💫 If you find Harpy useful, please give us a ⭐! It helps others discover the project and supports continued development.
Recommended for end-users.
uv venv --python=3.12 # set python version
source .venv/bin/activate # activate the virtual environment
uv pip install "git+https://github.com/saeyslab/harpy.git#egg=harpy-analysis[extra]" # use uv to pip install dependencies
python -c 'import harpy; print(harpy.__version__)' # check if the package is installedOnly 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]' # use uv to pip install dependencies
python -c 'import harpy; print(harpy.__version__)' # check if the package is installed
# make changes
python -m pytest # run the testsCheckout the docs for installation instructions using conda.
Explore how to use Harpy for segmentation, shallow and deep feature extraction, clustering, and spatial analysis of gigapixel-scale multiplexed data with these step-by-step notebooks:
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🚀 Basic Usage of Harpy
Learn how to read in data, perform tiled segmentation using Cellpose and Dask-CUDA, extract features, and carry out clustering. 👉 Tutorial
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🧩 Pixel and Cell Clustering
Learn how to perform unsupervised pixel- and cell-level clustering using
Harpytogether with FlowSOM. 👉 Tutorial
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🔬 Cell Segmentation
Explore segmentation workflows in
Harpyusing different tools:💡 Want us to add support for another segmentation method? 👉 Open an issue and let us know!
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🧠 Deep Feature Extraction
Discover how
Harpyenables fast, scalable extraction of deep, cell-level features from multiplex imaging data with the KRONOS foundation model for proteomics. 👉 Tutorial💡 Want us to add support for another deep feature extraction method? 👉 Open an issue and let us know!
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🔬 Shallow Feature Extraction
Learn to extract shallow features—such as mean, median, and standard deviation of intensities—from multiplex imaging data with
Harpy. 👉 Tutorial
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🧬 Spatial Transcriptomics
Learn how to analyze spatial transcriptomics data with
Harpy. For detailed information, refer to the SPArrOW documentation.
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🌐 Multiple samples and coordinate systems
Learn how to work with multiple samples, instrinsic and micron coordinates. 👉 Tutorial
📚 For a complete list of tutorials, visit the Harpy documentation.
Learn how Harpy can be integrated into your workflow.
See here for info on how to contribute to Harpy.
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.