow cell device (e.g., inlet gaskets). In some embodiments, the vision system is configured to determine an offset of the dispensing tip to a predetermined center position. In some embodiments, the predetermined center position may be determined during calibration of the vision system or the gantry and grabber system.

[0219] In some embodiments, the vision system is controlled by the processor of the sequencing system disclosed herein to communicate to the grabber and gantry system so that the gantry assembly can adjust the x and or y location of the dispensing tip to be at the predetermined center position or closer to the predetermined center position before the dispensing tip starts to descend to a lower z level along the z direction for insertion at least partly into the inlet gasket of the of the flow cell device.Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)|00220] FIG. 18 shows an example embodiment of the vision system 18000. In some embodiments, the vision system may comprise two cameras 18500, and a mirror 18600 that is used in combination to determine a location of the dispensing tip 17080 (e.g., at least in the x-y plane). In some embodiments, at least one camera remains static (e.g., caml, fixed camera) relative to the housing of the fluidic station, and one camera moves along with the dispensing tip (e.g., cam2, moving camera) relative to the housing of the fluidic station. In some embodiments, the vision system may include an alignment structure 17090 (which may also be referred to as a reference structure) with a hole. The alignment structure may be at a fixed position (e.g,, the center of the aperture may be aligned with the inlet gasket 17089 of the flow cell device). In some embodiments, the gasket of the inlet may be optional, and the such alignment of the aperture of the reference structure is directly with the inlet without the gasket,

[0221] In some embodiments, the center of caml 18500 defines an alignment center for alignment with the inlet or inlet gaskets of the flow cell device. The alignment structure 17090 may provide a physical reference at a known z plane or a z range, and the center of the hole defines a target x-y location for alignment with an inlet gasket of the flow cell device. Aligning the dispensing tip (e.g., its most distal end) with the alignment center may indicate the dispensing tip is centered with zero to minimal offset from the center of the inlet gasket. The camera (e.g., cam 2) may be configured to detect a relative position of the dispensing tip with an alignment structure 17090 to coarsely align the dispensing tip to be within a field of view that can be detected by the camera of the vision system (e.g., caml). The camera (e.g., cam 2) may be configured to detect a relative position of the dispensing tip with a center of the camera (e.g., cam 2). In some embodiments, cam2 is configured to image the dispensing tip and to determine a relative position of the dispensing tip with respect to a center of cam2, where cam2 moves together with the dispensing tip.

[0222] In some embodiments, using the vision system for aligning the dispensing tip includes moving the dispensing tip so that it is within a field of view of the fixed camera (cam 1) and positioning the dispensing tip at a predetermined z location corresponding to a plane of the alignment structure. The dispensing tip may also be within a predetermined range of z location that may be controlled by the gantry assembly. Based on the image captured by the fixed camera, e.g., caml, a projected position of the dispensing tip can be compared to the center of the alignment hole, thereby generating x-y offset information (e.g., a difference between coordinates (X1, Y1)Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)and (X3, Y3)).

[0223] In some embodiments, using the vision system for aligning the dispensing tip includes determining a fixed reference between the dispensing tip and the center of the moving camera, e.g., cam2, by acquiring an image of the dispensing tip using the moving camera.

[0224] In some embodiments, using the vision system for aligning the dispensing tip includes determining a fixed reference between the dispensing tip and the center of the moving camera, e.g., cam2, by acquiring an image of the dispensing tip using cam2 while the dispensing tip is positioned at the center of the alignment hole as determined by caml.

[0225] In some embodiments, using the vision system for aligning the dispensing tip includes calibrating the moving camera’s coordinates with the coordinates of the fixed camera.

[0226] In some embodiments, using the vision system for aligning the dispensing tip includes calibrating a coordinate system of the moving camera (cam2) with a coordinate system of the fixed camera (caml) based on the known x-y position of the dispensing tip relative to the alignment structure and the corresponding position of the dispensing tip detected by cam2.

[0227] In some embodiments, using the vision system for aligning the dispensing tip includes generating corrective movements for the dispensing tip based on the x-y offset information obtained from caml, the fixed spatial reference between the dispensing tip and cam2, and the calibration of the moving camera’s coordinate system relative to the fixed camera’s coordinate system.

[0228] After the dispensing tip is aligned (e.g., in the x-y plane), the dispensing tip may be controlled by the gantry assembly to descend along z direction and insert into the corresponding inlet gasket of the flow cell device.

[0229] In some embodiments, for openly dispensing fluid(s) via the dispensing tips, the gantry assembly may move the fluidic dispensing device with the dispensing tip (e.g., a clean dispensing tip) between two fluidic stations, move the fluidic dispensing device with the dispensing tip relative to the same fluidic station to align with different inlets of the flow cell device, and / or optionally, move the fluidic dispensing device with a dispensing tip (e.g., a clean dispensing tip) to the imaging station for dispensing into the flow cell device while it is at the imaging station.

[0230] In some embodiments, the gantry assembly may first coarsely move the dispensingAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)head assembly of the fluidic dispensing device with the dispensing tip so that the dispensing tip may be detectable by camera 1 to be within a predetermined location range (e.g., within a range that fine alignment can be performed). With the predetermined location range for fine alignment, two cameras work together to determine an offset of the dispensing tip to a predetermined camera center. In response to determining that the offset is within a threshold range, no fine alignment is required. In response to determine that the offset is not within the threshold range, a difference of dispensing tip location to the predetermined camera center is calculated and is provided as a feedback to the gantry assembly for moving the dispensing tip closer to or at the predetermined camera center.

[0231] In some embodiments, the threshold range in distance is from ± 5 mm to 0, from ± 5 mm to 0, from ± 4 mm to 0, from ± 3.5 mm to 0, from ± 3 mm to 0, from ± 2,5 mm to 0, from ± 2 mm to 0, from ± 1.5 mm to 0, from ± 1 mm to 0, or from ± 0.5 mm to 0. As disclosed herein, the inlet gaskets of the flow cell devices advantageously allow sealed coupling of the dispensing tip to the inlet gasket, and the mlet of the flow cell channels even if the dispensing tip is offset from a center of the inlet gasket within a distance within the threshold range. In some embodiments, an offset dispensing tip may insert at a second distance deeper than a first distance of a centered dispensing tip into the inlet gasket to form sealed coupling between the two. The second distance may be 0.1 mm, 0.2 mm, 0.3 mm, 0.5 mm, 0.6 mm, 0.8 mm, 1mm, 1.2 mm, 1.5 mm, 1.8 mm, 2 mm, 3 mm, 4 mm, 5 mm, 6 mm, 7 mm, or 8 mm greater than a first distance along the z direction. The first and second distance may be measured from a top surface of the inlet gasket along the z direction.

[0232] In some embodiments, the flow cell devices and systems are part of a sequencing system for next generation sequencing application of samples. In some embodiments, the flow cell devices and systems are enclosed within a housing of the sequencing system. In some embodiments, the flow cell system herein may include one or more of: a flow cell device, a manifold, one or more gaskets, one or more dispensing guides, a flow cell frame, mounting rails, a flow cell carrier, and a fluidic dispensing device. In some embodiments, the sequencing system or the flow cell system herein may include one or more valves, one or more pumps, one or more rotors.

[0233] FIGS. 5A-5C show an exemplary embodiment of the flow cell system 1000 having aAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)flow cell device 5000 with the flow cell frame 5100, flow cell carrier 5310, a first manifold 5500 (e.g., for coupling with the inlets), a second manifold 5590 (e.g., for coupling with the outlets in FIG. 5B), and mounting rails 5810. FIGS.4A-4D show an exemplary embodiment of the flow cell system 1000 with a flow cell device 4000, a first manifold 4500, a second manifold 4590, mounting rails 4810, the pump(s) 5900, and a by-pass reservoir 4591 for fluidic communication in the first manifold 4500 while by-passing the flow cell device 4500. The flow cell device (e.g., 4000, 5000) may include one or more channels defined by one or more substrates, where the one or more channels are configured to allow fluids to flow therethrough and optionally, to allow a bolus of gas to flow therethrough between one or more of the fluids. The flow cell device may have one or more inlets in the one or more substrates and in fluidic connection with the one or more channels; and one or more outlets in the one or more substrates and in fluidic connection with the one or more channels.

[0234] In some embodiments, the difference in flow cell devices 4000, 5000 in FIGS. 4A -5C in comparison to flow cell devices 200, 300 in their corresponding embodiments may be in one or more of: the number of channels, size / shape of channels, size / shape of inlet and / or outlet, and size / shape of open landing areas. For example, the height / shape of the dispensing guide along z axis may be different for flow cell devices 4000, 5000 in comparison to flow cell devices 200, 300. FIG. 5F shows a cross-sectional view of the flow cell device 5000 which includes a dispensing guide that has a height along z that is lower than the dispensing guide 4210. In some embodiments, the substrate(s), inlet(s), landing areas, outlet(s), and channels of flow cell devices 4000, 5000 are the same to the flow cell devices disclosed above, e.g., flow cell devices 200, 300, except the number of channels and the number of inlets and outlet. FIGS. 4A -5C show exemplary embodiments of the flow cell device with 6 channels.

[0235] In some embodiments, the substrate(s), inlet(s), outlet(s), and channels of flow cell devices 4000, 5000 are the same to the flow cell devices disclosed above, e.g., flow cell devices 200, 300.

[0236] In some embodiments, the one or more channels include six (6) channels (e.g., lanes 1-6 m FIGS. 4A-4B and 5A). In some embodiments, the one or more channels can include 2, 3, 4, 5, 6,7, 8, 9,10, 12, 16, 18, 20 or more channels at a same level along z-axis, e.g., within a same x- y plane. In some embodiments, each of the one or more inlets includes a landing area, e.g., 541 inAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)FIG. 5F. In some embodiments, the landing area is an area within the x-y plane where the dispensed fluids land first in the corresponding inlet. In some embodiments, one or more of the landing area has a diameter of less than 0.5 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, or 15 mm within the x-y plane. In some embodiments, the landing area is an open landing area shown in FIGS. 2E, 2J, or 5F. In some embodiments, the landing area is for open dispensing from above the inlet and above the top surface of the top substrate of the flow cell d evice and without any gasket, dispensing guide, or other structural elements that insert into the landing area and / or extend beyond the top surface of the top substrate. In some embodiments, the landing area is for closed dispensing with one or more of a gasket, dispensing guide, or other structural element that insert into the landing area and / or extend beyond the top surface of the top substrate. In such closed dispensing, the dispensing tip may insert at least partly into the gasket, dispensing guide, or other equivalent structural element to form a sealed connection for dispensing. In some embodiments, the dispensing tip may be above the top surface of the top substrate for such closed dispensing, e.g., as shown in FIG. 5F. In some embodiments, the dispensing tip may be at least partly inserted to be below the top surface of the top substrate for such closed dispensing.

[0237] As disclosed herein, “sealed,” “sealing” mean liquid tight only or both liquid tight and airtight. As disclosed herein, “sealed” means at least liquid tight with no passage of liquids (e.g., solutions, buffers, reagent but liquids excludes air or other gases) may occur. As disclosed herein, “fluids” may include liquids, air, and / or other gases that may flow.

[0238] In some embodiments, the inlet is coupled to a gasket, dispensing guide, or a functional equivalent for guiding dispensing and prevent leakage. An exemplary embodiment of the dispensing guide is shown as 5110 in FIGS. 5E-5F. In some embodiments, the one or more landing areas, e.g., 541 in FIG. 5F, lacks a hydrophobic coating. In some embodiments, the flow cell device (e.g., 4000, 5000) lacks a hydrophobic coating. In some embodiments, each of the one or more landing areas lacks any coating that facilitates flowing of fluids from the landing area into the one or more channels. In some embodiments, residuals are unlikely to accumulate at the landing area at least due to the negative pressure that can be apply via the cleaning outlet (e.g., 570 in FIG. 5F) and / or outlet of the flow cell device 4000, 5000 that may efficiently remove the residuals. In some embodiments, residuals are unlikely to accumulate at the landing area (e.g., 541 in FIG. 5F) due to the positive pressure that can be applied to the manifold and the common line, e.g., via a pump, alone or in combination with negative pressure that can be apply via the cleaningAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)outlet and / or outlet of the flow cell device that may efficiently remove the residuals. In some embodiments, the one or more substrates of the flow cell device 4000, 5000 lacks a hydrophobic coating.

[0239] In some embodiments, the one or more inlets (e.g., 540 in FIG. 5F) is coupled with a dispensing guide that extends along an axis orthogonal to the x-y plane but may or may not extend beyond the one or more substrates (e.g., top substrate 520 in FIG. 5F) of the flow cell device. Exemplary embodiments of the dispensing guide are shown in FIGS. 2A- 2J, FIGS. 3A-3D, and FIGS. 5E-5F. An exemplary embodiment of dispensing guide 5110 is shown in FIGS. 5E-5F. The top portion of the dispensing guide may extend beyond the flow cell device along the z axis with a height 5111. The height may be in a range from 0.1 mm to 1 cm. The height may be in a range from 0.5 mm to 8 mm. The height may be in a range from 1 mm to 6 mm.

