This repository contains scripts used to convert ISS data (.czi raw images) into starfish format , as well as some other scripts used to run Starfish itself For more information about MATLAB toolbox for Bio-Formats, see https://www.openmicroscopy.org/bio-formats/downloads/ (forked version included in this repo)

Xiaoyan, 2019

Three main folders are found:

• SpaceTxFormat: contains the script used to convert from .czi raw images into starfish format.
• Starfish: contains Starfish pipeline, developed by Starfish to do spatial transcriptomic analysis
• lib: repository containing all the functions used for implementing all