starfish: scalable pipelines for image-based transcriptomics

Jupyter Notebook Python wdl Submitted 29 June 2020Published 04 May 2021

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Shannon Axelrod, Matthew Cai (0000-0003-4998-6328), Ambrose J. Carr (0000-0002-8457-2836), Jeremy Freeman (0000-0001-7077-7972), Deep Ganguli, Justin T. Kiggins (0000-0002-4638-7015), Brian Long (0000-0002-7793-5969), Tony Tung, Kevin A. Yamauchi (0000-0002-7818-1388)


Axelrod et al., (2021). starfish: scalable pipelines for image-based transcriptomics. Journal of Open Source Software, 6(61), 2440,

@article{Axelrod2021, doi = {10.21105/joss.02440}, url = {}, year = {2021}, publisher = {The Open Journal}, volume = {6}, number = {61}, pages = {2440}, author = {Shannon Axelrod and Matthew Cai and Ambrose J. Carr and Jeremy Freeman and Deep Ganguli and Justin T. Kiggins and Brian Long and Tony Tung and Kevin A. Yamauchi}, title = {starfish: scalable pipelines for image-based transcriptomics}, journal = {Journal of Open Source Software} }
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xarray skimage microscopy imaging biology single cell biology spatial transcriptomics MERFISH In Situ Sequencing osmFISH smFISH BaristaSeq dartfish starmap seqFISH

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