scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images.
Please refer to our documentation, in particular:
Check out the docs for complete installation instructions. scPortrait currently supports Python 3.10 and 3.11.
To get started you can install scPortrait via pip:
pip install git+https://github.com/MannLabs/scPortrait
Currently the scPortrait framework is being developed using Linux and macOS, and only provides limited Windows support. Please refer to this GitHub issue for more information.
scPortrait was created by Sophia Mädler and Niklas Schmacke in the labs of Matthias Mann, Veit Hornung and Fabian Theis in 2024 and is actively being developed. If you are interested in contributing please reach out to the developers.
If you use our code please cite this manuscript:
SPARCS, a platform for genome-scale CRISPR screening for spatial cellular phenotypes Niklas Arndt Schmacke, Sophia Clara Maedler, Georg Wallmann, Andreas Metousis, Marleen Berouti, Hartmann Harz, Heinrich Leonhardt, Matthias Mann, Veit Hornung bioRxiv 2023.06.01.542416; doi: https://doi.org/10.1101/2023.06.01.542416
If you like this software, you can give us a star to boost our visibility! All direct contributions are also welcome. Feel free to post a new issue or clone the repository and create a pull request with a new branch. For an even more interactive participation, check out the discussions.