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 3.8 and should be installed from the GitHub repo inside a virtual environment:
$ mkdir starfish
$ cd starfish/
$ python3 -m venv starfish_venv
$ source starfish_venv/bin/activate
$ python3 -m pip install --upgrade pip setuptools wheel
$ python3 -m pip install napari[all]
$ python3 -m pip install notebook seaborn
$ python3 -m pip install git+https://github.com/shachafl/starfish.gitFor detailed installation instructions (currently not updated!), 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]