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.