TY  - JOUR
TI  - sc3D: A Comprehensive Tool for 3D Spatial Transcriptomic Analysis
AU  - Sendra, Miquel 
AU  - Bolondi, Adriano 
AU  - Guignard, Léo 
VL  - 16
IS  - 4
PY  - 2026
DA  - 2026/02/20
SP  - e5607
C1  - Bio-protocol 2026;16:e5607
DO  - 10.21769/BioProtoc.5607
UR  - https://doi.org/10.21769/BioProtoc.5607
AB  - 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 Hox gene expression. These results show that sc3D allows reproducible reconstruction and analysis of volumetric spatial omics data across different samples and experimental platforms.
KW  - sc3D
KW  - Spatial transcriptomics
KW  - Slide-seq
KW  - 3D reconstruction
KW  - Virtual in situ hybridization
KW  - Napari
KW  - Spatial differential expression
JF  - Bio-protocol
SN  - 2331-8325
PB  - Bio-protocol LLC.
BIO101  - False