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: Provided in some aspects are methods of patterning a surface in situ for producing an array on the surface, for example, by partitioning of beads comprising oligonucleotides into spatially predefined regions, to generate unique DNA sequences in spatial positions in the array. Compositions such as nucleic acid arrays produced by the methods are also disclosed.

Abstract: The present disclosure relates in some aspects to methods for manufacturing molecular arrays using a hybrid approach comprising microfluidics-based delivery and photolithography-guided oligonucleotide hybridization and ligation. In particular, the molecular arrays can be used for determining spatial patterns of abundance and/or expression of a biological target in a sample.

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: A tissue processing station includes a housing and a first heated plate that is either disposed on or forms a first horizontally oriented surface of the housing. The first heated plate is configured to either (i) contain water, or (ii) receive a dish containing water. The tissue processing station may also include a vertically-oriented heated well for heating slides. A second heated plate is either disposed on or forms an angled surface of the housing for supporting one or more laboratory slides. The angled surface is angled relative to the first horizontally oriented surface. A third heated plate is either disposed on or forms a second horizontally oriented surface of the housing for supporting one or more laboratory slides. The first and second horizontally oriented surfaces are defined at different elevations on the housing. The angled surface extends between the two horizontally oriented surfaces.

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: 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 station includes a housing and a first heated plate that is either disposed on or forms a first horizontally oriented surface of the housing. The first heated plate is configured to either (i) contain water, or (ii) receive a dish containing water. The tissue processing station may also include a vertically-oriented heated well for heating slides. A second heated plate is either disposed on or forms an angled surface of the housing for supporting one or more laboratory slides. The angled surface is angled relative to the first horizontally oriented surface. A third heated plate is either disposed on or forms a second horizontally oriented surface of the housing for supporting one or more laboratory slides. The first and second horizontally oriented surfaces are defined at different elevations on the housing. The angled surface extends between the two horizontally oriented surfaces.

Abstract: Methods for determining a location of a feature on an array include: (a) providing a first array with a first plurality of features immobilized on a first substrate; (b) providing a second array with a second plurality of features immobilized on a second substrate; (c) aligning the first array with the second array; (d) hybridizing a first barcoded oligonucleotide of the first array to a second barcoded oligonucleotide of the second array, thereby producing a combined nucleic acid that includes first and second spatial barcodes; (e) determining all or a portion of the sequence of the combined nucleic acid; and (f) identifying the second barcoded oligonucleotide associated with the first barcoded oligonucleotide in the combined nucleic acid, and determining the location of a second feature in the second array.

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: 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: Methods and systems for designing large sets of barcodes that ensure robust and efficient error correction capabilities are described. Also described are methods for assigning barcodes to target analytes that minimize optical crowding in in situ detection applications. Furthermore, methods for performing barcode error correction and for performing barcode-assisted image registration and alignment are also described.

Abstract: Methods and systems for designing large sets of barcodes that ensure robust and efficient error correction capabilities are described. Also described are methods for assigning barcodes to target analytes that minimize optical crowding in in situ detection applications. Furthermore, methods for performing barcode error correction and for performing barcode-assisted image registration and alignment are also described.

Abstract: Methods and systems for designing large sets of barcodes that ensure robust and efficient error correction capabilities are described. Also described are methods for assigning barcodes to target analytes that minimize optical crowding in in situ detection applications. Furthermore, methods for performing barcode error correction and for performing barcode-assisted image registration and alignment are also described.

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

Abstract: The present disclosure relates to compositions and methods for generating capture probes on a substrate for identifying the location of analytes in a biological sample.

Abstract: This disclosure provides methods for spatial profiling of biological analytes present in a biological sample. Methods include generating feature arrays using a master/copy format using recessed arrays, and methods for using such arrays. For example spatially-tagged analyte capture analytes can be used in spatial detection in methods to determine the location of analytes (e.g., proteins) in biological samples.

Abstract: A method for ascertaining differential accessibility of (TF) binding motifs in open chromatin regions of cells, comprising receiving a cell barcode genomic sequence dataset; aligning each of a plurality of fragment sequence reads to a reference sequence; identifying peaks defined by the aligned plurality of fragment sequence reads; generating a peak-barcode matrix that is comprised of peaks for each cell barcode; clustering cells with peaks having similar chromatin accessibility profiles into a cell cluster to form one or more cell clusters; generating a TF barcode matrix that maps each peak in the peak-barcode matrix to one or more given TF binding motif(s); performing a differential accessibility analysis, wherein the analysis identifies differences in accessibility of peaks and TF binding motifs associated with each identified cell cluster relative to all other identified cell clusters; and generating an output of one or more refined cell clusters based on the differential accessibility analysis.