Python package for processing segmented multi-channel images
Documentation is available at https://bodenmillergroup.github.io/imctoolkit
This package requires Python 3.8 or later.
Python package dependencies are listed in requirements.txt.
Optional Python package dependencies include:
- anndata for exporting single-cell data as AnnData object
- fcswrite for writing single-cell data as FCS file
- networkx for exporting spatial cell graphs to networkx
- python-igraph for exporting spatial cell graphs to igraph
- opencv-python for faster image processing
Using virtual environments is strongly recommended.
Install imctoolkit and its dependencies with:
pip install imctoolkit
To also install optional dependencies (see above):
pip install imctoolkit[all]
See Quickstart
Created and maintained by Jonas Windhager jonas.windhager@uzh.ch
quickstart
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