imctoolkit¶
Python package for processing segmented multi-channel images
Documentation is available at https://bodenmillergroup.github.io/imctoolkit
Requirements¶
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.
Installation¶
Install imctoolkit and its dependencies with:
pip install imctoolkit
To also install optional dependencies (see above):
pip install imctoolkit[all]
Usage¶
See Quickstart
Authors¶
Created and maintained by Jonas Windhager jonas.windhager@uzh.ch