Note: This package is still under very active development.

Recommended for end-users. Install the latest harpy-analysis PyPI package with the extra dependencies in a local Python environment. Note that the cellpose package is pinned to version 3. The recent Version 4 is compatible, but does not align yet with the current documentation.

uv venv --python=3.12 # set python version
source .venv/bin/activate # activate the virtual environment
uv pip install 'harpy-analysis[extra]' 'cellpose==3.1.1.2' # use uv to pip install dependencies and pin cellpose
python -c 'import harpy; print(harpy.__version__)' # check if the package is installed

Only for developers. Clone this repository locally, install the .[dev] instead of the [extra] dependencies and read the contribution guide.

# Clone repository from GitHub
uv venv --python=3.12 # set python version
source .venv/bin/activate # activate the virtual environment
uv pip install -e '.[dev]' 'cellpose==3.1.1.2' # use uv to pip install dependencies and pin cellpose
python -c 'import harpy; print(harpy.__version__)' # check if the package is installed
# make changes
python -m pytest # run the tests

Checkout the docs for more installation instructions.

Tutorials are available here.

Learn how Harpy can be integrated into your workflow in different ways.

See here for info on how to contribute to Harpy.

• https://github.com/ashleve/lightning-hydra-template

Check the license. Harpy is free for academic usage. For commercial usage, please contact Saeyslab.

If you encounter any problems, please file an issue along with a detailed description.