imctools
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BodenmillerGroup
Tools to handle IMC data
imctools
Deprecation note: This repository is not actively maintained. For a maintained IMC file parser implementation please refer to readimc.
Background
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
Requirements
This package requires Python 3.7 or later.
Using virtual environments is strongly recommended.
Installation
Install imctools and its dependencies with:
pip install imctools
Usage
See Quickstart
Authors
Created and maintained by Vito Zanotelli [email protected] and Anton Rau [email protected]
BodenmillerGroup