ArticleBio-protocol2026
sc3D: A Comprehensive Tool for 3D Spatial Transcriptomic Analysis.
Article in Bio-protocol, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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3 authors.
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Abstract
Serial spatial omics technologies capture genome-wide gene expression patterns in thin tissue sections but lose spatial continuity along the third dimension. Reconstructing these two-dimensional measurements into coherent three-dimensional volumes is necessary to relate molecular domains, gradients, and tissue architecture within whole organs or embryos. sc3D is an open-source Python framework that registers consecutive spatial transcriptomic sections, interpolates bead coordinates in three dimensions, and stores the result in an AnnData object compatible with Scanpy. The workflow performs slice alignment, 3D reconstruction, optional downsampling, and interactive visualization in a napari-sc3D-viewer, enabling virtual in situ hybridization and spatial differential gene expression analysis. We tested sc3D on Slide-seq and Stereo-seq datasets, including E8.5 and E16.5 mouse embryos, recovering continuous tissue morphologies, cardiac anatomical markers, and the expected anterior-posterior gradients of
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