starfish 0.4.0
Pipelines and pipeline components for the analysis of image-based transcriptomics data
Requires Python: <3.14,>=3.10
Keywords: single-cell, image-based, transcriptomics

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
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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 3.10-3.13 and can easily be installed from PyPI:

.. code-block:: bash

    $ 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):

.. code-block:: bash

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

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

.. code-block:: bash

    $ pip install starfish[napari]

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

.. code-block:: bash

    $ pip install starfish[jupyter]

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

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.

.. _`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: `starfish@chanzuckerberg.com <mailto:starfish@chanzuckerberg.com>`_