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

<p>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 &gt; Imaging Technique &gt; Dataset &gt; Tissue &gt; ROI.</p> <p>Each folder contains the corresponding metadata (including original sample information, cell type annotations, and neighborhood annotations) stored in a file named <code>cells.tsv</code>. Additionally, the module used to identify spatial pattern genes includes an <code>anndata</code> format file, named <code>adata_moran.h5ad</code>, which stores the integrated results of scRNA-seq and spatial proteomics.</p> <p>scProAtlas_analysis_code.tar.gz contains example codes for all analysis modules in scProAtlas. Here, we provide the example using <strong>SCP_CODEX1 - Large intestine. </strong>The codes include all the scripts used for the entire workflow, from image segmentation to scRNA-spatial proteomics integration, and spatial analysis.</p> <p>We have also uploaded the raw protein channel matrices with AnnData format in <strong>version 3 and 4.</strong></p>