Cell-level measurements, lineage annotations and clinical metadata for "Robust multicellular programs dissect the complex tumor microenvironment and track disease progression in colorectal cancer"

Cell-level measurements, lineage annotations and clinical metadata for "Robust multicellular programs dissect the complex tumor microenvironment and track disease progression in colorectal cancer"

Preprint: https://doi.org/10.48550/arXiv.2510.05083
Code: https://doi.org/10.5281/zenodo.17186802

Description:

• cell_table.csv: intensity measured per channel and per cell, and cell location and shape descriptors, after artefact filtering (plain text CSV). Use the column fov to map it to the metadata.
• adata_consensus_cell_types.h5ad: cell-level measurements including cell type annotation (AnnData format). Use obs['fov'] to map it to the metadata.
• summary_clinical_data_modified.csv: clinical annotation per sample (plain text CSV). Use the column TMA Localisation to map it to the measurements.

These files are proposed as entry points in reproducing or expanding our analyses. See the repository linked for the details of how the data is processed, and the preprint for scientific context. Multiplexed images and segmentation masks will be provided separately (BioImage Archive).