QUICHE reveals structural definitions of anti-tumor responses in triple negative breast cancer

Contains preprocessed single-cell imaging data and metadata for Spain, Stanford, and NeoTRIP TNBC cohorts. `.h5ad` objects can be accessed using the read_h5ad function in anndata. For access to the raw imaging data and cell segmentation masks, see the BioStudies imaging repository under the accession S-BIAD1507 at https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1507. 

Spain TNBC cohort (spain_preprocessed.h5ad) contains preprocessed MIBI-TOF imaging data of 314 primary TNBC tumors from five medical centers collected from the CNIO biobank. De-identified patient-level metadata can be found in `adata.obs`.

Stanford TNBC cohort (stanford_preprocessed.h5ad) contains preprocessed MIBI-TOF imaging data of 142 primary TNBC tumors collected from the Stanford hospital. De-identified patient-level metadata can be found in `adata.obs`.

NeoTRIP TNBC cohort from Ref. (https://doi.org/10.1038/s41586-023-06498-3) (nt_preprocessed.h5ad) was originally downloaded from the Zenodo data repository (https://doi.org/10.5281/zenodo.7990870) and contains 119 baseline samples profiled with imaging mass cytometry. De-identified patient-level metadata can be found in `adata.obs`.