GUI and CLI for DC data postprocessing
Project description
ChipStream is a graphical user interface for postprocessing deformability cytometry (DC) data. This includes background computation, event segmentation, and feature extraction.
Documentation
The documentation, is available at chipstream.readthedocs.io.
Installation
Installers for Windows and macOS are available at the release page.
If you have Python installed, you can install ChipStream from PyPI
# graphical user interface pip install chipstream[gui] # command-line interface pip install chipstream[cli] # both pip install chipstream[cli,gui]
Since version 0.6.0, you can also make use of torch-based segmentation models.
pip install chipstream[cli,gui,torch]
If you have a CUDA-compatible GPU and your Python installation cannot access the GPU (torch.cuda.is_available() is False), please use the installation instructions from pytorch (https://pytorch.org/get-started/locally/). For instance, if you have CUDA 12.1, you can install torch with this pytorch.org index URL:
pip install torch torchvision --index-url https://download.pytorch.org/whl/cu121
Execution
If you have installed ChipStream from PyPI, you can start it with
# graphical user interface chipstream-gui # command-line interface chipstream-cli
Citing ChipStream
Please cite ChipStream either in-line
(...) using the postprocessing software ChipStream version X.X.X (available at https://github.com/DC-analysis/ChipStream).
or in a bibliography
Paul Müller and others (2023), ChipStream version X.X.X: Postprocessing software for deformability cytometry [Software]. Available at https://github.com/DC-analysis/ChipStream.
and replace X.X.X with the version of ChipStream that you used.
Testing
pip install -e . pip install -r tests/requirements.txt pytest tests
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