The link to our GitHub page is here: https://github.com/Moldia

To process our images and data we grouped our current analysis software in different modules. This is because different steps of the process require different (and incompatible) Python packages. Each module requires the creation of a specific conda environment and a set of specific instructions for running.

ISS_preprocessing:
This module contains the necessary software for pre-processing your raw images from the microscope so they become compatible with the downstream steps. In this module your images are maximum-projected, stitched and aligned across cycles.

ISS_decoding:
This module contains the necessary software to take your preprocessed images and extract gene expression dots from them.

ISS_postprocessing:
This module contains the software you need to assign expression dots to individual cells and cluster the cells according to their transcriptomics signatures. It also contains functions for high-level spatial analysis.

ISS_deconvolution and ISS_CARE :
These are optional modules that can be run at different stages of the pipeline so to enhance image quality for improved dot extraction.