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.

• Starfish enterprise: finding RNA patterns in single cells, Nature Technology Feature, Aug 2019
• Developing a Computational Pipeline and Benchmark Datasets for Image-Based Transcriptomics, ASCB Science News, Dec 2018

Documentation

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

Installation

starfish supports python 3.9-3.12 and can easily be installed from PyPI:

$ pip install starfish[napari]

Some operating systems might need different dependencies for napari. For more detailed installation instructions, see here.

Python Version Notice

starfish will be dropping support for python 3.9 in future release when upstream dependencies will require a minimum python=3.10 version.

Contributing

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

Help, support, and questions

• Forum: ask on the Image.sc forum
• Email: starfish@chanzuckerberg.com