Abstract: A machine vision system for calibrating and/or positioning of various motion control modules of an opto-fluidic instrument/tool/instrument having integrated optics and fluidics modules configured for imaging of biological specimens is disclosed. The machine vision system includes determining 3D positions of an object within a reference coordinate system based on a plurality of stereo-images comprising the object; generating a transformation matrix based on the determined 3D positions of the object with respect to a reference position; and calibrating one or more motion control systems based on the determined transformation matrix. The methods also include determining a 3D position of an object within a reference coordinate system based on a stereo-image of the object; generating a 3D offset value between the determined 3D position and a reference location of the object; updating the 3D position using the 3D offset value; and positioning the object based on the corrected 3D position.

Abstract: An imaging system includes an optical mounting plate having an aperture disposed between a first portion and a second portion, an imaging sensor disposed on the first portion, an objective lens disposed on the second portion, and an illumination assembly arranged within the aperture and disposed between the imaging sensor and the objective lens. The imaging system includes a heat sink coupled to the illumination assembly and configured to transfer heat away from light sources of the illumination assembly via a working fluid that flows through the heat sink.

Abstract: An imaging system includes an optical mounting plate having an aperture disposed between a first portion and a second portion, an imaging sensor disposed on the first portion, an objective lens disposed on the second portion, and an illumination assembly arranged within the aperture and disposed between the imaging sensor and the objective lens. The imaging system includes a heat sink coupled to the illumination assembly and configured to transfer heat away from light sources of the illumination assembly via a working fluid that flows through the heat sink.

Abstract: An optical assembly of a machine vision system for calibrating and/or positioning of various motion control modules of an analytical system/tool/instrument having integrated optics and fluidics modules configured for imaging of biological specimens is disclosed. The optical assembly includes one or more light sources configured to generate a first light beam and a second light beam that intersects the first light beam at an intersection region to illuminate an object within the intersection region; a sensor array configured to receive the first light beam and the second light beam to thereby form a stereo-image based on received light from the first light beam and the second light beam; a first imaging mirror configured to reflect the first beam after the intersection region and towards the sensor array; and a second imaging mirror configured to reflect the second beam after the intersection region and towards the sensor array.

Abstract: Various embodiments of the present disclosure disclose mitigating internal and external vibrational disturbances in opto-fluidic instrument. In various embodiments, the resonance frequency ranges and/or the vibrational frequency ranges of various modules and components of the opto-fluidic instrument may be selected to avoid resonances from occurring in the opto-fluidic instrument, thereby mitigating vibrations from internal and external sources that may distort the imaging of samples in the opto-fluidic instrument.

Abstract: The present disclosure relates to systems and methods for thermal management of well plates. In various embodiments, an apparatus for performing thermal management includes a thermal transfer block configured to receive a well plate having a plurality of wells, wherein the thermal transfer block comprises a base and a plurality of protrusions arranged on a first side of the base in a configuration such that each of the plurality of wells is received between a set of adjacent protrusions, and wherein each protrusion of the set of adjacent protrusions has a surface that substantially matches a portion of an outer surface of each well that is received between the set of adjacent protrusions; and a cooling block disposed in contact with a second side of the base of the thermal transfer block, wherein the cooling block comprises a heat sink having a plurality of fins immersed in a fluid for cooling.

Abstract: Provided in some aspects are methods for light-controlled in situ surface patterning of a substrate using a minimal mask scheme. Systems and kits employing the methods are also disclosed. In some embodiments, a method disclosed herein comprises using photomasks and photoresist for photocontrollable hybridization and/or ligation of nucleic acid molecules, wherein photoresist removal allows hybridization and/or ligation of nucleic acid molecules at the exposed area. A large diversity of barcodes can be created in molecules on the substrate via sequential rounds of light exposure, hybridization, and ligation.

Abstract: An assembly includes a stage body, a cam plate disposed on the body, and a sample positioning plate having a sample positioning surface configured to receive a sample device. The surface has first, second, and third raised portions. The second raised portion is disposed between the first and third raised portions. The first, second, and third raised portions are configured to contact the sample device. The assembly includes a riser module disposed within the stage body. The riser module is coupled to the plate and the body. The assembly includes a lid configured to be coupled to the cam plate. The lid has a coupled configuration and an uncoupled configuration such that, when in the coupled configuration, a recess is formed by the lid and the plate. The assembly includes one or more light sources disposed in the cam plate that are configured to direct light within the recess.

