Image analysis scripts for PhD thesis (Heide F B Murray)

This release contains scripts utilized in data analysis and figure making in the thesis by Heide Murray (Harvard CB program, 2026). A total of three scripts are included: chromogenic_IHC-2.ipynb: quantifies and analyzes organoid slices stained with DAB stains for markers of interest, using edge-to-edge quantifiations of grayscale pixel intensity mask_and_quant.py: creates a mask from cell body stain and applies to channel of interest to quantify signal and count_puncta_nuclei.py: counts puncta, nuclei, and outputs relevant quantifications and metrics All scripts were utilized for image processing and quantification using standard algorithms and methods.