Abstract: A method for filtering open chromatin regions on a cell barcode genomic sequence dataset is provided, comprising receiving, by one or more processors, a cell barcode genomic sequence dataset, the method comprising a plurality of fragment sequence reads and barcodes associated with the plurality of fragment sequence reads. The method further comprising generating, by the one or more processors, an adjacency matrix that counts up pairs of adjacent fragment sequence reads and barcodes associated with each fragment sequence read. The method further comprising identifying, by the one or more processors, pairs of adjacent fragment sequence reads with different barcodes and annotating the pair as a multiplet pair. The method further comprising filtering, by the one or more processors, one fragment sequence read from each of the identified multiplet pairs. The method further comprising generating, by the one or more processors, a multiplet filtered cell barcode genomic sequence dataset.

Abstract: A method for conducting a customized analysis of open chromatin regions on a cell, comprising receiving an output file for a cell barcode genomic sequence dataset, the output file comprising a peak-barcode matrix, wherein each peak is defined by a plurality of fragment sequences aligned within a peak region, a unique barcode is associated with each fragment sequence in the dataset, and the peak-barcode matrix pairs each peak with the barcodes of the aligned fragments; and cell clusters with cells aggregated based on similarity in accessibility of specific transcription factor binding motifs associated with each cell, wherein the accessibility is determined via a differential accessibility analysis.

Abstract: A tissue processing system for processing a laboratory slide includes a slide holder for holding the slide, an outlet port positioned to direct a fluid stream onto the slide, and a device for moving the slide holder relative to the outlet port, or vice versa, to adjust a point on the slide at which the fluid stream is delivered onto the laboratory slide. The slide holder includes an absorbent pad configured to be positioned between one wall of the plurality of walls and a free edge of the slide for absorbing fluid travelling along the slide. A manifold of the system includes a first outlet port that directs a first fluid stream from a first fluid passageway onto the slide, and a second outlet port that directs a second fluid stream from a second fluid passageway onto a location of the slide that differs from the first fluid stream.

Abstract: A dataflow accelerator including a control/command core, a scratchpad and a coarse grain reconfigurable array (CGRA) according to an exemplary embodiment is disclosed. The scratchpad may include a write controller to transmit data to an input vector port interface and to receive data from the input vector port interface. The CGRA may receive data from the input vector port interface and includes a plurality of interconnects and a plurality of functional units.

Abstract: Systems and methods for spatial analysis of analytes include placing a sample on a substrate having fiducial markers and capture spots. Then, an image of the sample is acquired and sequence reads are obtained from the capture spots. Each capture probe plurality in a set of capture probe pluralities is (i) at a different capture spot, (ii) directly or indirectly associates with analytes from the sample and (iii) has a unique spatial barcode. The sequencing reads serve to detect the analytes. Sequencing reads include a spatial barcode of the corresponding capture probe plurality. Spatial barcodes localize reads to corresponding capture spots, thereby dividing them into subsets, each subset for a respective capture spot. Fiducial markers facilitate a composite representation comprising (i) the image aligned to the capture spots and (ii) a representation of each subset of sequence reads at respective positions within the image mapping to the corresponding capture spots.

Abstract: Systems and methods for spatial analysis of analytes are provided. A data structure is obtained comprising an image, as an array of pixel values, of a sample on a substrate having a identifier, fiducial markers and a set of capture spots. The pixel values are used to identify derived fiducial spots. The substrate identifier identifies a template having reference positions for reference fiducial spots and a corresponding coordinate system. The derived fiducial spots are aligned with the reference fiducial spots using an alignment algorithm to obtain a transformation between the derived and reference fiducial spots. The transformation and the template corresponding coordinate system are used to register the image to the set of capture spots. The registered image is then analyzed in conjunction with spatial analyte data associated with each capture spot, thereby performing spatial analysis of analytes.

Abstract: A tissue processing system for processing a laboratory slide includes a slide holder for holding the slide, an outlet port positioned to direct a fluid stream onto the slide, and a device for moving the slide holder relative to the outlet port, or vice versa, to adjust a point on the slide at which the fluid stream is delivered onto the laboratory slide. The slide holder includes an absorbent pad configured to be positioned between one wall of the plurality of walls and a free edge of the slide for absorbing fluid travelling along the slide. A manifold of the system includes a first outlet port that directs a first fluid stream from a first fluid passageway onto the slide, and a second outlet port that directs a second fluid stream from a second fluid passageway onto a location of the slide that differs from the first fluid stream.

Abstract: The present disclosure provides methods and systems for nucleic acid preparation and analysis. Nucleic acid molecules may be derived from one or more cells. Preparation of nucleic acid molecules may comprise generation of one or more mutations, such as strand-specific mutations. Nucleic acid molecules may be prepared for and analyzed by sequencing. Sequences may be identified with nucleic acid orientation information.

Abstract: Provided herein are methods of determining a location of a biological analyte in a biological sample.

Abstract: A visualization system comprising a persistent memory, storing a dataset, and a non-persistent memory implements a pattern visualizing method. The dataset contains discrete attribute values for each first entity of a first type in a plurality of first entities of the first type and discrete attribute values for each first entity of a second type in a plurality of first entities of the second type for each second entity in a plurality of second entities. The dataset is compressed by blocked compression and represents discrete attribute values in both compressed sparse row and column formats. The discrete attribute values are clustered to assign each second entity to a cluster in a plurality of clusters.

