Data

Tools

Indexes

Applications

Experiments

Open Source Science

starfish

starfish: scalable pipelines for image-based transcriptomics - Published in JOSS (2021)

https://github.com/spacetx/starfish

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in JOSS metadata
  • ✓
    Academic publication links
    Links to: nature.com
  • ✓
    Committers with academic emails
    1 of 30 committers (3.3%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

human-cell-atlas imaging python transcriptomics

Keywords from Contributors

bioinformatics anndata scanpy scverse neuroscience pypi annotations mesh

Scientific Fields

Engineering Computer Science - 40% confidence
Last synced: 4 months ago · JSON representation

Repository

starfish: unified pipelines for image-based transcriptomics

Basic Info
Statistics
  • Stars: 237
  • Watchers: 19
  • Forks: 70
  • Open Issues: 174
  • Releases: 44
Topics
human-cell-atlas imaging python transcriptomics
Created over 8 years ago · Last pushed 5 months ago
Metadata Files
Readme Changelog Contributing License

README.rst 

starfish: scalable pipelines for image-based transcriptomics
============================================================

.. image:: https://github.com/spacetx/starfish/blob/64add94b51dbf6f8f5fd614b02c4dfbf4b0d702d/docs/source/_static/design/logo.png?raw=True
    :alt: starfish logo
    :width: 312
    :height: 127
    :align: center

-----------------------------

.. image:: https://img.shields.io/badge/dynamic/json.svg?label=forum&url=https%3A%2F%2Fforum.image.sc%2Ftags%2Fstarfish.json&query=%24.topic_list.tags.0.topic_count&colorB=brightgreen&suffix=%20topics&logo=data:image/png;base64,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
    :target: https://forum.image.sc/tag/starfish
    :alt: Image.sc forum

.. image:: https://img.shields.io/pypi/v/starfish
    :target: https://pypi.org/project/starfish/
    :alt: PyPI

.. image:: https://img.shields.io/pypi/dm/starfish
   :target: https://pypistats.org/packages/starfish
   :alt: PyPI - Downloads

.. image:: https://readthedocs.org/projects/spacetx-starfish/badge/?version=latest
    :target: https://spacetx-starfish.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status

.. image:: https://github.com/spacetx/starfish/actions/workflows/starfish-prod-ci.yml/badge.svg?branch=master
    :target: https://github.com/spacetx/starfish/actions/workflows/starfish-prod-ci.yml
    :alt: starfish production CI

.. image:: https://codecov.io/gh/spacetx/starfish/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/spacetx/starfish
    :alt: Code Coverage

-------------------------------

**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 3.9-3.12 and can easily be installed from PyPI:

.. code-block:: bash

    $ pip install starfish[napari]

`Some operating systems might need different dependencies for napari. For more detailed installation instructions, see here `_.

Python Version Notice
---------------------

starfish will be dropping support for python 3.9 in future release when
upstream dependencies will require a minimum python=3.10 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 `_
- Email: `starfish@chanzuckerberg.com `_

Owner

  • Name: spacetx
  • Login: spacetx
  • Kind: organization

JOSS Publication

starfish: scalable pipelines for image-based transcriptomics
Published
May 04, 2021
DOI
Volume 6, Issue 61, Page 2440
Authors
Shannon Axelrod
Chan Zuckerberg Initiative
Matthew Cai ORCID
Chan Zuckerberg Initiative
Ambrose J. Carr ORCID
Chan Zuckerberg Initiative
Jeremy Freeman ORCID
Chan Zuckerberg Initiative
Deep Ganguli
Chan Zuckerberg Initiative
Justin T. Kiggins ORCID
Chan Zuckerberg Initiative
Brian Long ORCID
Allen Institute for Brain Science
Tony Tung
Chan Zuckerberg Initiative
Kevin A. Yamauchi ORCID
Chan Zuckerberg Biohub
Editor
Charlotte Soneson ORCID
Tags
xarray skimage microscopy imaging biology single cell biology spatial transcriptomics MERFISH In Situ Sequencing osmFISH smFISH BaristaSeq dartfish starmap seqFISH
View PDF Review Thread Software Archive

Papers & Mentions

Total mentions: 1

BARcode DEmixing through Non-negative Spatial Regression (BarDensr)
Last synced: 2 months ago

