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

for the most updated version install directly from Github (starfish release on PyPI might be a few months behind the repo's master branch):

$ pip install starfish@git+https://github.com/spacetx/starfish.git

To install starfish with napari (for interactive visualization), use:

$ pip install starfish[napari]

To install starfish with both napari and jupyter (for notebook support), use:

$ pip install starfish[jupyter]

For any difficulties with dependencies, see more detailed installation instructions at https://spacetx-starfish.readthedocs.io/en/latest/installation/.

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: [email protected]