[0240] In some embodiments, the dispensing guide herein (e.g,, 4210, 4310, 4410, 5110) may include one or more gaskets, and where each gasket corresponds to an inlet of the one or more inlets or an outlet of the one or more outlets of the flow cell device, FIGS. 2E, 2J, and 5F show exemplary embodiments of the dispensing guide. In FIG. 5F, the dispensing guide may be a ring gasket (e.g., O-ring) inserted at least partly into the flow cell frame 5100. In some embodiments, the dispensing guide may include a top portion that extends beyond the top surface 521 of the top substrate 520 with a height 5111, that may be configured to guide insertion of a dispensing tip at least partly into the gasket and / or inlet. In some embodiments, the gasket may sealingly couple with a manifold to allow sealed fluidic connection between the manifold and the flow cell device.

[0241] In some embodiments, the flow cell system 1000 may include a first manifold, e.g., 4500, 6500, configured to facilitate fluidic communication from the reagent cartridge to the flow cell device. In some embodiments, the manifold may include one or more fluidic pathways, e.g., 6110, and one or more openings. In some embodiments, the manifold includes a common line, e.g., 6120, and the one or more openings are at the end branches of the common line. For example, a common line may have 8 end branches, and each end branch has a corresponding opening at a surface of the manifold. In some embodiments, the common line connects at least one of the one or more fluidic pathways via the one or more openings to the inlets of the flow cell device. In some embodiments, the common line has a volume of less than 1 ul, 5 ul, 10 ul, 20 ul, 40 ul, 50 ul, 60 ul, 80 ul, 100 ul, 200 ul, 300 ul, 400 ul or more. In some embodiments, the common line has aAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)volume of less than 10%, 20%, 40%, 60%, or 80% of a second volume of a channel of the one or more channels of the flow cell device. In some embodiments, the manifold includes a solid manifold body that may have a thickness extending along the z axis when it is positioned in the flow cell system. In some embodiments, the one or more fluidic pathways and the common line are defined within the solid manifold body. In some embodiments, the manifold includes a first surface, and the one or more openings are in the first surface, e.g., the bottom surface facing the flow cell device, e.g., FIG. 6A. In some embodiments, the one or more openings are at a bottom surface of the manifold facing the flow cell device. In some embodiments, the one or more openings may each include a protrusion 6130 extending beyond the bottom surface of the manifold, e g., FIG. 6A. The protrusions may be configured to couple to the corresponding dispensing guide or directly couple to the corresponding inlet to enable sealed fluidic communication between the manifold and the flow cell device. In some embodiments, the one or more fluidic pathways may be located at least partly within the thickness of manifold along the z axis.

[0242] In some embodiments, the flow cell system further includes one or more second gaskets, and where the one or more second gaskets are coupled to the one or more openings, e.g., the protrusion. In some embodiments, the second gaskets may be configured to couple to the corresponding dispensing guide or directly couple to the corresponding inlet to enable sealed fluidic communication between the manifold and the flow cell device, (e.g., via pressure applied on the manifold relative to the flow cell device), thereby reducing leakage while the opening(s)s of the manifold and inlet(s) of the flow cell device are in fluidic communication or allow sealing of the fluidic connection therebetween. FIG. 5A shows an exemplary embodiment of the second gaskets 5115 that are coupled to the one or more openings and extending toward the flow cell device. The second gaskets 5115 may be of similar or different size / shape as the gaskets 5115 in FIG.5F, In some embodiments, the pressure applied to press the manifold relative to the flow cell device may be in a range from 0.5 kPa to 200 kPa. In some embodiments, the pressure applied to press the manifold relative to the flow cell device may be in a range from 1 kPa to 100 kPa.

[0243] In some embodiments, the flow cell system 1000 further includes one or more valves configured to enable selective fluidic connection between the one or more fluidic pathways and the common line of the manifold. In some embodiments, the one or more valves includes a rotary valve. In some embodiments, the rotary valve disclosed herein may include various valve designsAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)that allow that controls fluid flow by rotating a movable element (e.g., a rotor or disk) relative to a stationary valve body to selectively connect or disconnect fluidic pathways.

[0244] FIGS. 6A-6C shows an exemplary embodiment of the first manifold 4500. FIGS. 6A is a perspective view of the first manifold coupled to a valve 7001, e.g., a rotary valve. FIG. 6B is a close -up view of the distal end of the valve 7001 and the manifold with a transparent effect to show the fluidic pathways 6110 and the openings. FIG. 6C shows a bottom view of the surface at the cross section of AA’ in FIG. 6B. One end of each of the fluidic pathways may be in fluidic connection with a corresponding reagent compartment in the reagent cartridge or a washing buffer reservoir. Controlled by the valve, the other end of each of the fluidic pathways 6110 may be selectively connected (e.g., via 6111 in FIG. 6C) by the valve to the common line 6120 so that the corresponding fluidic pathway may be in fluidic communication with the common line. When connected with the common line, fluid may flow from one reagent compartment of the reagent cartridge to the connected fluidic pathway and via the valve to the common line. The fluid may exit the common line from all the openings at the end branches to corresponding channels of the flow cell device. In this particular embodiment, the fluids flow simultaneously through the common line to 6 different channels of the flow cell device. The flow rate in the common line or in the one or more channels of the flow cell device may vary depending on the channel size and shape. In some embodiments where each channel may have a volume less than 100 ul, then the flow rate in the common line or the one or more channels may be in a range from 1 ul to 500 ul. In some embodiments where each channel may have a volume less than 100 ul, then the flow rate in the common line or the one or more channels may be in a range from 5 ul to 300 ul.

[0245] In some embodiments, multiple fluidic pathways may be connected to the common line so that fluids from different reagent compartments may be premixed (e.g., at the valve) and flow into the common line. Such premixmg may advantageously save reagent mixing time and improves sequencing efficiency.

[0246] In some embodiments, the common line has a predetermined volume to minimize the dead volume and cross contamination between administration of different reagent in sequence. In some embodiments, the predetermined volume is in a range from 1 ul to 100 ul. In some embodiments, the predetermined volume is in a range from 5 ul to 80 ul. In some embodiments, the predetermined volume is in a range from 10 ul to 60 ul. In some embodiments, to enable flowAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)efficiency and desired flow rate (e.g., more than 100 ul to 500 ul per second), a negative pressure is applied at the outlet(s) of the channels(s) to pull the reagent(s) from the common line into the channels and facilitate fast and efficient transfer of reagent(s) from the common line to the flow cell device. The application of the negative pressure may also advantageously remove residuals of a first reagent in the common line and / or the inlets of the flow cell device (e.g., at the landing area(s)) that may cause cross contamination to the administration of a second reagent thereafter. The negative pressure may be applied via various mechanisms. In some embodiments, the flow cell system further includes one or more pumps in fluidic connection with the flow cell device. In some embodiments, the one or more pumps are configured to pull fluids (e.g., applying negative pressure to the fluids) from the manifold toward the flow cell device, and from the flow cell device to a reservoir (e.g., a waste container). For example, the negative pressure may be applied by one or more pumps 5900 as shown in FIG. 4B. Various pumps including but not limited to syringe pumps may be used.

[0247] In some embodiments, the first manifold, e.g,, 6500 in FIG. 4H, may have a different structure other than the first manifold 4500 in FIGS. 4A-4G. In such embodiments, the first manifold 6500 may couple with one or more channels of the flow cell device via one or more interfaces 6600. In such embodiments, the first manifold 6500 may include a simpler common line 6120__a than the common line 6120 of the first manifold 4500 shown in FIGS.4A-4G. The simpler common line 6120__a may have only one end branch and one opening as shown in FIG. 411. In some embodiments, the first manifold 6500 may be coupled to the flow cell device via the one or more interfaces 6600. Each of the one or more interfaces may include one or multiple end branches that allows fluidic communication from the common line 6120 a to one or more channels. The number of end branches may vary to accommodate flow cell devices with different number of channels or channels with different shapes or sizes. For example, as shown in FIG. 4H, two different interfaces 6600 may be coupled to the manifold 6500 and the flow cell device 4000 to allow fluidic flow from the reagent cartridge to either 4 channels (via the top interface 6600) or 2 channels (via the bottom interface 6600) of the same flow cell device 4000. In some embodiments, different interfaces may each be in the coupling of the manifold 6500 to allow fluidic flow from the reagent cartridge to different flow cell devices (not shown). The interface and the number of end branches can be customized to allow coupling to various numbers of channels in the same or different flow cell devices. The different interfaces herein may advantageously couple to a sameAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)manifold 6500 to allow fluidic communication to flow cell devices with a different number of channels or channels of different shapes and / or sizes. Such combination of different interfaces and the manifold may advantageously facilitate flexibility of fluidic communication from the reagent cartridge to various flow cell devices. Similarly, the fluidic communication via other fluidic pathways, e.g., 6110 a and / or 6110 b in FIGS. 4E-G, may also be flexible to accommodate different number of channels within the same flow cell device or among different flow cell devices via the interface(s) 6600. In some embodiments, the interface may include a first opening, e.g,, 6630_a in FIG. 4H, that may sealmgly couple to a corresponding opening 6130 of the manifold 6500. The interface may include one or more end branches, e.g,, 6621, each branch may be sealingly coupled to an inlet of a corresponding channel of the flow cell device. In some embodiments, the opening(s) of the interface(s) may comprise a gasket to enable sealed fluidic connection with the manifold or the corresponding channel(s). In some embodiments, the interface(s) may be disposable after a sequencing run. In some embodiments, the interface(s) and the flow cell device may be disposable while the manifold (e.g., 6500) may not be disposed, e.g., after a sequencing run. In some embodiments, the interface(s), the manifold, and / or the flow cell device may be disposable, e.g., after a sequencing run.

[0248] In some embodiments, the flow cell system may include a second manifold, e.g., 4590 and 5590. The second manifold may be of different or similar shape and / or size of the first manifold. The second manifold may be coupled to the one or more outlets of the flow cell device as shown m FIGS. 4D and 5B. In some embodiments, the second manifold may include one or more second fluidic pathways that may couple one or more second openings of the second manifold to the outlets of the flow cell device. The one or more second openings may be of similar shape / size as the one or more openings of the first manifold that is configured to couple to the inlets of the flow cell device. In some embodiments, the second manifold may have a common line. In some embodiments, the second manifold may have each of one or more fluidic pathways that are directly m communication to the corresponding openings, and such fluidic pathways may enable fluidic flow independent of other fluidic pathways. As a nonlimiting example, the one or more second fluidic pathways may be parallel to each other and may be connected to a corresponding pump of the one or more pumps 5900 at one end and may have a corresponding opening at the other end. In some embodiments, each of the second fluidic pathway may be connected to a valve that may control the connection and disconnection of the fluidic pathway toAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)the corresponding outlet of the flow cell device. An exemplary valve may be a two-way valve such as a solenoid valve.|00249] In some embodiments, the flow cell device may be at different positions relative to the manifold to enable hybrid fluidic communication, e.g., closed and open fluidic communication to the flow cell device. In some embodiments, the flow cell may be m the closed position. In such closed position, the one or more openings of the manifold are coupled to the one or more inlets of the flow cell device. In such closed position, the distance between the flow cell and manifold is the shortest among all different positions that the flow cell device may have. In some embodiments, the one or more openings of the manifold are coupled to the corresponding dispensing guides of the inlets of the flow cell device. In some embodiments, at the closed position, the one or more opening are sealingly coupled to the one or more inlets (e.g., coupled to the dispensing guides or gaskets coupled to the inlets) so that no liquid leakage is detectable by naked eyes when the flow cell device is in the closed position, A pressure, e.g., along z axis toward the flow cell device, may be applied to the manifold to enable the sealed coupling of the manifold to the flow cell device.FIGS. 4B, 5B and 5D shows the flow cell device 4000, 5000 in the closed position relative to the manifold 4500, 5500. e.g., via a pressure applied at the manifold. The pressure may be of various values that may not cause deformation of the flow cell device. In some embodiments, the pressure may be in a range from 0.01 kPa to 500 kPa. In some embodiments, the predetermined pressure may be in a range from 0.1 kPa to 200 kPa. In some embodiments, the predetermined pressure may be in a range from 1 kPa to 80 kPa.

