Abstract: Systems and methods for overlaying image data for a biological sample on spatial analyte data are provided. A first image of the sample on a first substrate and a second image of the sample on the first substrate overlayed on a second substrate are obtained. The second substrate includes spatial fiducials and capture spots. At least one of the first substrate and the second substrate is transparent. A registration for the first image and the second image is determined, using a first pattern of the sample in the first image and a second pattern of the sample in the second image. The registration is used to overlay the first image onto a spatial dataset including spatial analyte data for the capture spots from the sample. A frame of reference of the spatial dataset is known with respect to the second image, based on the spatial fiducials of the second image.

Abstract: Systems and methods for evaluating a biological sample on a substrate are provided. An image of the biological sample and glyphs on the substrate are displayed on a display as a plurality of pixels. Respective indications are received of coordinates within the image of the glyph locations. These and a reference fiducial pattern that includes the plurality of glyphs are used to calculate and display an initial alignment between the image and the fiducial pattern. The alignment is updated through manual user adjustments to glyph coordinates. A set of pixels in the plurality of pixels depicting the biological sample are received from a user. Identification of each capture spot in a plurality of capture spots encompassed by the set of pixels is outputted to an output file, with each respective capture spot being identified within the image for the output file based on the updated alignment.

Abstract: Provided herein are computer-implemented methods including receiving, by a processor, a data set comprising cellular data, and presenting an end user with a visualization tool, wherein the cellular data may include at least one of an antigen binding specificity value associated with a cell receptor and a unique molecular identifier (UMI) count associated with the cell receptor. The visualization tool can provide a dynamic display of the data set by generating a visual sequence from the data set, displaying at least a portion of the generated visual sequence, and displaying in response to a user interaction with the visualization tool, the antigen binding specificity value or the UMI associated with the cell receptor in conjunction with the at least a portion of the visual sequence. The visual sequences include sets of indicia corresponding paired chains of the cell receptor.

Abstract: Systems and methods for overlaying image data for a biological sample on spatial analyte data are provided. A first image of the sample on a first substrate and a second image of the sample on the first substrate overlayed on a second substrate are obtained. The second substrate includes spatial fiducials and capture spots. At least one of the first substrate and the second substrate is transparent. A registration for the first image and the second image is determined, using a first pattern of the sample in the first image and a second pattern of the sample in the second image. The registration is used to overlay the first image onto a spatial dataset including spatial analyte data for the capture spots from the sample. A frame of reference of the spatial dataset is known with respect to the second image, based on the spatial fiducials of the second image.