The algorithms described on this page are used to generate the cell-feature matrix files and associated metrics in the output bundle:
cell_feature_matrix.zarr.zipcsc_cell_feature_matrix.zarr.zipanalysis_summary.html: Analysis tabmetrics_summary.csv
To create the cell-feature matrix, the pipeline must ensure that transcripts are accurately assigned to cells. The pipeline uses the DAPI images that were acquired periodically throughout the instrument run to align data collected across cycles. For example, this process aligns the images acquired from one panel to the next in a WTA panel + Panel C configuration run.
Decoded and deduplicated transcripts in 3D with Q-Scores ≥ 20 are assigned to directly overlapping segmented cells to produce a cell-feature matrix. This matrix can be analyzed using conventional and novel single cell and spatial analysis approaches, facilitating integration with existing single cell and spatial datasets.