Abstract: A fluid-containing cartridge for a tissue processing apparatus includes a body defining a plurality of discrete fluid passageways, and a plurality of fluid-containing wells that are disposed on the body, wherein each fluid passageway of the body defines a fluid path between one of the fluid-containing wells and a fluid exit port that is configured to dispense fluid onto a laboratory slide.

Abstract: According to some embodiments, a dataflow accelerator comprises a control/command core, a scratchpad and a coarse grain reconfigurable array (CGRA). The scratchpad comprises a write controller to transmit data to an input vector port interface and to receive data from the input vector port interface. The CGRA receives data from the input vector port interface where the CGRA comprising a plurality of interconnects and a plurality of functional units.

Abstract: Methods and systems for estimating the flux of spheroidal particles through a pore in a vessel wall using Brownian dynamics (BD) simulation are provided. Also provided are methods of producing a particle based on the BD simulation to provide particles for use in delivering therapeutic agents to a target tissue.

Abstract: A fluid-containing cartridge for a tissue processing apparatus includes a body defining a plurality of discrete fluid passageways, and a plurality of fluid-containing wells that are disposed on the body, wherein each fluid passageway of the body defines a fluid path between one of the fluid-containing wells and a fluid exit port that is configured to dispense fluid onto a laboratory slide.

Abstract: A tissue processing system includes a plurality of processing stations. Each processing station includes a plurality of tissue receiving areas that are each configured to accommodate a tissue sample as well as physically isolate that tissue sample from other tissue samples at other receiving areas of the same processing station. Each processing station is configured to separately and individually process the tissue sample at each receiving area to either reduce or eliminate any potential for cross-contamination between the tissue samples undergoing processing at the same processing station. For each receiving area of each processing station, the system is configured to immerse a tissue sample at a particular receiving area in processing fluid for a pre-determined time according to a pre-defined protocol that is based upon parameters of that tissue sample.

Abstract: A tissue processing system includes a plurality of processing stations. Each processing station includes a plurality of tissue receiving areas that are each configured to accommodate a tissue sample as well as physically isolate that tissue sample from other tissue samples at other receiving areas of the same processing station. Each processing station is configured to separately and individually process the tissue sample at each receiving area to either reduce or eliminate any potential for cross-contamination between the tissue samples undergoing processing at the same processing station. For each receiving area of each processing station, the system is configured to immerse a tissue sample at a particular receiving area in processing fluid for a pre-determined time according to a pre-defined protocol that is based upon parameters of that tissue sample.

Abstract: A slide stainer and a method for operating the slide carrier is disclosed. The slide stainer includes a slide carrier that carries one or more laboratory slides; a vessel that is capable of carrying fluid for staining the laboratory slides and that is sized to accommodate the laboratory slides; a slide transporter that moves the slide carrier into and out of the vessel; and a spring loaded pin that engages with a surface of the slide stainer to limit free-fall translation of the slide carrier in an event of a power loss. Additionally, during an agitation phase of a slide staining process, the slide transporter is configured to translate the slide carrier in an upward direction to a pre-determined height that is set by a user of the slide stainer, and the slide transporter translates the slide carrier in a downward direction back into the vessel.

Abstract: A configurable tissue processing system is disclosed that includes a plurality of configurable tissue processing stations, each station configured to receive tissue samples and selectively configurable to heat, agitate and apply either a positive pressure or a vacuum pressure to the received tissue samples; a transport mechanism that is configured to transport the tissue samples between the plurality of configurable tissue processing stations; and a control unit coupled to the plurality of configurable tissue processing stations and to the transport mechanism, the control unit controlling the transport mechanism to selectively position the tissue samples in the plurality of configurable tissue processing stations, and the control unit configuring each of the plurality of configurable tissue processing stations to heat, agitate and apply either a positive pressure or a vacuum pressure to the received samples. Also disclosed is a method of configuring the plurality of tissue processing stations.

Abstract: A tissue processing system includes a plurality of processing stations. Each processing station includes a plurality of tissue receiving areas that are each configured to accommodate a tissue sample as well as physically isolate that tissue sample from other tissue samples at other receiving areas of the same processing station. Each processing station is configured to separately and individually process the tissue sample at each receiving area to either reduce or eliminate any potential for cross-contamination between the tissue samples undergoing processing at the same processing station. For each receiving area of each processing station, the system is configured to immerse a tissue sample at a particular receiving area in processing fluid for a pre-determined time according to a pre-defined protocol that is based upon parameters of that tissue sample.

Abstract: A slide stainer and a method for operating the slide carrier is disclosed. The slide stainer includes a slide carrier that carries one or more laboratory slides; a vessel that is capable of carrying fluid for staining the laboratory slides and that is sized to accommodate the laboratory slides; a slide transporter that moves the slide carrier into and out of the vessel; and a spring loaded pin that engages with a surface of the slide stainer to limit free-fall translation of the slide carrier in an event of a power loss. Additionally, during an agitation phase of a slide staining process, the slide transporter is configured to translate the slide carrier in an upward direction to a pre-determined height that is set by a user of the slide stainer, and the slide transporter translates the slide carrier in a downward direction back into the vessel.