Processed CODEX Datasets from - Discovery and Generalization of Tissue Structures from Spatial Omics Data

This entry provides access to processed CODEX data files of four studies analyzed in the article "Discovery and Generalization of Tissue Structures from Spatial Omics Data". Details of datasets can be found in the STAR Methods section of the article.

For each dataset, a zip file containing multiple comma-separated values (CSV) files is included.

Each region is assigned an unique identifier (e.g., DKD_kidney_001), and its related data files are:

`{region_id}.cell_data.csv`, a table containing three columns: "CELL_ID", "X", and "Y". This table provides centroid locations for all cells segmented in this region.

`{region_id}.expression.csv`, a table containing multiple columns: "CELL_ID", "DAPI", "CD45", etc. This table provides detailed protein biomarker expression quantified for all cells in this region.

`{region_id}.scgp_annotations.csv`, a table containing two columns: "CELL_ID" and "SCGP". This table provides SCGP/SCGP-Extension annotations for all cells in this region.

Code base for SCGP is also included in this entry. Please refer to https://gitlab.com/enable-medicine-public/scgp for the latest codes, questions, and/or issues. Raw CODEX data and images will be accessible through links posted at the code base. Raw data will also be available from lead contact (A.E.T.) upon request.