Multiplex imaging of breast cancer lymph node metastases identifies prognostic single-cell populations independent of clinical classifiers

This repository contains the raw IMC data of ZTMA 26 as continuation of dataset 10.5281/zenodo.7494413. The zip files starting with ZTMA contain the raw IMC measurements (mcd and txt) of those parts of the TMA. The TMA measurements are split up into parts in order to avoid huge files.

Additionally, this repository contains the metadata of the patients analyzed in this study, the panel information and the single-cell data that was extracted from the multiplexed images together with the associated metadata in SingleCellExperiment format for analysis in R.

The analysis.zip folder contains files that were written out during the analysis according to the scripts in https://github.com/BodenmillerGroup/BC_LN_metastses.

The single-cell and other data outputs from CellProfiler can be found in the cpout.zip file.

The IF_whole_sections.zip file contains the IF images of the primary breast cancer sections (czi files) and the extracted single-cell data.