ArticleNature communications2023
STalign: Alignment of spatial transcriptomics data using diffeomorphic metric mapping.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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Who cites it
92 citing papers in PubMed.
- Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular heterogeneity.PLoS computational biology · 2026Article
- The lipidomic architecture of the mouse brain.Nature · 2026Article
- OT-knn: A neighborhood-aware optimal transport framework for aligning spatial transcriptomics data.PLoS computational biology · 2026Article
- STcompare: comparative spatial transcriptomics data analysis of structurally matched tissues to characterize differentially spatially patterned genes.Bioinformatics (Oxford, England) · 2026Article
- Uncovering smooth structures in single-cell data with neighbor embeddings guided by predictability-computability-stability.Patterns (New York, N.Y.) · 2026Article
- A spatial multi-omics atlas of immunosenescence reveals germinal-center B cell dysfunction in human lymph nodes.Cell press blue · 2026Article
- LYNX: a deep generative model for linking spatial dynamics and cell interactions in multimodal spatial data.bioRxiv : the preprint server for biology · 2026Article
- H&E-Referenced Multiplex Immunofluorescence Interpretation in TMA Cores: Spatial Co-localization, Cell Feature Validation, and Virtual H&E Generation.Research square · 2026Article
- Computational analysis in spatial transcriptomics: methods and perspectives.Briefings in bioinformatics · 2026Review
- Riemannian metric learning for alignment of spatial multiomics.Bioinformatics (Oxford, England) · 2026Article
- Article
- Spatial transcriptomics in cancer research: insights into tumorigenesis, diagnosis and therapeutics.Cell death discovery · 2026Review
- Fault-tolerant 3D reconstruction from 2D spatial proteomics sections.bioRxiv : the preprint server for biology · 2026Article
- Integrative cross-sample alignment and spatially differential gene analysis for spatial transcriptomics.Nature communications · 2026Article
- Atlas-Level Single-Cell and Spatial Transcriptomics Data Integration via PRIME.bioRxiv : the preprint server for biology · 2026Article
- Spatiotemporal cell type deconvolution leveraging tissue structure.Research square · 2026Article
- A spatial code governs olfactory receptor choice and aligns sensory maps in the nose and brain.Cell · 2026Article
- SPOmiAlign: a modality-agnostic computational framework for multimodal spatial omics alignment enabled by a feature matching foundation model.Briefings in bioinformatics · 2026Article
- Interpretable, flexible and spatially aware integration of multiple spatial transcriptomics datasets from diverse sources.Nature genetics · 2026Article
- Article
32 more citing papers are in PubMed but not listed here.
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9 authors.
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Abstract
Spatial transcriptomics (ST) technologies enable high throughput gene expression characterization within thin tissue sections. However, comparing spatial observations across sections, samples, and technologies remains challenging. To address this challenge, we develop STalign to align ST datasets in a manner that accounts for partially matched tissue sections and other local non-linear distortions using diffeomorphic metric mapping. We apply STalign to align ST datasets within and across technologies as well as to align ST datasets to a 3D common coordinate framework. We show that STalign achieves high gene expression and cell-type correspondence across matched spatial locations that is significantly improved over landmark-based affine alignments. Applying STalign to align ST datasets of the mouse brain to the 3D common coordinate framework from the Allen Brain Atlas, we highlight how STalign can be used to lift over brain region annotations and enable the interrogation of compositional heterogeneity across anatomical structures. STalign is available as an open-source Python toolkit at https://github.com/JEFworks-Lab/STalign and as Supplementary Software with additional documentation and tutorials available at https://jef.works/STalign .
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.