scProAtlas: an atlas of multiplexed single-cell spatial proteomics imaging in human tissues

All analysis results for the spatial proteomics imaging techniques in the scProAtlas database are stored in compressed files named accordingly. Within each compressed file, the folders are organized in a fixed storage structure in the following order: Analysis module > Imaging Technique > Dataset > Tissue > ROI. Each folder contains the corresponding metadata (including original sample information, cell type annotations, and neighborhood annotations) stored in a file named cells.tsv. Additionally, the module used to identify spatial pattern genes includes an anndata format file, named adata_moran.h5ad, which stores the integrated results of scRNA-seq and spatial proteomics. scProAtlas_analysis_code.tar.gz contains example codes for all analysis modules in scProAtlas. Here, we provide the example using SCP_CODEX1 - Large intestine. The codes include all the scripts used for the entire workflow, from image segmentation to scRNA-spatial proteomics integration, and spatial analysis. We have also uploaded the raw protein channel matrices with AnnData format in version 3 and 4.