Installation

Installation#

Install package#

InterSCellar can be installed via pip from PyPI:

pip install interscellar

Or install from source:

git clone https://github.com/hms-dbmi/InterSCellar.git
cd InterSCellar
pip install -e .

Requirements#

InterSCellar requires Python 3.8 or higher and the following dependencies:

  • numpy >= 1.20.0

  • pandas >= 1.3.0

  • scipy >= 1.7.0

  • scikit-image >= 0.18.0

  • opencv-python >= 4.5.0

  • zarr >= 2.10.0

  • dask[array] >= 2021.0.0

  • matplotlib >= 3.4.0

  • seaborn >= 0.11.0

  • tqdm >= 4.62.0

Optional dependencies:

  • anndata >= 0.8.0 (for AnnData integration)

  • napari >= 0.4.0 (for visualization)

  • duckdb >= 0.6.0 (for database operations)

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