Starfish

Introduction

Starfish is a Python library that lets you build scalable and modular pipelines for processing image-based transcriptomics data. Starfish is developed in the open in collaboration with SpaceTx. SpaceTx is a consortium effort to benchmark image based transcriptomic methods by applying 10 different methods on a common tissue source, standardizing the raw data formats and using standardized analysis pipelines.

For detailed information on installation and usage, see the documentation.

Quickstart

We are currently in pre-alpha, finishing proof of concept pipelines for each of the spaceTx contributors that leverage starfish's shared object model. Follow the links in the table below to see starfish in action on particular assay types. Or, browse our our notebooks directory here.

Assay	Loads Data	Single-FoV Pipeline	Multi-FoV Pipeline
MERFISH	[x]	[x] mer	in process
ISS	[x]	[x] iss	[x]
osmFISH	[x]	[x] osm	[ ]
smFISH	[x]	[x] 3ds	[x]
BaristaSeq	[x]	[x] bar	[ ]
DARTFISH	[x]	[x] dar	[ ]
ex-FISH	[x]	[ ]	[ ]
StarMAP	[x]	[x] str	[ ]
seq-FISH	[x]	in process: seq	[ ]
FISSEQ	no data	no pipeline	[ ]

Contributing

We are very interested in contributions! See our contributing.rst and documentation for more information.

Contact Starfish

You can get in touch with the starfish authors a variety of ways.

1. We can be reached by email.
2. We have an active slack channel on czi-science slack, which you can sign up for here. When you've joined, #starfish-users and #starfish-dev are good places to get fast feedback from our team.
3. The best place to discuss design issues or bug reports is on github.