[0250] In some embodiments, the flow cell device may be in a decoupled position so that the fluidic communication between the manifold and the flow cell device is cut off and the flow cell device only has a displacement along z direction from its closed position. In some embodiments, the decoupled position may be optional. In some embodiments, the one or more openings of the manifold are configured to be at a first distance only along a first direction to the one or more inlets when the flow cell device is in the decoupled position. The first distance may be at least along the z axis. The first distance may include at least a z component that is greater than zero. The first distance may only be along the z axis. The first distance may be in a range from 0.1 mm to 10 cm. The first distance may be in a range from 0.1 mm to 5 cm. The first distance may be in a range from 2 mm to 3 cm. The first distance may be in a range from 2 mm to 2 cm. FIGS. 5A, and 5E show exemplary embodiments of the flow cell device 5000 in the decoupled position. The firstAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)distance in the embodiment shown in FIGS. 5 A and 5E is only along z axis, i.e., only with a z component, dl __z, which is greater than zero. In some embodiments, when in the decoupled position, the manifold may at least partly obstruct access to the inlets from the z direction, e.g., by a dispensing tip of the dispensing device. In some embodiments, when in the decoupled position, the manifold may obstruct access to all the inlets from the z direction as shown in FIGS. 5A and 5E. For example, a dispensing tip, e.g., a pipette tip or dispensing tip, may not be able to access any of the inlets from above the inlets (or from any direction that has a z-direction component) in the decoupled position,

[0251] In some embodiments, the flow cell device may be at an open position. In embodiments when the flow cell device is in an open position, the one or more openings of the manifold are at a second distance at least along a second direction to the one or more inlets of the flow cell device. The second direction is different from the first direction. The second direction may be orthogonal to the first direction. FIGS.4A, 4C and 5C show exemplary embodiments of the flow cell device 4000, 5000 in the open position relative to the manifold 4500, 5500. In the open position, some or all of the inlets of the flow cell device may not be obstructed by the manifold from access along the z direction. In some embodiments, the flow cell device may have multiple open positions so that a different number of inlets may be exposed for access along z axis, e.g., by a pipette tip. For example, the flow cell device may move from a decoupled position in FIG. 5A to a first open position (e.g., a first stop point along the mounting rail) in which only the right most inlet is not obstructed by the manifold, and a dispensing tip may dispense a library preparation reagent into the right most inlet via open dispensing. After that, the manifold may move to a second open position (e.g., a second stop point along the mounting rail) in which all 6 inlets are not obstructed by the manifold along z direction as shown in FIG. 5C, a dispensing tip array of 2 to 5 tips may simultaneously administer a different library preparation reagent into the corresponding 2-5 inlets but not the right most inlet. As another example, a single dispensing tip may sequentially dispense a same reagent into multiple inlets by moving the flow cell at multiple open positions (e.g., multiple stop point along the mounting rail), and at each open position, the dispensing tip may access an individual inlet along z axis by at least partly inserting into the individual inlet. Since the movement of the flow cell and the dispensing tip(s) can be relative, instead of moving the flow cell at multiple positions along the mounting rails while keep the pipette tips fixed to the fluidic station or housing of the sequencing system, the flow cell may be at a single open position, e.g.Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WO)shown in FIGS.4A, 4C and 5C, and the dispensing tips may move from inlet to inlet in a sequence for dispensing same or different reagents to the inlets.

[0252] Referring to FIG. 4A, in the open position, the first distance is along z axis, and the second distance is along y axis, i.e., with a y component d2_y. The second distance in the embodiment in FIG.4A may also have an x component (not shown). In this embodiment, as shown in FIG. 4A, the manifold may not obstruct access to any the inlets from the z direction by the dispensing tips.

[0253] In embodiments where the flow cell device may be in an open position relative to the manifold. At the open position, the distance between the flow cell device and manifold may include at least a first distance along z and a second distance along a direction within x-y plane. In such embodiments, the access to the flow cell device via some or all of its inlets along z axis is not obstructed by the manifold, e.g., FIG. 4A.

[0254] In some embodiments, the flow cell device may have only a closed position (e.g,, FIG.4B) and an open position (FIG. 4A), but not any decoupled position separate from the open positions as shown in FIGS. 5A and 5C (the decoupled position may be only with only z displacement between the flow cell device and the manifold from each other). However, having a decoupled position including only a first distance along z axis ( which is not also an open position) may simplify control and actuation of movement of the manifold / flow cell device from the closed position to the decoupled position (e.g., only along z axis) and from the decoupled position to the open position (e.g., only within x-y plane) thus reducing system complexity, cost, and reliability.

[0255] In some embodiments, the manifold is configured to move at least along the z direction bi-directional relative to the flow cell device, e.g., from the closed position to the decoupled position or open position. In some embodiments, the manifold is configured to move at least along the z direction bi-directional relative to a fluidic station. In some embodiments, the manifold is configured to move at least along the z direction bi-directional relative to a housing of the flow cell system.

[0256] In some embodiments, movement of the manifold may be actuated using various mechanisms including but not limited to magnetic or electromagnetic forces, pneumatic forces, and mechanical forces. For example, a spring may be used to bias the manifold toward a decoupled position, and a magnetic or mechanical force may be used to move the manifold to the closedAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)position. In some embodiments, movement of the manifold may be actuated using similar mechanisms as that for actuation of the flow cell device. Nonlimiting examples of the mechanisms may include a continuous track, a belt, a slidable stage, a screw, gears, magnets, etc.

[0257] In some embodiments, the flow cell device is configured to move at least along a direction bi-directionally within an x-y plane relative to the manifold, the fluidic station, or the housing of the sequencing system. In some embodiments, the flow cell device is configured to move at least along a z direction bi-directionally relative to the manifold, the fluidic station, or the housing of the sequencing system.

[0258] In some embodiments, the manifold is configured to move at least along a direction within the x-y plane or along a direction in 3D bi-directional relative to a fluidic station to switch between two different positions, e.g., from the closed position to the open position. In some embodiments, the manifold is configured to move at least along a direction within the x-y plane along a direction in 3D bi-directional relative to a housing of a sequencing system comprising the flow cell system to switch between two different positions. In some embodiments, movement of the manifold is relative to the flow cell device, the fluidic station, or the housing.

[0259] In some embodiments, the manifold moves when the flow cell device remains still relative to the fluidic station or housing to switch between two different positions. In some embodiments, the flow cell device moves when the manifold remains still relative to the fluidic station or housing to switch between two different positions. In some embodiments, both the flow cell device and manifold moves relative to the fluidic station or housing to switch between two different positions.

[0260] In some embodiments, since the movement of the flow cell device and manifold is relative, one or both of them may move in ID, 2D, or 3D relative to the fluidic station or the housing to result in separation of the flow cell device and the manifold, e.g., by the first distance or second distance. In some embodiments, since the movement of the flow cell device and manifold is relative, one or both of them may move in ID, 2D, or 3D relative to the fluidic station or the housing to result m switching of the flow cell device between two different positions relative to the manifold.

[0261] In some embodiments, the distance (e.g., first distance) is greater than 1 mm, 2 mm, 5 mm, 8 mm, 10 mm, 12 mm, 15 mm, 18 mm, 20 mmm or more. In some embodiments, the one orAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)more openings are configured to be at a second distance at least along a direction at least within the x-y plane relative to the one or more inlets when the flow cell device is in an open position. In some embodiments, the second distance is at least 2x, 4x, 6x, 8x, 10x, 15x, 20x, 30x, 40x, or 50x greater than the first distance. In some embodiments, the second distance may vary depending on the size and shape of the flow cell device. In some embodiments, the second distance is at least 0.2 cm, 0.5 cm, 1 cm, 2 cm, 4 cm, 6 cm, 8 cm, 10 cm, 15 cm, 20 cm, 30 cm, or greater.

[0262] FIG. 4C shows an exemplary second distance that has at least an x component, d2_x. The second distance in this embodiment may also have an y component (not shown). FIG. 5C shows an exemplary second distance that has at least an x component, d2 x. In some embodiments, the x and / or y component of the second distance is at least 2x, 4x, 6x, 8x, 10x, 15x, 20x, 30x, 40x, or 50x greater than the first distance.

[0263] In some embodiments, the first distance may be zero or close to zero (e.g., less than 1 mm, 0.5 mm, or 0.2 mm) at least along the z direction. In some embodiments, the first distance may be zero or close to zero, and the difference between the closed position and the decoupled position may be in the pressure applied to the manifold relative toward the flow cell device. In some embodiments, the pressure that applied to the manifold and / or flow cell device may be completely removed to switch the flow cell device from the closed position to the decoupled position. In some embodiments, at least 99% 90%, 80%, 70% 60%, 50%, or 40% of the pressure that is applied to the manifold and / or flow cell device at the closed position may be removed so that the flow cell device may switch from the closed position to the decoupled position. Although in embodiments herein pressure may be applied only to the manifold toward the flow cell device, it is worth nothing that it is equivalent to apply pressure to the flow cell device only, or to the flow cell device and the manifold to arrive at the same closed position of the flow cell device and the same sealed coupling of the inlets and the openings.

[0264] The top portion of the dispensing guide may couple with a matching gasket coupled to the openings of the manifold or the protrusions of the openings to form a sealed fluidic communication between the manifold and the flow cell device. The matching gasket or protrusion may also have a matching top portion extending beyond a bottom surface of the manifold along the z -axis, e.g., 5115 m FIG. 5A, that facilitate the sealed coupling of the dispensing guide of the flow cell device and the gasket of the manifold.Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)|00265] In some embodiments, the flow cell device further includes one or more cleaning outlets, and where each cleaning outlet corresponds to a corresponding inlet of the one or more inlets of the flow cell device and is in fluidic connection therewith. Exemplary’ embodiments of the cleaning outlet are shown in FIGS. 2C and 2G. In some embodiments, the flow cell device may comprise at least a cleaning outlet that may correspond to multiple inlets of the flow cell device and is in fluidic connection therewith. The cleaning outlet may be configured to remove residual left in the inlet, e.g., on the landing area, to avoid contamination of a subsequently administered reagent via the inlet to the one or more channels.

[0266] In some embodiments, the flow cell device 4000, 5000 lacks any cleaning outlet, e.g., as shown in FIGS. 2C and 2G. As a non-limiting example, FIG. 5F shows a cross section of the flow cell device 5000 without any cleaning outlet.

[0267] In some embodiments, the flow cell device may be in a by-pass position relative to the manifold as shown m FIG. 41). In the by-pass position, the flow cell device may be at the same location as in the open position, but the difference from the open position is that the manifold is in fluidic communication with the by-pass reservoir 4591, and fluids may flow from the manifold into the by-pass reservoir by-passing the flow cell device. In such embodiments, the manifold may be primed or washed with various fluids, e.g., buffer(s) and / or reagent(s), and such fluids may be collected to a waste container 4595. The one or more pumps may apply a negative pressure to pull the fluids from the manifold toward the by-pass reservoir 4591 and the waste reservoir 4595. The by-pass reservoir may include ports that are similar to the inlets of the flow cell device to enable sealed coupling to the openings of the manifold. Relative movement of the manifold to the by-pass reservoir may be enabled by motors or driving mechanisms similar to those disclosed herein elsewhere. For example, the by-pass reservoir may travel along the same mounting rails as the flow cell device or stay at the same location within the x-y plane. The manifold may move at least along the z direction to sealingly couple with the by-pass reservoir.

[0268] In some embodiments, the by-pass reservoir may be positioned within a same x-y plane as the flow cell device, e.g., as shown in FIG.4E. In some embodiments, moving the flow cell out of coupling along the mounting rails simultaneously moves the by-pass reservoir 4591 toward the manifold 4500 so that the by-pass reservoir 4591 may be coupled to the manifold allowing priming, washing, or otherwise fluidic communication therebetween while by-passing the flow cell device,Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)e.g., as shown in FIG. 4E. In such embodiments, the flow cell device and the by-pass reservoir may be m a relative fixed position with respect to each other along x, y, and z directions.|00269] In some embodiments, the by-pass reservoir may be positioned at a different z level as the flow cell device. For example, the by-pass reservoir may be positioned underneath the flow cell device. FIG. 41 shows cross sectional view of an exemplary embodiment of the flow cell device 4000, the first manifold 4500, the second manifold 4590, and the by-pass reservoir 4591. The cross sections in FIG. 41 are at one channel of the flow cell device. The flow cell device is in a decouple position relative to the first manifold as shown in the top panel of FIG. 41. The flow cell device is in a closed position relative to the first manifold as shown in the middle panel of FIG. 41. The flow cell device is in an open position relative to the first manifold as shown in the bottom panel of FIG. 41,

[0270] During sequencing, the manifold 4500 may be coupled to the flow cell device 4000 as disclosed herein, e.g., in the closed position as shown in FIG 4B and in the middle panel of FIG.41. In such position, the by-pass reservoir is not fluidically connected to the first manifold and / or the second manifold. In such position, the flow cell device is not fluidically connected to the bypass reservoir. In some embodiments, the flow cell device 4000 may be moved from the decoupled position to the open position, e.g., after a sequencing cycle, or completion of a sequencing run. The gasket(s) 4313 attached to the flow cell device 4000 may move along with the flow cell device. In some embodiments, moving the flow cell device out of coupling along the mounting rails within the x-y plane does not move the by-pass reservoir 4591 at least within the x-y plane. After moving flow cell device along the mounting rails (e.g., to the open position), the flow cell device is not located between the manifold 4500 and the by-pass reservoir, and the by-pass reservoir 4591 may be coupled to the manifold to allow priming, washing, or otherwise fluidic communication therebetween while by-passing the flow cell device, e.g., as shown in the bottom panel of FIG. 41. In some embodiments, the manifold 4500 may move along the z direction relative to the by-pass reservoir to enable coupling therebetween. In some embodiments, the manifold 4500 may move along the z direction relative to the housing of sequencing system while the by-pass reservoir may remain in a fixed position relative to the housing of the sequencing system. In some embodiments, the by-pass reservoir may move along the z direction relative to the housing of sequencing system while the manifold may remain in a fixed position relative to the housing of the sequencing system to allow coupling of the manifold to the by-pass reservoir as shown in the bottom panel of FIG.Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)41.

