Segmentation aware probabilistic phenotyping of single-cell spatial protein expression data

This repository contains raw and processed data of the original datasets generated for Lee et al. "Segmentation aware probabilistic phenotyping of single-cell spatial protein expression data". The files Dilution_3_ROI02.ome.tiff, Dilution_3_ROI02_mask.ome.tiff, st_reclustered_expr_data.h5ad contain raw data (as ome tiff), a mesmer-generated segmentation mask, and single-cell quantification in anndata format of the cell pellet data generated for the study. The file tonsil-for-zenodo.tar.gz contains all raw and processed data of the IMC data of the 16 human tonsil ROIs: imc contains raw tiff stacks of the acquisition mask contains mesmer-generated masks channel.yml contains channel info exp_mat/dc/ contains single cell quantifications using mesmer segmentation