Abstract: Various embodiments of the present disclosure disclose a system for forming a sealed chamber for preparing samples therein. In particular, various embodiments present an assembly that includes a sample device and a lid for forming a sealed chamber that can be used for, among other things, incubating samples therein. When the lid engages with the sample device, a plurality of snap joint elements of the lid engage with a respective plurality of snap joint elements to form a seal between the lid and the sample device.

Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate configured to rotate. The open substrate can comprise an array of immobilized analytes. A solution comprising a plurality of probes may be directed, via centrifugal force, across the array during rotation of the substrate, to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via continuous rotational area scanning of the substrate.

Abstract: Systems and methods for dispensing a liquid on a substrate are disclosed. The system may be used to coat a substrate and/or a sample (e.g., a biological sample) with a liquid. The system includes a rotating device configured to rotate about an axis and a substrate disposed on the rotating device. The substrate comprises a well configured to hold a liquid and the substrate is positioned on a surface of the rotating device perpendicular to and concentric with the axis. The system further includes a liquid handler configured to dispense the liquid into the well. The rotating device is configured to rotate at a speed sufficient to disperse the liquid within the well.

Abstract: Flowcell devices configured for reversible assembly, and methods of assembly, disassembly, and use thereof are provided. The methods and devices allow the interior of the flowcell device to be accessed without damaging, or otherwise disturbing sensitive samples and surfaces.

Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate configured to rotate. The open substrate can comprise an array of immobilized analytes. A solution comprising a plurality of probes may be directed, via centrifugal force, across the array during rotation of the substrate, to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via continuous rotational area scanning of the substrate.

Abstract: Devices (e.g., flow cell holders) and methods for flow cell assembly and disassembly are provided. The flow cell holders and methods can be used to join or separate the bottom and top layers of a flow cell.

Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate configured to rotate. The open substrate can comprise an array of immobilized analytes. A solution comprising a plurality of probes may be directed, via centrifugal force, across the array during rotation of the substrate, to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via continuous rotational area scanning of the substrate.

Abstract: Systems and methods for detection of a signal from droplets of an emulsion. An exemplary system may comprise a fluid transporter having a tube with an open end for aspirating droplets, a singulator to arrange the droplets in single file and to space the single-file droplets from one another, and a detection channel in optical communication with a detector configured to detect a signal from droplets. In some embodiments, the singulator may have a channel junction at which a stream of droplets in single file is combined with a stream of spacing fluid, and a tapered spacing channel extending downstream from the channel junction toward the detection channel. In some embodiments, the fluid transporter may suck droplet-containing fluid and spacing fluid through the detection channel from respective sources. In some embodiments, droplets may be subjected to a disaggregation routine before they are passed through the detection channel.

Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate configured to rotate. The open substrate can comprise an array of immobilized analytes. A solution comprising a plurality of probes may be directed, via centrifugal force, across the array during rotation of the substrate, to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via continuous rotational area scanning of the substrate.

Abstract: Systems and methods for detection of a signal from droplets of an emulsion. An exemplary system may comprise a fluid transporter having a tube with an open end for aspirating droplets, a singulator to arrange the droplets in single file and to space the single-file droplets from one another, and a detection channel in optical communication with a detector configured to detect a signal from droplets. In some embodiments, the singulator may have a channel junction at which a stream of droplets in single file is combined with a stream of spacing fluid, and a tapered spacing channel extending downstream from the channel junction toward the detection channel. In some embodiments, the fluid transporter may suck droplet-containing fluid and spacing fluid through the detection channel from respective sources. In some embodiments, droplets may be subjected to a disaggregation routine before they are passed through the detection channel.

Abstract: Provided in some aspects are methods for light-controlled in situ surface patterning of a substrate. Compositions such as nucleic acid arrays produced by the methods are also disclosed. In some embodiments, a method disclosed herein comprises using photoresist for photocontrollable hybridization and/or ligation of nucleic acid molecules, wherein photoresist removal allows hybridization and/or ligation of nucleic acid molecules at the exposed area. A large diversity of barcodes can be created in molecules on the substrate via sequential rounds of light exposure, hybridization, and ligation.

Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate. The open substrate may be configured to rotate or otherwise move. The open substrate can comprise an array of individually addressable locations, with analytes immobilized thereto. The substrate may be spatially indexed to identify nucleic acid molecules from one or more sources, and/or sequences thereof, with the respective one or more sources. A solution comprising a plurality of probes may be directed across the array to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via scanning of the substrate while minimizing temperature fluctuations of the substrate or optical aberrations caused by bubbles.