[0271] To enable coupling shown in the bottom panel of FIG. 41, the manifold (e.g., first manifold 4500 or second manifold 4590) or the by-pass reservoir 4591 may move relative to each other along z direction. In some embodiments, the coupling of the manifold to the by-pass reservoir may include one or more gaskets 4313 to enabling sealed fluidic communication in between. In some embodiments, the one or more gasket may include gasket(s), e.g., 4599, attached to the by¬ pass reservoir. In some embodiments, the coupling between the manifold and the by-pass reservoir may be formed using various mechanisms including but not limited to mechanical pressuring along z direction and clamping along z direction and / or x-y plane. In some embodiments, the flow cell device 4000 is in the open position relative to the first manifold 4500 when the first manifold (and the second manifold 4590) is coupled to the by-pass reservoir (e.g., as shown in FIGS. 4D and 41). In some embodiments, the flow cell system 1000 may further comprise one or more fluid pathways, e.g., 6110_a and / or 6110_b in FIGS.4E-4G, that is independent to the fluidic pathways 6110 of the manifold disclosed herein. Such fluidic pathway(s) may be utilized independent of the manifold and its corresponding fluidic pathways 6110 therewithin. Such fluidic pathway(s) may comprise at least part of the common line and the one or more openings of the manifold, e.g., 6120 and 6130 in FIGS.4E and 4G. Such fluidic pathway] s) may be at least partly external to the manifold to enable flexibility in connection to various sources of reagent(s) or otherwise fluidic solutions different from the fluidic sources (e.g., reagent cartridge) in fluidic communication with the fluidic pathways 6110. In some embodiments, such fluidic pathway(s) may be at least partly within the manifold or completely within the manifold to enable compact and efficient fluidic communication. Such fluidic pathway(s) may be utilized for one or more functions that are different from the function(s) of allowing closed and sealed fluidic communication to the flow cell device from the reagent cartndge(s), which is a function of the fluidic pathways 6110 of the manifold.

[0272] In some embodiments, the flow cell system 1000 may further comprise the fluid pathway, e.g., 6110 a in FIGS. 4E-4F, that is independent to the fluidic pathways 6110 of the manifold disclosed herein. In some embodiments, the fluidic pathway 6110 a may be connected to an open port 6118 a configured to enable flow of fluids to the fluidic pathway 6110 a. The open port may be coupled to a gasket to enable sealed fluidic connection with a dispensing tip, e.g., the dispensing tip shown in FIGS. 3A, 3C and 5F. The fluidic pathway 6110 a may beAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)connected to the one or more valves 7001, e.g., the rotary valve, so that the fluids may flow via the fluidic pathway 6110 a to the flow cell device in a controlled manner via control by the one or more valves. For example, the rotary valve may connect the fluidic pathway 6110 a to the common line 6120 of the manifold, thus allowing flow of fluids entering the open port 6118 a to simultaneously go into the one or more channels of the flow cell device, e.g., as shown in FIG.4G. In some embodiments, the fluidic pathway 6110_a enables fluids introduced by the dispensing tip via the open port 6118 to go through the manifold 4500 and arrive at the one or more channels of the flow device at the same time. In some embodiments, the fluidic pathway external to the manifold 6110_a may allow simultaneous fluidic flow to the channels of the flow cell device from a source that is different from the reagent cartridge. For example, the source can be various reagent(s), buffer, or otherwise fluids that may be introduced through the open port 6118_a. In comparison to fluidic communication via the dispensing tip(s) in the open position in FIG. 4D, introduction of reagents from the open port 6118 and the fluidic pathway 6110_a can be faster (without the need to move a dispensing tip from one channel to another for dispensing) and more efficient (without the need to use multiple dispensing tips to enable simultaneous fluidic delivery to multiple channels). Further, in comparison to fluidic communication via the dispensing tip(s) in the open position in FIG. 4D, such fluidic delivery may occur in the closed position (e.g., FIG.4F) but not in the open position, therefore removing the need to move the manifold and the flow cell device from the closed position to the open position. The fluidic pathway 6110 a may be used in the open position to allow fluidic flow from the open port 6118 a to wash or prime the fluidic pathway similar as the one or more fluidic pathways of the manifold 4500, e.g., in FIG. 4F. |00273] In some embodiments, the fluidic pathway 6110 a external to the manifold 4500, 6500 may help reduce variation in fluid delivery from the open port 6118 a to the one or more channels of the flow cell device in comparison to dispensing individually via dispensing tip(s) to the channels at the open position. For example, the variation in reagent flow rate, flow speed, spatial distribution of reagent concentration across the channel may be reduced when the reagent is introduced into the flow cell device via the fluidic pathway 6110 a external to the manifold 4500, e.g., simultaneously during RCA.

[0274] In some embodiments, the open port 6118_a may have a funnel shape. The funnel shape may have variously-sized top opening, and the bottom opening of the funnel shape may match the opening size and shape of the open port 6118_a. The funnel shape may extend along the z directionAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)from the open opening to the bottom opening. The size and volume of the funnel shape may be customized based on the volume of the one or more fluidic pathways of the manifold and / or the size and volume of the channels of the flow cell device. For example, the funnel shape may have a size to hold a volume of fluids that is greater than the volume of the fluidic pathways of the manifold so that the volume is sufficient to wash or prime the manifold. As another example, the funnel shape may have a size to hold a volume of fluids that is greater than the total volume of channels in the flow cell device so that the volume is sufficient to wash the flow cell device. As yet another example, the funnel shape may have a size to hold a volume of fluids that is greater than a required volume of reagents for all channels in the flow cell device, so that the volume is sufficient to deliver the reagent during sequencing.

[0275] In some embodiments, the funnel shape may allow a dispensing tip (or other open fluidic delivery) to deliver a bolus of fluid(s) therewithin, and fluidic transmission for priming the manifold when the flow cell device is not in the closed position, FIG. 4E shows an exemplary embodiment of using the open port 6118_awith the funnel shape to temporarily hold fluids after the fluids are dispensed in the funnel. The fluids in the funnel may then exist the funnel to enter into the fluidic pathways of the manifold, via various driving forces including but not limiting to gravity, positive pressure applied to the funnel, and negative pressure applied via the fluidic pathways (e.g., via a vacuum)

[0276] In some embodiments, the open port 6118 a may have a funnel shape that may allow a dispensing tip to deliver a bolus of fluid(s) therewithin and deliver of fluid(s) into the flow cell device when the flow cell device is in the closed position. FIG. 4F shows an exemplary- embodiment of using the open port 6118a with the funnel shape to temporarily hold fluids after the fluids are dispensed in the funnel. The fluids in the funnel may then exist the funnel to enter into the fluidic pathways of the manifold, via various driving forces including but not limiting to gravity, positive pressure applied to the funnel, and negative pressure applied via the fluidic pathways (e.g., via a vacuum).

[0277] In some embodiments, the flow cell system 1000 may further comprise a fluid pathway, e.g., 6110 b in FIGS. 4G, that is independent to the fluidic pathways 6110 of the manifold disclosed herein. In some embodiments, the fluidic pathway 6110_b may be connected to a closed port 6118 b configured to enable flow of fluids to the fluidic pathway in a closed and sealedAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)manner (e.g., airtight). The closed port 6118 b may be connected to a fluidic source to enable sealed fluidic connection to the flow cell device independent of the manifold and its corresponding fluidic pathways 6110. The fluidic pathway 6110 b may be connected to the one or more valves 7001, e.g., the rotary valve, so that the fluids may flow via the fluidic pathway 6110 b to the flow cell device in a controlled manner via control by the one or more valves. For example, the rotary valve may connect the fluidic pathway 6110__b to the common line of the manifold, thus allowing flow of fluids, e.g., air entering from the source to simultaneously go into the one or more channels of the flow cell device in a sealed manner. In some embodiments, the fluidic pathway 6110_b may be used for various functions before or during sequencing. For example, the fluidic pathway 6110_b and the closed port 6118_b may be used in sealed connection with a source to detect air and / or l iquid leakage in one or more of: the common line 6120, the coupling of the manifold 6500 to the flow cell device, and the one or more channels before starting a sequencing run. Such leakage detection may also be used after a new flow cell is manufactured or assembled or after an error in sequencing has been detected that may be caused by leakage during a sequencing run. In some embodiments, such leakage detection may be when the manifold is in the closed position (e.g., in FIG. 4G) and / or in the open position (not shown).

[0278] In some embodiments, the flow cell system 1000 further includes one or more mounting rails configured to allow moveable mounting of the flow cell device thereon.

[0279] Exemplary embodiments of the mounting rails are shown as 4810, 5200, 5810 in FIGS.4G, 5A and 5C. In some embodiments, the flow cell system 1000 may comprise a motor that actuates the flow cell device to move along the mounting rails. Various moving mechanisms may be used to move the flow cell device along the mounting rails when driven by a motor or an actuator. Nonlimiting examples of the mechanisms may include a continuous track, a belt, a slidable stage, a screw, gears, a spring, a magnet, an electromagnet, etc. FIG. 5C shows a lead screw and threaded nut 5820 that when rotates by a motor, translate the flow cell device along the mounting rails within the x-y plane.

[0280] In some embodiments, the flow cell frame is configured to contain the flow cell device at least partly therewithin. In some embodiments, the flow cell system further includes a flow cell carrier configured to: hold the flow cell frame or the flow cell device in a fixed position relative to the carrier; and move in 1 dimension, 2 dimensions, or 3 dimensions relative to a housing of aAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)sequencing system comprising the flow cell system. FIGS. 5A-5C shows an exemplary embodiment of the flow cell frame 5100 and flow cell carrier. In some embodiments, the flow cell frame includes one or more alignment holes 5112(FIGS. 5 A and 5C) configured to couple to one or more protrusions (not shown) on the flow cell carrier 5310. In some embodiments, the flow cell frame includes one or more alignment holes configured to couple to one or more protrusions (not shown) on the flow cell device. In some embodiments, the flow cell frame may include a cover that may open to receive the flow cell device at least partly therewithin. In some embodiments, the one or more gaskets are coupled on the flow cell frame, the flow cell carrier, or both to enable sealed coupling of the one or more openings of the manifold to the one or more inlets of the flow cell device. In some embodiments, the one or more mounting rails are configured to allow moveable mounting of the flow cell carrier along with the flow cell device at least partly within the flow cell frame. In some embodiments, the flow cell device, the flow cell frame, and the flow cell carrier may be disposable after a sequencing run. In some embodiments, one or more of the flow cell device, the flow cell frame, and the flow cell carrier may be disposable after a sequencing run.

[0281] In some embodiments, disclosed herein is the flow cell system comprising: a flow cell device comprising: one or more channels defined by one or more substrates, where the one or more channels are configured to allow fluids to flow therethrough and to allow a bolus of gas to flow therethrough between one or more of the fluids; one or more inlets in the one or more substrates and in fluidic connection with the one or more channels; and one or more outlets in the one or more substrates and in fluidic connection with the one or more channels; and a manifold comprising: one or more fluidic pathways; one or more openings that can be in fluidic connection with the one or more fluidic pathways (e.g., enabled and controllable by a valve in between them), where the one or more opening are configured to couple to the one or more inlets when the flow cell device is a closed position, and where the one or more inlets are configured to receive open administration of fluid when the flow cell is in an open position, and where the open administration of fluid is not blocked by the one or more openings at least along a first direction at the open position.

[0282] In some embodiments, disclosed herein is the flow cell system comprising: a flow cell device comprising: one or more channels defined by one or more substrates, where the one or more channels are configured to allow fluids to flow therethrough and to allow a bolus of gas to flowAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)therethrough between one or more of the fluids; one or more inlets in the one or more substrates and in fluidic connection with the one or more channels; and one or more outlets in the one or more substrates and in fluidic connection with the one or more channels; and a manifold comprising: one or more fluidic pathways; one or more openings in fluidic connection with the one or more fluidic pathways (e.g., such connection may be enabled and controlled by a valve in between); one or more motors configured to move the flow cell device to be in a closed position, optionally a decoupled position, and an open position relative to the manifold, where the one or more motors spatially displace the one or more openings from the one or more inlets in a first direction; and where the one or more motors spatially displace the one or more openings from the one or more inlets in a second direction orthogonal to the first direction.

[0283] In some embodiments, the sequencing system herein may further comprise the fluid storage device (e.g., reagent cartridge) having one or more fluidic compartments. In some embodiments, at least one of the one or more fluidic compartments contains a cycling reagent for sequencing or a washing buffer. In some embodiments, at least one of the one or more fluidic compartments lacks any non-cycling reagent for sequencing. In some embodiments, at least one of the one or more fluidic compartments contains at least a non-cycling reagent for sequencing. In some embodiments, the manifold, the fluidic storage device, or both are disposable, e.g., after a sequencing run.Methods of using the hybrid flow cell systems

[0284] In some embodiments, disclosed herein are methods of using the flow cell system for hybrid fluidic communication with reagents or other fluids, e.g., during a sequencing run in one or more sequencing cycles. In some embodiments, the method of using the flow cell system for hybrid fluidic communication may comprise performing a sequencing run with one or more sequencing cycles comprising one or more operations disclosed herein. In some embodiments, one or more operations are within a same or different sequencing cycles of the sequencing run.

