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IMC segmentation pipeline

Posted: Wed Apr 11, 2018 6:14 pm
by votti
This thread should collect question about the IMC segmentation pipeline developed in the Bodenmiller lab, described here: ... onPipeline

The open source software based pipeline combines the powerful CellProfiller segmentation software ( and the supervised pixel classifier Ilastik ( using custom CellProfiller modules ( and a script based IMC file format converter ( to extract quantitative information from the single cell cuts in the IMC images.

This pipeline is routinely used in the lab to quantify hundreds of IMC images and was so far used for the following publications:
  • histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data, Schapiro & Jackson et al., Nature Methods, 2017
  • Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry, Schulz et al, Cell Systems, 2017
  • Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry, Chevrier, Crowell & Zanotelli et al, Cell Systems, 2017