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Tools to handle Fluidigm IMC data

Project description


PyPI PyPI - Python Version PyPI - License GitHub Workflow Status (branch)

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


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 and Anton Rau







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