[0285] In some embodiments, the sequencing system, e.g., 100 in FIG. 1, herein may comprise one or more hardware processors; one or more data storage devices storing instructions executable by the one or more hardware processors to cause the one or more hardware processors to control or perform one or more operations.Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)

[0286] The methods disclosed herein can include some or all of the operations disclosed herein. The operations may be performed in but is not limited to the order that is described herein.

[0287] The methods can be performed or controlled by one or more processors disclosed herein. In some embodiments, the processor can include one or more of: a processing unit, e.g., a CPU, a reconfigurable logic device, an integrated circuit that is not reconfigurable, or their combinations. For example, the processing unit can include a central processing unit (CPU). The reconfigurable logic device can include one or more FPGA devices. The integrated circuit can include a chip such as an Al chip or an ASIC chip.

[0288] An exemplary embodiment of the method of using the flow cell system 1000 for hybrid fluidic communication is shown as 7000 in FIG. 7. In some embodiments, the method 7000 may include an operation 7010 of (a) coupling one or more inlets defined in the one or more substrates of a flow cell device to one or more openings of a manifold so that the flow cell device is in a closed position. In some embodiments, the operation 7010 of (a) coupling one or more inlets defined in the one or more substrates of a flow cell device to one or more openings of a manifold so that the flow cell device is in a closed position includes: moving the one or more inlets of the flow cell device relative to the one or more openings; and pressing the one or more inlets of the flow cell device to the one or more openings to form a sealed coupling. In some embodiments, pressing the one or more inlets of the flow cell device to the one or more openings to form a sealed coupling is using relative pressure of the manifold on the flow cell device. The pressure may be of various values that may not cause deformation of the flow cell device. In some embodiments, the pressure may be in a range from 0.01 kPa to 500 kPa. In some embodiments, the predetermined pressure may be in a range from 0.1 kPa to 200 kPa. In some embodiments, the predetermined pressure may be in a range from 1 kPa to 80 kPa.

[0289] In some embodiments, the method 7000 may include an operation 7020 of (b) flowing fluid from a fluidic storage device toward one or more channels defined in the one or more substrates of the flow cell device via one or more fluidic pathways of the manifold and via the coupling of the one or more inlets and the one or more openings.

[0290] In some embodiments, the operation 7020 of (b) flowing fluid from a fluidic storage device toward one or more channels defined in the one or more substrates of the flow cell device via one or more fluidic pathways of the manifold and via the coupling of the one or more inletsAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)and the one or more openings include: fluidically connecting at least one of the one or more fluidic pathways in the manifold to the common line in the manifold via a valve; and flowing the fluid from the fluidic storage device to the one or more channels of the flow cell device via one or more fluidic pathways of the manifold, the common line, and the coupling of the one or more inlets and the one or more openings so that at least a first volume of fluids exit the fluid storage device. In some embodiments, one or multiple fluidic pathways may be connected simultaneously to the common line using the valve, e.g., a rotary valve.

[0291] In some embodiments, the operation 7020 of (b) flowing fluid from a fluidic storage device toward one or more channels defined in the one or more substrates of the flow cell device via one or more fluidic pathways of the manifold and via the coupling of the one or more inlets and the one or more openings include: flowing fluid from a fluidic storage device toward one or more channels while simultaneously applying a negative pressure via the one or more outlets of the flow cell device via one or more pumps,

[0292] In some embodiments, the method 7000 may include an operation 7030 of (c) decoupling the one or more inlets of the flow cell device from the one or more openings of the manifold by moving the one or more openings away from the one or more inlets at least in a first direction so that the flow cell device is in a decoupled position.

[0293] In some embodiments, the method 7000 may include an operation 7040 of (d) moving the one or more inlets of the flow cell device relative to the one or more openings at least in a second direction orthogonal to the first direction so that the flow cell device is in an open position relative to the manifold.

[0294] In some embodiments, the operation 7040 of (d) moving the one or more inlets of the flow cell device relative to the one or more openings at least in a second direction orthogonal to the first direction so that the flow cell device is in an open position relative to the manifold includes: moving the flow cell device along the one or more mounting rails from a start point to a first stop point so that at least one of the one or more inlets are not obstructed by the manifold along a z direction. In some embodiments, the operation 7040 of (d) further includes moving the flow cell device along the one or more mounting rails from a first stop point to a second stop point so that at least one of the one or more inlets are not obstructed by the manifold along a z direction. For example, the start point may be when the flow cell is in a decoupled position as shown in FIG.Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)5A, the flow cell device may move toward the right in FIG. 5A to expose at least one inlet, at the first stop point, to allow access to the exposed inlet by a dispensing tip at least along a z direction. The flow cell device may then move to a second stop point, e.g., as shown in FIG. 5C, where all the inlets are exposed and allow access by dispensing tips at least along a z direction for dispensing reagents therefrom to the channels. In this example, the second stop point is when the flow cell device is at the open position.

[0295] In some embodiments, instead of operation 7040, the method may include an operation of moving the flow cell device relative to the manifold to be in an open position, where access of the one or more inlets of the flow cell device along z direction is not blocked by the manifold when the flow cell device is in the open position.

[0296] In some embodiments, the method 7000 may include an operation 7050 of (e) dispensing, using one or more dispensing tips of a fluidic dispensing device, one or more types of fluids via the one or more inlets to the one or more channels of the flow cell device.

[0297] In some embodiments, the operation 7050 of (e) dispensing, using one or more dispensing tips of a fluidic dispensing device, one or more types of fluids via the one or more inlets to the one or more channels of the flow cell device include: inserting the one or more dispensing tips at least partly through the gaskets or dispensing guides of the one or more inlets; and simultaneously dispensing one or more types of fluids via the one or more inlets to the one or more channels of the flow cell device. In some embodiments, the operation 7050 of (e) dispensing, using one or more dispensing tips of a fluidic dispensing device, one or more types of fluids via the one or more inlets to the one or more channels of the flow cell device include: (1) inserting one of the one or more dispensing tips at least partly through a corresponding gasket of one of the one or more dispensing tips; (2) pressing one or more dispensing tips of the fluidic dispensing device toward the dispensing guide to form a sealed coupling between the dispensing tip and the dispensing guide; (3) dispensing one or more types of fluids via the one inlet to a corresponding channel of the flow cell device; and repeating (1) (2), and / or 3 for one or more repetitions, each repetition for a same or different inlet of the one or more inlets of the flow cell device. For example, a single dispensing tip may be used to sequentially dispense a same reagent or fluid to multiple inlets of the flow cell devices. As another example, a first dispensing tip may be used to firstly dispense a first reagent or fluid to one or more inlets of the flow cell device, and a secondAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)dispensing tip may be used to then dispense a second reagent or fluid to one or more different inlets of the flow cell device. In some embodiments, the distal end of the dispensing tip (the end toward the flow cell device) is above the top surface of the top substrate of the flow cell device. In some embodiments, the distal end of the dispensing tip (the end toward the flow cell device) is below the top surface of the top substrate of the flow cell device. In some embodiments, the distal end of the dispensing tip is above the top surface of the top substrate of the flow cell device. In some embodiments, the dispensing tip is at least partly inserted into the dispensing guide to form the sealed coupling. In some embodiments, the pressure to press the dispensing tip on the dispensing guide is in a range from 0.1 kPa to 500 kPa, In some embodiments, the pressure to press the dispensing tip on the dispensing guide is in a range from 0,5 kPa to 200 kPa.

[0298] In some embodiments, the method 7000 may include an operation 7060 of (f) repeating one or more operations of operations 7010 to 7050, e.g., (a) to (e), for at least one time. In some embodiments, operations 7010-7060 occurs within a single sequencing cycle of a sequencing run. In some embodiments, operations 7010-7050 occurs within a single sequencing cycle of a sequencing run.

[0299] In some embodiments, the method 7000 and one or more of the operations 7010-7060 may be performed (a) to (f) while the flow cell device is positioned on a fluidic station or a nest bank. In some embodiments, the method 7000 and all of the operations 7010-7060 may be performed while the flow cell device is positioned on a fluidic station or a nest bank. It is advantageous to keep all the operations of method 7000 to be on the fluidic station or nest bank to avoid contamination or damage to the imaging station. In some embodiments, the method 7000 may further include an operation of controlling a temperature, using a thermal module of the fluidic station or nest bank, of the flow cell device while the flow cell device is on the fluidic station or nest bank.

[0300] In some embodiments, the method 7000 further include: aspirating at least a portion of the fluids flew toward the one or more channels back toward the fluidic storage device so that at least a second volume of fluids travels back to the fluidic storage device. In some embodiments, the second volume is at least 30% to 90 % of the first volume.

[0301] In some embodiments, the one or more types of fluids in method 7000 include a noncycle reagent for sequencing. In some embodiments, the one or more types of fluids include aAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)library preparation reagent. In some embodiments, the one or more types of fluids include a paired end sequencing reagent. In some embodiments, the one or more types of fluids lacks any washing buffer or cycling reagent.

[0302] In some embodiments, the method 7000 may further include an operation of moving the flow cell device, the flow cell frame, and the flow cell carrier together as a unit from the fluidic station or nest bank to an imaging station so that the sample(s) immobilized on the flow cell device may be imaged. In some embodiments, the manifold stays still relative to the fluidic station or the housing while the flow cell device is moved to the imaging station.

[0303] In some embodiments, the method 7000 may further include an operation of moving a stage, e.g., the x-y stage, of the imaging station and flow cell device fixed thereon relative to an optical system of a sequencing system to allow positioning a region of interest of the sample(s) to be in focus and ready to be imaged,

[0304] In some embodiments, the method 7000 may further include an operation of imaging one or more samples of the flow cell device using the optical system while flowing fluid to a second flow cell device on the fluidic station or nest bank. The sequencing systems herein, e.g., 100 in FIG, 1, advantageously allow fluidic communication needed before imaging to be handled at the fluidic station of the second flow cell device whiting imaging of the flow cell device at the imaging station. The flow cell device at the image station may have completed fluidic preparation for imaging at the fluidic station. The sequencing systems herein may advantageously increase system efficiency, throughput, and enable separation the fluidic manipulation from the imaging station to keep the imaging station dry and clean to avoid damages or contamination.

[0305] In some embodiments, the method 7000 further include: positioning a second flow cell device on the fluidic station, while the second flow cell device is in the open position or decoupled position; and moving the second flow cell device relative to the manifold so that the second flow cell device is in the closed position and ready for fluidic communication with the fluid storage device.Coatings

[0306] In some embodiments, the flow cell device, e.g., 200, 300, the dispensing guide, and / orAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)the one or more dispensing tips may be at least partly coated with a coating. The coating may be a hydrophobic coating. The coating may be a slippery coating. The coating may facilitate transfer of fluids on the coating comparing with the surfaces / structures without the coating.

[0307] In some embodiments, the flow cell device, e.g., 200, 300, the dispensing guide, and / or the one or more dispensing tips may lack any coating disclosed herein. For example, the landing area 241 of flow cell device 200 may lack any hydrophobic or slipper coating in order to reduce residual or dead volume build up.

[0308] In some embodiments, the manifold lack any coating disclosed herein.

[0309] In some embodiments, the coating 249, 349 can include any liquid-repelling coating. In some embodiments, the coating 249, 349 can include an omniphobic coating. In some embodiments, the coating 249, 349 include a slippery omniphobic covalently attached liquid (SOCAL) coating. In some embodiments, the coating 249, 349 include a liquid-like polymer brush surface that is covalently attached to the one or more substrates. In some embodiments, the coating 249, 349 is formed by acid-catalyzed graft polycondensation of one or more saline monomers. The one or more saline monomers can comprise dimethyldimethoxysilane (PDMS) In some embodiments, the one or more saline monomers can have a low surface energy that is below about 10, 15, 20, 25, or 20 mJ / m2

[0310] The coating, e.g., 249, 349, can be formed using various methods. For example, the coating can be formed by impregnating lubricants in one or more porous surfaces. In some embodiments, the coating include a slippery liquid-infused porous surface (SLIPS). In some embodiments, the lubricants comprise a liquid with a low surface energy, where the low surface energy is below a predetermined threshold. The predetermined threshold can be about 20 milliJoule per square meter (mJ / m2). In some embodiments, the predetermined threshold can be about 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, or 30 mJ / m2, inclusive of all ranges and subranges therebetween. In some embodiments, the lubricants comprise a silicone oil. In some embodiments, the coating include low surface energy that is below about 10, 15, 20, 25, or 20 mJ / m2, inclusive of all ranges and subranges therebetween.SamplesAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)

[0311] In some embodiments, the one or more samples, e.g., the samples immobilized on the one or more substrates, include biological analytes to be sequenced. In some embodiments, the biological analytes include nucleic acids or DNA strands to be sequenced. In some embodiments, the one or more samples include a cellular sample containing cell(s) and / or tissue(s). In some embodiments, the one or more samples include in situ sample(s). In some embodiments, In some embodiments, the sequencing system including the optical system herein advantageously enable sequencing and imaging of biological analytes (e.g., target analyte(s)) or features while they remain intact inside the cell or tissue. In some embodiments, the cell or tissue and the targets (e.g., target analytes, structure elements, organelles, etc.) therewithin remain intact during sequencing and / or imaging. In some embodiments, the one or more samples being imaged using the optical systems herein can be 2D or 3D samples. The 3D samples can include in situ samples such as cells, tissues, or the like. In some embodiments, the cells or tissue samples are immobilized on the flow cell device or otherwise substrate for sequencing and / or imaging without modifying the spatial locations of targets within the cells or tissue. In some embodiments, the cells or tissue samples are immobilized on the flow cell device or otherwise substrate for sequencing or imaging without modifying the spatial relationship of biological analytes (e.g., targets or target analytes) within the cells or tissue. In some embodiments, the cells and / or tissue are immobilized with the morphological features, RNA, mRNA, and protein targets of the samples intact inside the cell(s) or tissue during sequencing and / or imaging. In some embodiments, the spatial locations or relationships of the target analytes or targets remain intact during sequencing and / or imaging. In some embodiments, the spatial locations or relationships of the target analytes or targets during sequencing and / or imaging are not manually reconstructed using artificially added structure or features m the sample(s). For example, the nucleus, cell membrane, mitochondria, and extracellular matrix can retain their relative spatial relationship to each other in the sample(s) during imaging and / or sequencing.

