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 3.10-3.13 and can easily be installed from PyPI:
$ pip install starfishfor 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.gitTo 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]Python Version Notice
starfish will be dropping support for python 3.10 in future release when upstream dependencies will require a minimum python=3.11 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
4 maintainers
Metadata
4 maintainers
Release files for starfish 0.4.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| starfish-0.4.0.tar.gz | 282.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| starfish-0.4.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 681.2 kB
Release files / starfish-0.4.0.tar.gz
| Download URL | starfish-0.4.0.tar.gz |
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| Size | 282.7 kB |
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Release files / starfish-0.4.0-py3-none-any.whl
| Download URL | starfish-0.4.0-py3-none-any.whl |
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| Size | 398.5 kB |
| Tags | Python 3 |
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twine/6.2.0 CPython/3.10.19
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