All datasets used in this study are already published and were obtained from public data repositories. The SPOTS mouse spleen data was obtained from the GEO repository (accession no. GSE198353, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE198353) 4, the Stereo-CITE-seq mouse thymus data from BGI and the spatial-ATAC-RNA-seq mouse brain data from AtlasXplore (https://web.atlasxomics.com/visualization/Fan) 3. The details of all datasets used are available in the Methods section. The raw data used in this study have been uploaded to Zenodo and is freely available at https://zenodo.org/record/7879713#.ZE3aOnZByUk.