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    starfish: unified pipelines for image-based transcriptomics

    spacetx spacetx Last update: Nov 04, 2023

    starfish: scalable pipelines for image-based transcriptomics

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    starfish is a Python library for processing images of image-based spatial transcriptomics. It lets you build scalable pipelines that localize and quantify RNA transcripts in image data generated by any FISH method, from simple RNA single-molecule FISH to combinatorial barcoded assays.

    Documentation

    See spacetx-starfish.readthedocs.io for the quickstart, user guide, examples, and API.

    Installation

    starfish supports python 3.7 and above and can easily be installed from PyPI:

    $ pip install starfish[napari]

    For more detailed installation instructions, see here.

    Python Version Notice

    starfish will be dropping support for python 3.6 in the next release due to minimum python=3.7 version requirements in upstream dependencies.

    Contributing

    We welcome contributions from our users! See our contributing.rst and developer guide for more information.

    Help, support, and questions

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    spacetx

    spacetx
    GitHub Repository https://github.com/spacetx
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