ArticleNature communications2024
SANTO: a coarse-to-fine alignment and stitching method for spatial omics.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- STcompare: comparative spatial transcriptomics data analysis of structurally matched tissues to characterize differentially spatially patterned genes.Bioinformatics (Oxford, England) · 2026Article
- Spatial ecotype in tumor immune exclusion: from spatial architecture to therapeutic strategies.Molecular cancer · 2026Review
- Computational analysis in spatial transcriptomics: methods and perspectives.Briefings in bioinformatics · 2026Review
- Integrative cross-sample alignment and spatially differential gene analysis for spatial transcriptomics.Nature communications · 2026Article
- Spatiotemporal cell type deconvolution leveraging tissue structure.Research square · 2026Article
- Alignment of spatial transcriptomics slices across diseases, platforms and conditions.Genome medicine · 2026Article
- Single-Cell and Spatial Omics: Methods and Applications.MedComm · 2026Review
- 3d-OT: a deep geometry-aware framework for heterogeneous slices alignment of spatial multi-omics.Nature methods · 2026Article
- Network model for alignment, stitching and slice-to-volume 3D reconstruction of large-scale spatially resolved slices.Nature communications · 2026Article
- Multimodal spatial alignment and morphology mapping with MOSAICField.bioRxiv : the preprint server for biology · 2026Article
- GALA: a unified landmark-free framework for coarse-to-fine spatial alignment across resolutions and modalities in spatial transcriptomics.Briefings in bioinformatics · 2026Article
- Expansion omics: from expansion microscopy to spatial omics.Molecular systems biology · 2026Review
- Robust characterization and interpretation of rare pathogenic cell populations from spatial omics using GARDEN.Nature communications · 2026Article
- Multimodal landscape of atherosclerotic plaques: A spatial omics approach with mass spectrometry imaging.Analytica chimica acta · 2025Review
- Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA.Genome research · 2025Article
- Benchmarking multi-slice integration and downstream applications in spatial transcriptomics data analysis.Genome biology · 2025Article
- Cancer therapy resistance from a spatial-omics perspective.Clinical and translational medicine · 2025Review
- Spatial Insights in Cardiovascular Aging.Aging and disease · 2025Review
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Authors and funding
9 authors.
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Abstract
With the flourishing of spatial omics technologies, alignment and stitching of slices becomes indispensable to decipher a holistic view of 3D molecular profile. However, existing alignment and stitching methods are unpractical to process large-scale and image-based spatial omics dataset due to extreme time consumption and unsatisfactory accuracy. Here we propose SANTO, a coarse-to-fine method targeting alignment and stitching tasks for spatial omics. SANTO firstly rapidly supplies reasonable spatial positions of two slices and identifies the overlap region. Then, SANTO refines the positions of two slices by considering spatial and omics patterns. Comprehensive experiments demonstrate the superior performance of SANTO over existing methods. Specifically, SANTO stitches cross-platform slices for breast cancer samples, enabling integration of complementary features to synergistically explore tumor microenvironment. SANTO is then applied to 3D-to-3D spatiotemporal alignment to study development of mouse embryo. Furthermore, SANTO enables cross-modality alignment of spatial transcriptomic and epigenomic data to understand complementary interactions.
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