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starfish: scalable pipelines for image-based transcriptomics

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Image.sc forum PyPI PyPI - Downloads Documentation Status https://travis-ci.com/spacetx/starfish.svg?branch=master

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 3.6 and above (python 3.7 recommended) and can easily be installed from Pypi:

$ pip install starfish[napari]

For more detailed installation instructions, see here.

Contributing

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

Help, support, and questions