|ChipStream|
============
|PyPI Version| |Build Status| |Coverage Status| |Docs Status|
**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 <https://chipstream.readthedocs.io>`__.
Installation
------------
Installers for Windows and macOS are available at the `release page
<https://github.com/DC-analysis/ChipStream/releases>`__.
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
.. |ChipStream| image:: https://raw.github.com/DC-analysis/ChipStream/master/docs/artwork/chipstream_splash.png
.. |PyPI Version| image:: https://img.shields.io/pypi/v/ChipStream.svg
:target: https://pypi.python.org/pypi/ChipStream
.. |Build Status| image:: https://img.shields.io/github/actions/workflow/status/DC-analysis/ChipStream/check.yml?branch=master
:target: https://github.com/DC-analysis/ChipStream/actions?query=workflow%3AChecks
.. |Coverage Status| image:: https://img.shields.io/codecov/c/github/DC-analysis/ChipStream/master.svg
:target: https://codecov.io/gh/DC-analysis/ChipStream
.. |Docs Status| image:: https://img.shields.io/readthedocs/chipstream
:target: https://readthedocs.org/projects/chipstream/builds/
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