"Chemotherapy-driven intestinal dysbiosis and indole-3- propionic acid rewire myelopoiesis to promote a metastasis-refractory state" IMC dataset

This upload contains the raw and processed IMC dataset from the publication. The files include: Raw IMC dataset in the archive "imc_raw.zip" Command list to preprocess the file using steinbock docker package in "commandList.txt" Segmentation masks for each slide obtained used steinpose napari plugin in "masks.zip", cellpose v2 parameters included Manual cell annotation table in "annotation_manual.zip", parameters included Fully analyzed R dataset in "spe_analyzed.rds" Analysis and visualization script in "analysis_script.R" Differential abundance results for celltypes and neighborhoods in "cells_statistics.xlsx"