The link to our GitHub page is here:

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.
General workflow of a ISS project
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.
This module contains the necessary software to take your preprocessed images and extract gene expression dots from them.
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 andĀ ISS_CAREĀ :
These are optional modules that can be run at different stages of the pipeline so to enhance image quality for improved dot extraction.

Follow this website

You need to create an Owlstown account to follow this website.

Sign up

Already an Owlstown member?

Log in