[0312] In some embodiments, the one or more samples herein may include one or more cells which may be cultured on a support, e.g., a flow cell, or on a surface that is transferred to a support, e.g., the flow cell. In some embodiments, a cell may be an adherent cell. I some embodiments, a cell may be a confluent cell. In some embodiments, a cell may be a suspended cell. In some embodiments, a suspended cell may be adhered to the surface by a specific capture mechanism such as an antigen-antibody interaction, or a receptor-ligand interaction, especially including anAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)interaction of a known surface receptor with a known ligand; an unknown surface receptor with a known ligand, a known ligand with an unknown ligand, or an unknown receptor with an unknown ligand. In some embodiments, a suspended cell may be adhered to a surface by interaction with a specific carbohydrate binding interaction, a specific protein or peptide binding interaction, or a specific lipid-lipid interaction, lipid-peptide interaction, or lipid-carbohydrate interaction. In some embodiments, a suspended cell may be adhered to a surface by a nonspecific interaction with said surface, such as by use of a charged surface (e.g., a polylysine, polyarginine, polyglutamic acid, polyaspartic acid surface or the like, or a charged polymer surface, such as a polyethylenimine surface; or a plasma-treated or ion-treated glass or polystyrene surface, or the like). It will be understood by one of skill in the art that in addition to surfaces disclosed herein, any surface useful for, or conventionally used for, cell culture, will be useful for capture of adherent cells. In particular embodiments, a surface useful for capture of adherent cells will comprise at least one of polyethylene oxide, streptavidin, protein A, or any combination thereof. In some embodiments, a suspended cell may be introduced to a flow cell by flow through the flow cell, by direct pipetting or liquid transfer onto a surface of the flow cell, by gravitational precipitation, by centrifugation, or by any method known in the art for bringing cells into contact with a surface.

[0313] In some embodiments, the one or more samples include biological analytes (e.g., target analyte(s)) that are located inside the sample(s) or on the membrane of the sample(s). In some embodiments, the one or more samples include target analyte(s) that are on the exterior or interior surface of the cell. In some embodiments, the one or more samples include target analyte(s) that are on the exterior or interior surface of the cell membrane. In some embodiments, In some embodiments, the one or more samples include target analyte(s) that are part of the extracellular matrix. In some embodiments, the one or more samples include target analyte(s) that are part of and / or located on one or more organelles within the cell or tissue. In some embodiments, the one or more samples include target analytes that are on or in the glycocalyx or belong to part of the glycocalyx.

[0314] In some embodiments, the biological analyte or target analyte(s) comprise at least one polypeptide, lipid, nucleic acid or polysaccharide. In some embodiments, the biological analyte or target analyte(s) comprise at least one polypeptide, enzyme or lipid located anywhere in the sample(s) including without limits the cytoplasm and nucleus. In some embodiments, the biological analyte or target analyte(s) comprise at least one polypeptide, enzyme or lipid locatedAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)in or on a cellular structure including without limits any cellular membrane, nucleus, nucleolus, mitochondria, chloroplast, Golgi apparatus, ribosome, endoplasmic reticulum, microtubules, peroxisome and lysosome.

[0315] In some embodiments, the one or more samples herein include analytes (e.g., nucleic acids, DNA, RNA, mRNA, and / or proteins) obtained from cell or tissue with preserved spatial information to undergo sequencing and / or imaging outside the cell or tissue. In some embodiments, the one or more samples herein include analytes (e.g., nucleic acids, DNA, RNA, and / or proteins) removed from cell or tissue so that the analytes are not inside the cell or tissue anymore to undergo sequencing and / or imaging outside the cell or tissue, while keeping the rest of the cell or tissue, e.g., the structure of the cell or tissue, intact while the analytes are outside. In some embodiments, the one or more samples include analytes (e.g., nucleic acids, DNA, RNA, and / or proteins) transferred to the outside of the cell or tissue with artificially reconstructed spatial information to undergo sequencing and / or imaging outside the cell or tissue.

[0316] In some embodiments, the one or more sample(s) include a cell, a plurality of cells, a section of a cell, an intact tissue, an organ, a tissue section, an intact tumor, or a tumor section. In some embodiments, the sample(s) include a fresh cellular sample, a freshly-frozen cellular sample, a sectioned cellular sample, or an FFPE cellular sample. In some embodiments, the sample(s) include one or more living cells or non-living cells. In some embodiments, the sample(s) can be obtained from a virus, fungus, prokaryote or eukaryote. In some embodiments, the sample(s) can be obtained from an animal, fungus, plant, yeast, or bacterium. In some embodiments, the animal is a mammal or an insect. In some embodiments, the sample(s) include one or more virally-infected cells. In some embodiments, the sample(s) include transfected cells or displaced cells. In some embodiments, the sample(s) include mammalian transfected or displaced cells. In some embodiments, the sample(s) include a biofilm, i.e., a consortium of microorganisms that adhere together. In some embodiments, the sample(s) can be obtained from any organism including human, simian, ape, canine, feline, bovine, equine, murine, porcine, caprine, lupine, ranine, piscine, plant, insect, or bacterium. In some embodiments, the sample(s) can be obtained from any organ including head, neck, brain, breast, ovary, cervix, colon, rectum, endometrium, gallbladder, intestines, bladder, prostate, testicles, liver, lung, kidney, esophagus, pancreas, thyroid, pituitary, thymus, skin, heart, larynx, or other organs.Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)

[0317] The methods, devices, and systems disclosed herein may allow sequencing and analysis of various samples and sources. The samples may include nucleic acids extracted from any of a variety of biological samples, e.g., blood samples, saliva samples, urine samples, cell samples, tissue samples, and the like. In some embodiments, the samples here may include a variety of different cell, tissue, or sample types known to those of skill in the art. For example, the sample(s) may be from eukaryotes (such as animals, plants, fungi, protista), archaebactena, or eubacteria. In some embodiments, the sample(s) may include prokaryotic or eukaryotic cells, such as adherent or non-adherent eukaryotic cells. In some embodiments, the sample(s) may be from, for example, primary or immortalized rodent, porcine, feline, canine, bovine, equine, primate, or human cell lines. In some embodiments, the sample(s) may include a variety of different cell, organ, or tissue types (e.g., white blood cells, red blood cells, platelets, epithelial cells, endothelial cells, neurons, glial cells, astrocytes, fibroblasts, skeletal muscle cells, smooth muscle cells, gametes, or cells from the heart, lungs, brain, liver, kidney, spleen, pancreas, thymus, bladder, stomach, colon, or small intestine). In some embodiments, the sample(s) may include normal or healthy cells. Alternately or in combination, the sample(s) may include diseased cells, such as cancerous cells, or from pathogenic cells that are infecting a host. In some embodiments, the sample(s) may include a distinct subset of cell types, e.g., immune cells (such as T cells, cytotoxic (killer) T cells, helper T cells, alpha beta T cells, gamma delta T cells, T cell progenitors, B cells, B-cell progenitors, lymphoid stem cells, myeloid progenitor cells, lymphocytes, granulocytes, Natural Killer cells, plasma cells, memory cells, neutrophils, eosinophils, basophils, mast cells, monocytes, dendritic cells, and / or macrophages, or any combination thereof), undifferentiated human stem cells, human stem cells that have been induced to differentiate, rare cells (e.g., circulating tumor cells (CTCs), circulating epithelial cells, circulating endothelial cells, circulating endometrial cells, bone marrow cells, progenitor cells, foam cells, mesenchymal cells, or trophoblasts). Other cells are contemplated and consistent with the disclosure herein.

[0318] In some embodiments, the sample(s) harbors a plurality of target analytes including polypeptides, lipids, nucleic acids and polysaccharides, or a mixture thereof.

[0319] In some embodiments, the sample(s) harbors 2-10,000 different target analytes. In some embodiments, the target analytes comprise a plurality of target polypeptides. In some embodiments, the plurality of target polypeptides have different sequences. In some embodiments, the sample(s) harbors 1-25 different target polypeptide, or harbors 25-50 different targetAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)polypeptides, or harbors 50-75 different target polypeptides, or harbors 75-100 different target polypeptides, or harbors any range therebetween of different target polypeptides. In some embodiments, the sample(s) harbors more than 100 different target polypeptides, or more than 250 different target polypeptides, or more than 500 different target polypeptides, or more than 1000 different target polypeptides. In some embodiments, the sample(s) harbors more than 10,000 different target polypeptides.

[0320] In some embodiments, the sample(s) can be deposited (e.g., seeded) onto a support which is passivated with a coating that promotes cell adhesion. In some embodiments, the sample(s) can be deposited on a support that lacks immobilized capture primers which can bind target polynucleotide analytes from the sample(s). In some embodiments, the support can be coated with one or more compounds that generate a charged coated surface. In some embodiments, the support is coated with a lysine compound, poly-lysine compound, arginine compound, polyarginine compound, or an ami no-terminated compound (e.g., including amino-terminated PEG), The support can be coated with an unbranched compound, a branched compound, or a mixture of unbranched and branched compounds. In some embodiments, the support can be coated with modified peptides, including, for example and without limitation, cationic anti -microbial peptides or dual surface anti-microbial peptides. In some embodiments, the support can be coated with polycyclic peptide antibiotics comprising thioether amino acids lanthionine or methyllanthiomne and / or unsaturated ammo acids dehydroalanine and 2-aminoisobutryic acid. In some embodiments, the support can be coated with at least one small peptide such as melittin. In some embodiments, the support can be coated with a compound that promotes integrm-mediated cell adhesion. For example, and without limitation, the support can be coated with tripeptide arginyl-gly cyl-aspartic acid (Arg-Gly-Asp; also known as RGD). In some embodiments, the support can be coated with amines or polymers having -NH2 groups which promote cell adhesion, including for example polyethyleneimine (PEI) or polydopamine (PDA).Calibration with capacitance sensing

[0321] In some embodiments, the sequencing system disclosed herein includes a grabber and gantry system configured to move the flow cell device among fluidic stations and imaging station(s) of the sequencing system, e.g., during a sequencing run. In some embodiments, theAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)grabber and gantry system is configured to perform one or more operations comprising: grab the flow cell device from one of: the fluidic station(s) and the imaging station(s); move the flow cell device between the fluidic station(s) and the imaging station(s); and position the flow cell device on another one of: the fluidic station(s) and the imaging station(s) for imaging the one or more samples immobilized thereon or for fluidic communication with the one or more reagent reservoirs. In some embodiments, positioning of the flow cell device by the grabber and gantry system may be automatic. In some embodiments, positioning of the flow cell device by the grabber and gantry system may be in a controlled manner controlled by a hardware processor of the sequencing system. In some embodiments, positioning of the flow cell device by the grabber and gantry system may be based on: a first calibrated position of the fluidic station; a second calibrated position of the imaging station, or both. In some embodiments, the first calibrated position and the second calibrated position are determined during an automatic calibration using at least part of the grabber as a sensor,

[0322] In some embodiments, a grabber and gantry system include: a grabber configured to engage the flow cell device, e.g., grab the flow cell securely while not damaging the flow cell device; a gantry assembly configured to mechanically support the grabber and move the grabber along one or more axis or rotate about one or more axis, where the gantry assembly may be connected and actuated by one or more motors; a sensing system configured to detect one or more changes in an electrical signal when the grabber approaches and touches the fluidic station or the imaging station with movement along one or more axis or rotation about one or more axis, where at least part of the grabber forms an electrode of the sensing system; and a hardware processor configured to determine the first calibrated position of the fluidic station or the second calibration position of the imaging station based on the detected one or more changes in the electrical signal.

[0323] In some embodiments, the first calibrated position of the fluidic station and the second calibrated position of the imaging station are determined during an automatic calibration using at least part of the grabber and gantry system as a sensor or as an electrode of the sensor.

[0324] In some embodiments, the positioning of the flow cell device on the fluidic station or imaging station is performed within a single cycle. In a particular embodiment in which a sequencing system include two fluidic stations and a single imaging station and two flow cell devices, the gantry' and grabber system may need to perform movements of the flow cell devicesAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)multiple times including, but not necessarily m this order: position the first flow cell device of the two flow cell devices on a first fluidic station; position the second flow cell device of the two flow cell devices on a second fluidic station; move the first flow cell device to the imaging station and then move it back to the first fluidic station; and move the second flow cell device to the imaging station and them move it back to the second fluidic station. Such movements of the flow cell device(s) may be repeated in each cycle of more than 20, 50, 80, 100, 200, 300, or 500 sequencing cycles. Thus, there is a need for accurate and reliable movement of the flow cell device to the imaging station(s) and the fluidic station(s) to ensure proper imaging of the samples immobilized thereon and / or proper fluidic communication with the fluidic station and the reservoirs for sequencing reactions to take place.

