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

See spacetx-starfish.readthedocs.io 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.

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.

• Forum: ask on the Image.sc forum
• Email: [email protected]