Spatial analysis of human colorectal tumors reveals organized immune hubs at the stromal/epithelial interface
This repository contains the analysis code used to generate the figures in the manuscript ”Spatial analysis of human colorectal tumors reveals organized immune hubs at the stromal/epithelial interface.”
The repository is organized by figure and includes representative notebooks illustrating the analytical workflows used in the study. It is not intended to be a fully automated end-to-end reproduction pipeline for all datasets.
Citation will be added upon publication.
| Directory | Figure | Description |
|---|---|---|
fig1_segmentation_and_cell_typing/ |
Figure 1 | Baysor segmentation, hierarchical cell typing (coarse → fine), cross-sample harmonization, and GLMM marker analysis |
fig2_pathology_annotations/ |
Figure 2 | Pathology region annotations |
fig3_tessera_tissue_regions/ |
Figure 3 | Tessera spatial tiling and tissue region identification |
fig4_interface_analysis/ |
Figure 4 | Tumor–immune interface construction and MSI vs MSS / hub+ vs hub− comparisons |
fig5_colocalization/ |
Figure 5 | Spatial colocalization and neighborhood composition analyses |
Each directory contains its own README.md with further details.
Input data required to run these notebooks are not included in this repository. Data will be made available upon publication.