CytoPix is a graphical user interface for manually segmenting deformability cytometry (DC) images. The mask data (labeled images) can be used for training machine-learning based segmentation algorithms and are also generally useful for benchmarking segmentation algorithms.

Documentation

The documentation is available at cytopix.readthedocs.io.

Installation

Installers for Windows and macOS are available at the release page.

If you have Python installed, you can install CytoPix from PyPI

# graphical user interface
pip install cytopix

Execution

If you have installed CytoPix from PyPI, you can start it with

cytopix
# or
python -m cytopix

Citing CytoPix

Please cite CytoPix either in-line

(...) using the pixel-based segmentation software CytoPix version X.X.X
(available at https://github.com/DC-analysis/CytoPix).

or in a bibliography

Paul Müller and others (2025), CytoPix version X.X.X: Pixel-based
manual segmentation of deformability cytometry images [Software].
Available at https://github.com/DC-analysis/CytoPix.

and replace X.X.X with the version of CytoPix that you used.

Testing

pip install -e .
pip install -r tests/requirements.txt
pytest tests