Deprecation note: This repository is not actively maintained. For a maintained IMC file parser implementation please refer to readimc.
An IMC file conversion tool that aims to convert IMC raw data files (.mcd, .txt) into an intermediary ome.tiff, containing all the relevant metadata. Further it contains tools to generate simpler TIFF files that can be directly be used as input files for e.g. CellProfiller, Ilastik, Fiji etc.
Documentation is available at https://bodenmillergroup.github.io/imctools
This package requires Python 3.7 or later.
Using virtual environments is strongly recommended.
Install imctools and its dependencies with:
pip install imctools
See Quickstart
Created and maintained by Vito Zanotelli vito.zanotelli@uzh.ch and Anton Rau anton.rau@uzh.ch