ttung / starfish

starfish: standardized pipelines for image-based transcriptomics

Starfish

Introduction

The goal of starfish is to prototype a reference pipeline for the analysis of image-based transcriptomics data that works for each image-based transcriptomic assay. This is a work in progress and will be developed in the open.

We are currently in pre-alpha, finishing proof of concept pipelines for each of the spaceTx contributors that leverage starfish's shared object model. At this time starfish is mature enough to support computational developers interested in adapting other assays to starfish's object model.

Assay	Loads Data	Single-FoV Pipeline	Multi-FoV Pipeline
MERFISH	[x]	[x]	in process
ISS	[x]	[x]	in process
osmFISH	[x]	in process	[ ]
allen_smFISH	[x]	in review	[ ]
BaristaSeq	[x]	in process	[ ]
DARTFISH	[x]	in review	[ ]
ex-FISH	[x]	[ ]	[ ]
StarMAP	[ ]	[ ]	[ ]
FISSEQ	no data	no pipeline	[ ]
seq-FISH	[ ]	[ ]	[ ]
Imaging Mass. Cyto.	[x]	[ ]	[ ]

Concept

See this document for details. The diagram below describes the core pipeline components and associated file manifests that this package plans to standardize and implement.

Documentation

For more information on installation, usage, and the starfish API and CLI, please see the documentation