Immunotherapy response induces divergent tertiary lymphoid structure morphologies in hepatocellular carcinoma

This repository contains imaging mass cytometry (IMC) data and associated files for the publication "Immunotherapy response induces divergent tertiary lymphoid structure morphologies in hepatocellular carcinoma". Code used to analyze these data can be found at https://github.com/FertigLab/HCCTLS. Raw IMC data have been uploaded as .mcd files (n=10). The file "IMCpanel.xlsx" indicates the antibodies used for each IMC channel. In addition, we have uploaded .tiff files (n=38) generated from each .mcd, which were used to identify and annotate individual tertiary lymphoid structures (TLS) as some ROI had multiple TLS. The file "Updated Catalogue of TLS with S numbers.xlsx" indicates which TLS correspond to each ROI in the .mcd files. To determine the area of each TLS, .tiff files were annotated using ImageJ and the area of each TLS was exported and stored in the file, "TLS_selection_area_pixels.csv". The XY coordinates of individual TLS were obtained by using FlowJo software to annotate .fcs files resulting from single cell segmentation of each ROI.