starfish: scalable pipelines for image-based transcriptomics

starfish is a Python library for analysis of image-based transcriptomics.

For a brief survey of the package, you can read the Introduction. For more comprehensive instructions on how to use starfish, see the Getting Started section.

Starfish’s documentation also contains instructions on creating image-based transcriptomics processing pipelines, tutorials on running starfish using the API, and a worked example of contributing code to starfish. Finally, advanced users can examine the Data Structures and Help & Reference sections to learn more details about _starfish_ and its object models.

Starfish user support is hosted on the forum where questions and discussion will serve as a continually expanding resource for starfish users. Please post any help or support requests on with the starfish tag.

To see the code or report a bug, please visit the github repository.

To see what improvements the developers have planned for starfish, please see the Roadmap.


  • Filtering: API

  • Spot-Finding: API

  • Decoding: API

  • Segmenting: API