[0325] In some embodiments, the first calibrated position of the fluidic station and the second calibrated position of the imaging station advantageously allow the grabber and gantry system to repeatedly and accurately position the flow cell device on the fluidic station and the imaging station.

[0326] In some embodiments, the first calibrated position and the second calibrated position are determined during the automatic calibration. The automatic calibration may be performed whenever needed. For example, the automatic calibration may be performed during initial set-up of the sequencing system. As another example, the automatic calibration may be performed as needed after the initial set-up. For example, the automatic calibration may be performed after some mechanical disturbance occurred to the sequencing system, e.g., moving the system to a different location, experiencing an earthquake, replacing one parts of the grabber and gantry system, e.g., the grabber.

[0327] The existing manual calibration that may be performed by a user, e.g., by a service engineer during initial set-up, can be time-consuming and the calibrated position may vary depending on how or who is doing the calibration. The automatic calibration described herein advantageously removes user-dependent variability, reduces calibration time, and improves repeatability and consistency of the calibrated positions across different instruments and calibration operations.

[0328] In embodiments where the sequencing system includes multiple fluidic stations and / or imaging systems, a calibrated position may be determined for each of the additional stations in aAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)similar manner as determining the first and second calibrated positions disclosed herein.

[0329] In some embodiments, the sensing system of the grabber and gantry system include one or more sensors. In some embodiments, the one or more sensors includes a capacitive sensor. In some embodiments, at least part of the grabber is a part of a sensor of the sensing system. In some embodiments, at least part of the grabber is a part of an electrode of the sensor. In some embodiments, at least part of the grabber can be used as an electrode of the sensor so that no additional external sensors, e.g., camera, needs to be added to the grabber.

[0330] In some embodiments, the electrical signal include a capacitance signal measured between the grabber and a reference electrical path and may be represented as capacitance, charge, current, or a derived signal over time.

[0331] In some embodiments, using the grabber or a portion of the grabber as the electrode is advantageous because it reduces the mechanical and electrical complexity of the grabber, eliminates the need for additional external sensing components, and reduces overall cost. Using the grabber as the electrode or sensor may also improve sensing stability by minimizing wiring, connections, and alignment tolerances that may otherwise introduce noise or variability. System reliability may also be improved since fewer components and connection are required in comparison to using additional external sensors or electrodes on the grabber.

[0332] In some embodiments, at least part of the grabber include metal. In some embodiments, at least part of the grabber is electrically conductive. For example, the one or more arms (e.g., 17212) of the grabber may be metal or electrically conductive. / Xs another example, the one or more engagement features or fingers (e.g., 17211) may be metal or electrically conductive. As yet another example, the portions of or the entire grabber (e.g., 17200) may be made of metal and electrically conductive.

[0333] In some embodiments, the sensing system measures capacitance between the grabber and a reference electrical path including the one or more pins or a grounded reference through a resistive coupling.

[0334] In some embodiments, the grabber is mechanically connected via a connector to a gantry assembly of the grabber and gantry system, where the connector is electrically insulating thereby electrically isolating the grabber from the gantry assembly. In some embodiments, theAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)connector is configured to prevent electrical conduction between the grabber and the gantry assembly.

[0335] FIGS. 17A-17B shows an exemplary embodiment of the grabber and gantry system (e.g., 17000) comprising: a gantry assembly (e.g., 17100) configured to move a grabber (e.g., 17200) in 3D relative to a housing of the sequencing system (e.g., 8005). The grabber is connected to the gantry system via a connector 17300.

[0336] In some embodiments, the imaging station include one or more first pins that are electrically conductive. In some embodiments, the fluidic station include one or more second pins that are electrically conductive. In some embodiments, the grabber is configured to contact at least some of the one or more first pins and a first non-conductive location of the fluidic station sequentially for determining the first calibrated position of the fluidic station. In some embodiments, the grabber is configured to contact at least some of the one or more second pins and a second non-conductive location of the imaging station sequentially for determining the second calibrated position of the imaging station. In some embodiments, the first non-conductive location is comprised at a surface of the fluidic station. In some embodiments, the second non-conductive location is comprised at a surface of the imaging station.

[0337] FIGS. 19A -19G shows an exemplary embodiment the one or more first pins 19100 of the fluidic station 19090, and the first non-conductive location 19200 of the fluidic station. The second pins and the second non-conductive location may be at similar relative locations of the imaging station (not shown). In some embodiments, the first and second non-conductive locations may be various locations on the surface of the fluidic station and imaging station, respectively as shown by the indicated circled areas of each figure. In some embodiments, the first and second non-conductive locations are in a region of the imaging station or fluidic station that is electrically isolated from the conductive pins. In some embodiments, contacting the non-conductive location(s) with the grabber is configured to produce an electrical response different from that from a conductive contact with the pin(s).

[0338] In some embodiments, a non-conductive location include a region that is electrically isolated from the one or more pins and configured to produce an electrical response different from that produced by conductive contact with the one or more pins.

[0339] During automatic calibration, the grabber is configured to sequentially move towardAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)the fluidic station or imaging station along a plurality of directions and contact the fluidic station or imaging station a plurality of times to determine the first calibrated position of the fluidic station or the second calibrated position of the imaging station. Each movement of the grabber in the sequence may include starting from an initial position and moving along a direction until a contact event occurs. The grabber then may return to be in close proximity to (e.g., less than ± 5 mm) or at the initial position and move along a second direction until a second event occurs. Such movement may repeat multiple times, until a plurality of contact or touch events occur. The initial position may be a predetermined estimate of where the fluidic station or imaging station is. For example, the predetermined estimate may be based on the computer-aided design (CAD) of the sequencing system. In some embodiments, a contact, contact event, or touch event is determined by detecting the electrical signal exceeding a predetermined threshold corresponding to a physical contact between the grabber and the fluidic station or imaging station.

[0340] In some embodiments, the contact or touch event herein is determined by detecting a change in the electrical signal being sensed. In some embodiments, the contact or touch event herein is determined by detecting an electrical signal exceeding a predetermined threshold corresponding to physical contact or touch event.

[0341] In some embodiments, contacting the fluidic station or imaging station the plurality of times include at least a non-conductive contact and a conductive contact. In some embodiments, contacting the fluidic station or imaging station the plurality of times include at least a non-conductive contact with the non-conductive location (e.g., non-contact location] s) of the surface of the fluidic station or imaging station) and a conductive contact with at least some of the one or more first pins or second pins. In some embodiments, the plurality of directions comprise along an x axis, a y axis, and a z axis. In some embodiments, one direction of the plurality of directions comprise at least along the z axis, at least along the y axis, and / or at least along the x axis. In some embodiments, the first, second, and third axes correspond to x, y, and z axes, respectively.

[0342] In some embodiments, the sensor of the sensing system detects a first change in capacitance corresponding to a non-conductive contact between the grabber and the first non-conductive location of the fluidic station. In some embodiments, the sensor detects a second change in capacitance corresponding to a conductive contact between the grabber and the one or more first pins. In some embodiments, the non-conductive contact is at the end of movement ofAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)the grabber at least along the first axis, e.g., the z axis.

[0343] In some embodiments, the automatic calibration determines the calibrated position of the fluidic station or imaging station. In some embodiments, the calibrated position may be in the coordinate system corresponding to the grabber and gantry assembly. In some embodiments, the calibrated position may be in various coordinate systems relative to fixed datum features, such as the housing of the sequencing system. In some embodiments, the calibrated position, e.g., the first or second calibrated position, may be in the form of coordinates in a reference coordinate system. For example, the calibrated position may be (xl,yl,zl) in the reference coordinate system. In some embodiments, the calibrated position, e.g., the first or second calibrated position, may be in the form of offsets relative to a reference location. For example, the calibrated position may be (delta_xl, delta_y1, delta_zl) relative to a reference location (xO, yO, zO). In some embodiments, the reference coordinate system, e.g., its origin, the reference location, may be predetermined,

[0344] In some embodiments, the calibrated position is represented in a reference coordinate system of the sequencing system as one or more coordinates or offsets relative to a reference location,

[0345] In some embodiments, the automatic calibration determines a rotational alignment of the grabber relative to the fluidic station or the imaging station. The rotational alignment may be about z axis (e.g., theta), about an axis in the x-y plane, or any 3D axis. In some embodiments, the rotational alignment include at least a theta rotation about a z axis.

[0346] In some embodiments, the grabber include one or more alignment configured to contact the fluidic station and the imaging station during the automatic calibration. In some embodiments, the alignment features comprise one or more of: a first tip at a first arm, a second tip at a second arm, the first arm, and the second arm of the grabber. In some embodiments, same or different alignment features may be used in contacting the fluidic station or imaging station in different touch events. For example, a touch event in the automatic calibration may be by a first arm with a non-conductive location of the surface of the fluidic station, and another touch event may be by a first tip at the first arm of the grabber with a first pin of the fluidic station, and yet another touch event may be by a first tip at the second arm of the grabber with a second pm of the fluidic station.

[0347] FIGS. 19A-19G shows an exemplary embodiment of the automatic calibration comprising sequentially moving the grabber and contacting the fluidic station a plurality of times.Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)

[0348] In some embodiments, each contact (e.g., touch event) may provide information (e.g., change in electrical signal) for determining a coarse or refined position at least along an axis in 3D. In some embodiments, the automatic calibration includes: determining a first coarse position of the fluidic station or a second coarse position of the imaging station; and determining the first calibrated position or the second calibration position based on the first coarse position or the second coarse position. In some embodiments, determining the first or second coarse position include: sensing a change in the electrical signal (e.g., capacitance change over time) as the grabber approaches a first non-conductive location of the fluidic station or second non-conductive location of the imaging station. In some embodiments, determining the first or second calibrated position include: detecting a change in the electrical signal (e.g., capacitance change over time) as the grabber makes a conductive contact with the one or more first pins of the fluidic station or the one or more second pins of the imaging station,

[0349] In some embodiments, the sequencing system further include a second fluidic station, where the grabber and gantry system is configured to: grab / engage the flow cell device from one of the fluidic station, the second fluidic station, and the imaging station; move the flow cell device between the fluidic station, the second fluidic station, and the imaging station; and position the flow cell device on another one of the fluidic station, the second fluidic station, and the imaging station for fluidic communication with the one or more reagent reservoirs or imaging, where positioning of the flow cell device is based on a first calibrated position of the fluidic station, a second calibrated position of the imaging station, or a third calibrated position of the second fluidic station. The third calibrated position may be determined similarly as the first or second calibrated position.

[0350] In some embodiments, disclosed herein is a method for automatic calibration of positions of one or more fluidic stations and one or more imaging stations in the sequencing system. In some embodiments, the methods include one or more operations during automatic calibration. In some embodiments, some or all of the operations may be controlled by the hardware processor of the sequencing system. In some embodiments, some or all of the movements of the grabber may be actuated by the gantry assembly of the grabber and gantry system, which in term may be actuated by one or more motors. In some embodiments, the one or more operations during automatic calibration may be performed in the order disclosed herein but are not limited to be performed in the order disclosed herein. In some embodiments, one or more operations duringAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)automatic calibration may be repeated one or more times as needed for accurate and reliable calibration. For example, each touch event may be repeated 1 to 5 times, and the calibrated positions may be averaged for improved accuracy or reliability.

[0351] In some embodiments, the operations may include moving a grabber of the grabber and gantry system toward the fluidic station or imaging station; sensing, using a sensor comprising at least part of the grabber, a change in an electrical signal as the grabber moves; detecting a touch event between the grabber and fluidic station or the imaging station based on the sensed change in the electrical signal; recording a position of the grabber corresponding to the touch event; and determining, at least along a first axis or about a first rotational axis, a first calibrated position of the fluidic station or a second calibrated position of the imaging station based on the recorded position,

[0352] In some embodiments, the operations of moving the grabber, sensing the change in the electrical signal; detecting the touch event; and recording a position of the grabber may be repeated for multiple times, each repetition of the operations may be used to determine a coarse position or refined position at least along an axis, e.g., z or any axis in the x-y plane. Multiple repetitions may be used to define the calibrated position (e.g,, (xl, yl, z 1 )) of the fluidic station or imaging station in 3D.

[0353] In some embodiments, moving the grabber toward the fluidic station or imaging station includes: sequentially moving the grabber toward the fluidic station or the imaging station along a plurality of directions and contacting the fluidic station or imaging station a plurality of times. In some embodiments, moving the grabber toward the fluidic station or imaging station is at least along the first axis (e.g., z axis), a second axis (e.g., y axis), or a third axis (e.g., x axis).

[0354] FIGS. 19A-19G shows an exemplary embodiment of the operation of sequentially moving the grabber toward the fluidic station along a plurality of directions and contact the fluidic station a plurality of times. As shown in FIG. 19A, the grabber moves along z axis toward the fluidic station until a touch event, a non-conductive contact, with the surface of the fluidic station occurs. During this operation, the sensing of capacitance change, detection of touch event may also occur. Then the operation of recording the position of the grabber may occur, followed by determining a z location of the grabber.

