utils

a collection of open-source useful utility scripts for processing CODEX data; processing modules are organized by folder and each have their own README.md for step-by-step guidelines

in brief:

• celesta: includes template scripts for batch celesta processing and integrated visualization of assignments, proteomic images, and histology
• pathology: implements post-processing of histology images for figure generation
• segmentation: provides wrappers around mesmer and cellpose for segmentation and cell measurement quantification
• visualization: incorporates various visualization utilities for figure generation

the above were tested using python/3.9.4