starfish: scalable pipelines for image-based transcriptomics
starfish is a Python library for processing images of image-based spatial transcriptomics. It lets you build scalable pipelines that localize and quantify RNA transcripts in image data generated by any FISH method, from simple RNA single-molecule FISH to combinatorial barcoded assays.
- Starfish enterprise: finding RNA patterns in single cells, Nature Technology Feature, Aug 2019
- Developing a Computational Pipeline and Benchmark Datasets for Image-Based Transcriptomics, ASCB Science News, Dec 2018
starfish supports python 3.6 and above (python 3.7 recommended) and can easily be installed from Pypi:
$ pip install starfish[napari]