[0355] In FIGS. 19B-19C, the grabber moves along y axis (e.g., horizontal axis) and touchesAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)the left pin on the surface of the fluidic station sequentially with two different part of the grabber (e.g., the first tip of the first arm, and a part near the mid-point of the first arm). The arrows show movement directions of the grabber. During this operation, the sensing of capacitance change over time, detection of touch events also occur. Then the operation of recording the position of the grabber may occur, followed by determining of a coarse location of the grabber, e.g., along the y axis. Optionally, the two different y locations corresponding to the two different touch events may also be used to estimate a coarse rotation about z axis (e.g., theta rotation). For example, if the two different y locations are identical, the coarse rotation about z axis may be close to zero, but if not, there may be a rotation about z axis of the fluidic station relative a reference orientation of the fluidic station, e.g., a reference orientation according to the CAD,

[0356] In FIGS, 19D-19E, the grabber moves along x axis (e.g., vertical axis) and touches the left pin on the surface of the fluidic station with the first arm and touches the right pm on the surface with the second arm. During this operation, the sensing of capacitance change over time, detection of touch events also occur. The operation of recording the position of the grabber may occur, followed by determining of a coarse or refined location of the grabber, e.g., along the x axis. Optionally, the two different z locations corresponding to the two different touch events may also be used to estimate a refined rotation about z axis (e.g., theta rotation).

[0357] In FIGS.19F-19G, the grabber moves along y axis (e.g., horizontal axis) again and touches the left pin on the surface of the fluidic station with the tip of the first arm and touches the right pin on the surface with the tip of the second arm. The two touches may be toward opposite direction along the same axis, as shown by the arrows. During this operation, the sensing of capacitance change over time, detection of touch events also occur. The operation of recording the position of the grabber may occur, followed by determining of a refined location of the grabber, e.g., along the x axis.

[0358] Similarly, the refined location of the grabber along z axis may be determined using movement of the grabber along z axis toward the first and second pins and touch events by touching the first pm with the first tip and touching the second pm with the second tip.

[0359] In some embodiments, the sensing operation, using the sensor comprising at least part of the grabber, the change in the electrical signal as the grabber moves includes: sampling the electrical signal at a sampling rate determined based on a speed of the grabber movement; andAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)determining the change in the electrical signal from a baseline electrical signal. In some embodiments, the speed of the grabber may vary, e.g., depending on the sequencing time requirement. In some embodiments, the sampling rate is s...

Claims

Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)What is currently claimed:

1. A sequencing system comprising:a flow cell device comprising:one or more channels defined by one or more substrates, wherein the one or more channels are configured to allow one or more types of fluids to flow therethrough; one or more inlets in the one or more substrates and in fluidic communication with the one or more channels; andone or more outlets in the one or more substrates and in fluidic communication with the one or more channels;a fluidic station comprising:a manifold comprising:one or more fluidic pathways; andone or more openings;one or more reagent reservoirs;an actuation mechanism configured to move the flow cell device to:a closed position, at least along a z direction, wherein the one or more inlets of the flow cell device and the one or more openings of the manifold are sealingly coupled to each other for fluidic communication from the one or more reagent reservoirs to the flow cell device; andan open position, wherein the one or more inlets are accessible by a dispensing tip for fluidic communication from the dispensing tip to the flow cell device;an imaging station comprising:a sample stage for positioning the flow cell device thereon; anda sample stage actuator that moves the sample stage and the flow cell device at least alone the z direction for focusing the flow cell device;andAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)a grabber and gantry system configured to:grab the flow cell device from one of the fluidic station and the imaging station; sense coupling of the flow cell device to the grabber and gantry system;andmove the flow cell device between the fluidic station and the imaging station such that the flow cell device is positioned for imaging or for fluidic communication with the one or more reagent reservoirs,wherein the flow cell system comprises a sequencing system, the grabber and gantry system is configured to move the flow cell device to one of the fluidic station and the imaging station within a single sequencing cycle of a sequencing run and move a second flow cell device to the other one of the fluidic station and the imaging station within the single sequencing cycle.A sequencing system comprising:a flow cell device comprising:one or more channels defined by one or more substrates, wherein the one or more channels are configured to allow one or more types of fluids to flow therethrough; one or more inlets in the one or more substrates and in fluidic connection with the one or more channels; andone or more outlets in the one or more substrates and in fluidic connection with the one or more channels;a manifold comprising:one or more fluidic pathways; andone or more openings;a fluidic station comprising:one or more reagent reservoirs;Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)an actuation mechanism configured to move the flow cell device to:a closed position, at least along a z direction, wherein the one or more inlets of the flow cell device and the one or more openings of the manifold are coupled to each other for fluidic communication from the one or more reagent reservoirs to the flow cell device;one or more open positions, wherein at least one of the one or more inlets is accessible by a dispensing tip for fluidic communication from the dispensing tip to the flow cell device;a grabber position, wherein the flow cell device is decoupled from the fluidic station and is configured to be accessible by a grabber for moving the flow cell device away from the fluidic station;a loading or unloading position, wherein the flow cell device is accessible by a user; anda decoupled position that is optional, wherein the flow cell device is decoupled from the manifold and at a same location in a plane orthogonal to the z direction as the closed position,an imaging station;anda grabber and gantry’ system including the grabber and configured to:grab the flow cell device from one of the fluidic station and the imaging station; sense coupling of the flow cell device to the grabber; andmove the flow cell device between the fluidic station and the imaging station so as to position the flow cell device in one of the imaging station for imaging or for fluid communication with one or more reagent reservoirs of the flow cell system.

3. The system of any one of the preceding claims, wherein the one or more channels include at least 6 channels.Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)4. The system of any one of the preceding claims, wherein a / the grabber and gantry system includes a flow cell carrier configured to hold the flow cell device therein.

5. The system of claim 4, wherein the flow cell carrier is configured to couple to a grabber of the grabber and gantry system when the flow cell device is moved by the grabber.

6. The system of claim 4, wherein the flow cell carrier include a first coupling element configured to couple to a coupling element of a / the fluidic station.

7. The system of claim 4, wherein the flow cell carrier includes a first or a second coupling element configured to couple to a coupling element of a / the imaging station.

8. The system of any one of the preceding claims, wherein the one or more inlets are facing upwards with an opening in a top surface of the flow cell device.

9. The system of any one of the preceding claims, wherein the one or more outlets are facing upwards with an opening in a top surface of the flow cell device.

10. The system of any of claims 4-9, wherein the flow cell carrier includes a top cover and a flow cell frame that mechanically couples to the one or more substrates of the flow cell device independently.

11. The system of claim 10, wherein the top cover include:a top anchor element that mechanically couples to the one or more substrates;one or more through holes that allow one or more gaskets to fit through, wherein the one or more gaskets are configured to contact a top surface of the one or more substrate and sealingly couple to the manifold.Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)12. The system claim 11, wherein the one or more gaskets include one or more inlet gaskets and one or more outlet gaskets.

13. The system of claims 11 or 12, wherein the one or more gaskets are compatible with flow cell devices that are used in flow cell systems with only closed fluidic communication between the manifold and the flow cell device via the one or more gaskets.

14. The system of any of claims 11-13, wherein the one or more gaskets are configured to enable sealed fluidic communication from the manifold to the one or more inlets or from the one or more outlets to a second manifold.

15. The system of any of claims 11-14, wherein the one or more gaskets are configured to sealingly couple to the dispensing tip when the flow cell device is in the open position and sealingly couple to the manifold when the flow cell device is the closed position.

16. The system of any of claims 11-15, wherein each gasket of the one or more gaskets include a cone shaped cavity therewithin.

17. The system of any of claims 11-16, wherein the one or more gaskets are configured to sealingly couple to the dispensing tip when the dispensing tip is at least 0.1mm, 0.2mm, 0.3mm, 0.4mm, 0.5mm, 0.6mm, 0.8mm, or 1mm off a predetermined alignment with the one or more inlets of the flow cell device.

18. The system of any of claims 11-17, wherein the one or more gaskets are configured to sealingly couple to the dispensing tip when the one or more openings are at least 0.1mm, 0.2mm, 0.3mm, 0.4mm, 0.5mm, 0.6mm, 0.8mm, or 1mm off a predetermined alignment with the one or more inlets of the flow cell device.Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)19. The system of any of claims 12-18, wherein the manifold further include a manifold barb at each of the one or more openings.

20. The system of claim 19, wherein the manifold barb is tapered at an end thereof, and wherein the manifold barb is configured to insert at least partly into a corresponding gasket of the one or more inlet gaskets or one or more outlet gaskets.

21. The system of claim 19 or 20, wherein the manifold barb is configured to enable face seal of the one or more openings of the manifold and the flow cell device.

22. The system of any of claims 19-21, wherein the manifold is movably coupled to a housing of a / the fluidic station.

23. The system of any claims 2-22, wherein the manifold moves at least in a direction orthogonal to the z direction to sealingly couple to the one or more inlets of the flow cell device.

24. The system of claims 22 or 23, wherein the flow cell system further include a second manifold comprising:one or more second fluidic pathways; andone or more second openings,wherein:the one or more outlets of the flow cell device and the one or more second openings of the manifold are coupled to each other for fluidic communication from the flow cell device to at least a waste reservoir when the flow cell device is m the closed position;orAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)the one or more outlets of the flow cell device and the one or more second openings of the manifold are coupled to each other for fluidic communication from the flow cell device to at least a waste reservoir when the flow cell device is in the open position.

25. The system of any one of the preceding claims, wherein the grabber and gantry system include:a gantry assembly configured to move a grabber in 3D relative to a housing of the flow cell system; andthe grabber comprising:one or more arms that are configured to contact and engage the flow cell device; one or more engagement features extending from each of the one or more arms; one or more sensors mounted to the one or more arms; anda support body supporting the one or more arms and attaching the one or more arms to the gantry assembly,wherein the one or more arms are configured to move relative to the support body to engage the flow cell device.

26. The system of any one of the preceding claims, wherein the grabber and gantry system is configured to perform one or more operations, within a single sequencing cycle of a sequencing run, comprising:moving the flow cell device from a / the fluidic station to a / the imaging station; position the flow cell device on the imaging station for imaging;move the flow cell device from the imaging station to the fluidic station;position the flow cell device on the fluidic station;move a second flow cell device from the second fluidic station to the imaging station;Atorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)position the second flow cell device on the imaging station for imaging;move the second flow cell device from the imaging station to the second fluidic station;andposition the second flow cell device on the second fluidic station.

27. The system of any of claims 2-26, wherein the manifold is configured to move at least along a z axis bi-directionally relative to a housing of the fluidic station or a housing of the flow cell system to switch the flow cell device between two positions selected from the closed, decoupled, and open positions.

28. The system of any of claims 2-27, wherein the manifold is configured to move at least along a direction within an x-y plane bi-directionally relative to a housing of the fluidic station or a housing of the flow cell system to switch the flow cell device between two positions selected from the closed, decoupled, and open positions.

29. The system of any one of claims 2-28 wherein the flow cell device is configured to move at least along a / the z axis bi-directional relative to a housing of the fluidic station or a housing of the flow cell system to switch the flow cell device between two positions selected from the open, decoupled, and closed positions.

30. The system of any of claims 2-29, wherein the flow cell device is configured to move at least along a direction within an / the x-y plane bi-directionally relative to a housing of the fluidic station or a housing of the flow cell system to switch the flow cell device between two positions selected from the closed, decoupled, and open positions,31. The system of any of claims 2-30, wherein the manifold is configured to move at least along a / the z axis bi-directionally relative to a housing of the fluidic station or a housing of the flow cell system while the flow cell device is fixed relative to the housing of the fluidic station or the housing of the flow cell system to switch the flow cell device betweenAtorney Docket No. 43914-02780 / US (ELEM-081 / 001WQ)two positions selected from the closed, decoupled, and open positions.

32. The system of any of claims 2-31, wherein the flow cell device is configured to move at least along a / the z axis bi-directional relative to a housing of the fluidic station or a housing of the flow cell system while manifold is fixed relative to the fluidic station or housing of a flow cell system to switch the flow cell device between two positions selected from the closed, decoupled, and open positions.

33. The system of any of claims 10-32, wherein the flow cell system further include one or more mounting rails configured to allow moveable mounting of the flow cell device thereon.

34. The system of any of claims 10-32, wherein the flow cell system further include one or more mounting rails configured to allow moveable and reversible mounting of a flow cell carrier along with the flow cell device thereon, and wherein the flow cell device is at least partly within the flow cell frame.

35. The system of claims 33 or 34, wherein the flow cell device further include a motor for driving movement of the flow cell device on the one or more mounting rails.

36. The system of any one of the preceding claims, wherein the flow cell system further include a flow cell frame configured to contain the flow cell device at least partly therewithin.

37. The system of any of claims 4-36, wherein the flow cell carrier is configured to:hold a flow cell frame or the flow cell device in a fixed position relative to the carrier; and move in 1 dimension, 2 dimensions, or 3 dimensions relative to a housing of the flow cell system.

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