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 <https://www.nature.com/articles/d41586-019-02477-9>_, Nature Technology Feature, Aug 2019
• Developing a Computational Pipeline and Benchmark Datasets for Image-Based Transcriptomics <https://www.ascb.org/science-news/developing-a-computational-pipeline-and-benchmark-datasets-for-image-based-transcriptomics/>_, ASCB Science News, Dec 2018

Documentation

See spacetx-starfish.readthedocs.io <https://spacetx-starfish.readthedocs.io/en/latest/>_ for the quickstart <https://spacetx-starfish.readthedocs.io/en/latest/gallery/quick_start/plot_quick_start.html>, user guide <https://spacetx-starfish.readthedocs.io/en/latest/user_guide/>, examples <https://spacetx-starfish.readthedocs.io/en/latest/gallery/>, and API <https://spacetx-starfish.readthedocs.io/en/latest/api/>.

Installation

starfish supports python 3.7 and above and can easily be installed from PyPI:

.. code-block:: bash

$ pip install starfish[napari]

For more detailed installation instructions, see here <https://spacetx-starfish.readthedocs.io/en/latest/installation/>_.

Python Version Notice

starfish will be dropping support for python 3.6 in the next release due to minimum python=3.7 version requirements in upstream dependencies.

Contributing

We welcome contributions from our users! See our contributing.rst_ and developer guide_ for more information.

.. _developer guide: https://spacetx-starfish.readthedocs.io/en/latest/developer_guide/ .. _contributing.rst: https://github.com/spacetx/starfish/blob/master/CONTRIBUTING.rst

Help, support, and questions

• Forum: ask on the Image.sc forum <https://forum.image.sc/tag/starfish>_
• Email: [email protected] <mailto:[email protected]>_