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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.


See for the quickstart, user guide, examples, and API.


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.


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

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