biopsy_spatial_CosMx_longitudinal.h5ad

CosMx 1000-plex RNA-ISH dataset of formalin-fixed, paraffin-embedded (FFPE) colon biopsies from healthy controls and patients with ulcerative colitis pre and post treatment, responders and non-responders. Fine_annotation_3 used for manuscript. Addendum 8/29/24 raw fov_positions_file, transposed_exprMat_file, and metadata were added to read into squidpy. Addendum 8/3/24 transcript coordinate file was generated and uploaded as CosMx_unfilteredtranscriptCoords.csv, this does not have negative probes.