GitHub Events

Total
  • Create event: 36
  • Release event: 3
  • Issues event: 28
  • Watch event: 7
  • Delete event: 29
  • Issue comment event: 40
  • Push event: 43
  • Pull request review comment event: 6
  • Pull request review event: 42
  • Pull request event: 77
  • Fork event: 3
Last Year
  • Create event: 36
  • Release event: 3
  • Issues event: 28
  • Watch event: 7
  • Delete event: 29
  • Issue comment event: 40
  • Push event: 43
  • Pull request review comment event: 6
  • Pull request review event: 42
  • Pull request event: 77
  • Fork event: 3

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 1,450
  • Total Committers: 30
  • Avg Commits per committer: 48.333
  • Development Distribution Score (DDS): 0.723
Past Year
  • Commits: 39
  • Committers: 4
  • Avg Commits per committer: 9.75
  • Development Distribution Score (DDS): 0.385
Top Committers
Name Email Commits
Tony Tung t****g@m****g 402
Tony Tung t****g@c****m 300
Ambrose J Carr a****r 208
Deep Ganguli d****i@g****m 127
shanaxel42 s****d@c****m 111
Justin Kiggins j****s@g****m 63
Josh Moore j****h@g****m 41
Nicholas Mei n****i@o****m 36
mattcai 3****i 31
dependabot[bot] 4****] 27
shachafl 6****l 24
kevinyamauchi k****i@g****m 16
freeman-lab t****b@g****m 16
Marcus Kinsella m****a@c****m 11
Kira Evans c****t@k****e 6
sofroniewn s****n@g****m 5
Deep Ganguli d****i@s****m 5
Brian Long b****l 4
Charlotte Soneson c****n@g****m 3
Olga Botvinnik o****k@g****m 2
nickeener 3****r 2
Markus J. Ankenbrand m****s@a****e 2
xchang1 3****1 1
sgratiy 3****y 1
Ola Tarkowska 1****a 1
Jan Eglinger j****r@g****m 1
Gökçen Eraslan g****n@g****m 1
MikeDMorgan m****n@s****k 1
Dany 7****u 1
Chris Roat 1****t 1
Committer Domains (Top 20 + Academic)
chanzuckerberg.com: 3 sanger.ac.uk: 1 ankenbrand.me: 1 stitchfix.com: 1 kne42.me: 1 glencoesoftware.com: 1 merly.org: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 49
  • Total pull requests: 161
  • Average time to close issues: 4 months
  • Average time to close pull requests: 3 months
  • Total issue authors: 20
  • Total pull request authors: 18
  • Average comments per issue: 1.43
  • Average comments per pull request: 1.32
  • Merged pull requests: 97
  • Bot issues: 0
  • Bot pull requests: 71
Past Year
  • Issues: 20
  • Pull requests: 72
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 4 days
  • Issue authors: 2
  • Pull request authors: 5
  • Average comments per issue: 0.35
  • Average comments per pull request: 0.56
  • Merged pull requests: 61
  • Bot issues: 0
  • Bot pull requests: 22
View more stats
Top Authors
Issue Authors
  • shachafl (21)
  • vals (7)
  • iimog (4)
  • mattcai (2)
  • neuromusic (1)
  • ora-lv (1)
  • sebherbert (1)
  • ambrosejcarr (1)
  • mstemmer (1)
  • giovp (1)
  • johnfmarkham (1)
  • ryandikdan (1)
  • shanaxel42 (1)
  • juliomateoslangerak (1)
  • hziyin (1)
Pull Request Authors
  • dependabot[bot] (89)
  • shachafl (59)
  • ttung (12)
  • berl (6)
  • neuromusic (5)
  • njmei (4)
  • nickeener (3)
  • iimog (3)
  • chaichontat (2)
  • mattcai (2)
  • sgratiy (1)
  • ivanmilevtues (1)
  • ora-lv (1)
  • haoxusci (1)
  • pjb7687 (1)
Top Labels
Issue Labels
bug (38) docs (5) dependencies (5) feature (2) high priority (1) python (1)
Pull Request Labels
dependencies (89) python (15) docs (3) github_actions (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 2,771 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 5
  • Total versions: 52
  • Total maintainers: 4
pypi.org: starfish

Pipelines and pipeline components for the analysis of image-based transcriptomics data

  • Versions: 52
  • Dependent Packages: 1
  • Dependent Repositories: 5
  • Downloads: 2,771 Last month
Rankings
Stargazers count: 4.6%
Forks count: 5.4%
Dependent repos count: 6.6%
Average: 9.6%
Dependent packages count: 10.1%
Downloads: 21.4%
Maintainers (4)
tonytung ambrosejcarr shanaxel42 shachafl
Last synced: 4 months ago

Dependencies

.github/workflows/starfish-prod-ci.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
docker/Dockerfile docker
  • python 3.7-slim-stretch build