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imctoolkit

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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 [email protected]

Contributing

Contributing

Changelog

Changelog

License

MIT

Contents

quickstart
api_reference
CONTRIBUTING
CHANGELOG
LICENSE

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