Cancer-associated fibroblast phenotypes predict patient outcome in non-small cell lung cancer

Data for the manuscript "Cancer-associated fibroblast phenotypes are associated with patient outcome in non-small cell lung cancer " containing RAW IMC acquisition data (mcd files and .txt files), single cell objects (raw and annotated), cell and tumour-stroma segmentation masks, output from CellProfiler (panel, Cells, Image, acquisition metadata), necessary clinical data and patient stratification (into high and low, prognostic patient groups).

Clinical data can be found within the metadata (colData) of the single cell experiment (sce).

The masks for 178B had to be regenerated later due to initial data loss due to server migration and wrong saving that was only discovered much later. Regenerating the masks resulted in slightly altered masks with a slight mismatch of cell numbers between the single cell experiment and the cell masks. However: The tissue structure of the masks is exactly the same as in the raw data images and when plotting the coordinates of the cells, coloured by cell_category, there's a mismatch of only 5-15 cells between the number of cells in the sce file and in the new masks. Please consult TMA178_clarification.pdf for this. The data in the SCE is however correct as it was generated from the original masks that back then were checked for the marker expression of all cells.