This repository accompanies the paper "Spatial single-cell multiomics reveals peripheral immune dysfunction in Parkinson’s and inflammatory bowel disease". The CosMx assays use include CMx Hs Univ Cell Panel RNA kit and CMx Hs IO Panel protein kit. The README files contain all scripts, data structures, and figure-generation code used for this paper. There are also two files containing all computational environment requirments for either R or python used for the analysis of these data. The same information can also be found at: https://github.com/ibd-bcn/CosMx-Bolen/tree/main. This repository also contains an image of the entire tissue microarray, viusalizing the morphology markers contained within the NanoString provided morphology kit: PanCK (green), CD68 (yellow), BM2 (blue), and CD45 (pink). These data were generated in the lab of Dr. Malú Tansey by Dr. MacKenzie L. Bolen. The custom code was written by Marc Buendia, mentored by Dr. Azuecena Salas. If using data or code from this folder, cite: Bolen et al., 2025. Spatial single-cell multiomics reveals peripheral immune dysfunction in Parkinson’s and inflammatory bowel disease.