Example Pipelines

Starfish pipelines tailored for image data generated by groups using various image-based transcriptomics assays. When adapting these examples for other data sets, be cognizant that pipelines must be designed for the imaging system properties, sample characteristics, as well as the assay used.

ISS Processing Workflow

ISS Processing Workflow

Processing sequential smFISH in 3D

Processing sequential smFISH in 3D

STARmap processing example

STARmap processing example

Reproduce published osmFISH results with starfish

Reproduce published osmFISH results with starfish

Reproduce published MERFISH results with starfish

Reproduce published MERFISH results with starfish

BaristaSeq Processing Workflow

BaristaSeq Processing Workflow

Reproduce DARTFISH results with starfish

Reproduce DARTFISH results with starfish