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