ArticleBMC genomics2020
Seamless integration of image and molecular analysis for spatial transcriptomics workflows.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 162 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
162 citing papers in PubMed, 271 citations in OpenAlex.
- Unlocking the full potential of spatial omics in plants: practical challenges, solutions, and a path forward.The Plant cell · 2026Review
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- IL-33/IL1RL1 (ST2) signalling drives immune suppression in squamous intraepithelial hyperplasia.Tumour virus research · 2026Article
- Ten quick tips for spatial transcriptomics analysis.PLoS computational biology · 2026Review
- Profiling maize embryonic leaf development and discovering new genes using high-resolution spatial long-read isoform sequencing.Nature plants · 2026Article
- STcompare: comparative spatial transcriptomics data analysis of structurally matched tissues to characterize differentially spatially patterned genes.Bioinformatics (Oxford, England) · 2026Article
- Spatiotemporal transcriptomics of human cardiovascular progenitors in pig hearts identifies Midkine as a positive regulator of neovascularization.Nature cardiovascular research · 2026Article
- Computational analysis in spatial transcriptomics: methods and perspectives.Briefings in bioinformatics · 2026Review
- Spatial transcriptomics reveals compartment-specific cytotoxic T cell crosstalk with AT2 and goblet cells in advanced COPD.Biomarker research · 2026Article
- SINTER3D: continuous 3D reconstruction of spatial transcriptomics via implicit neural representations.Genome biology · 2026Article
- MLN2SVG: domain-aware spatially variable gene detection using contrastive variational autoencoder and multi-level neighbor search.Briefings in bioinformatics · 2026Article
- Serial Spatial Transcriptomes Reveal Regulatory Transitions in Maize Leaf Development.Plant biotechnology journal · 2026Article
- Spatial predictors of response to chemo-immunotherapy in microsatellite stable metastatic colorectal cancer.Nature communications · 2026Article
- Spatial omics in high-grade glioma: study design, analytical pitfalls, and standards for reproducible neuro-oncology.Acta neuropathologica communications · 2026Review
- Dissecting the coordinated progression of cell states in spatial transcriptomics with CoPro.bioRxiv : the preprint server for biology · 2026Article
- Article
- Spatial transcriptomics reveals tumor microenvironment-driven subtypes of invasive lobular carcinoma.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A spectral dimension reduction technique that improves pattern detection in multivariate spatial data.Bioinformatics (Oxford, England) · 2026Article
- Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies.Nature communications · 2026Article
- SHEST: single-cell-level artificial intelligence from haematoxylin and eosin morphology for cell-type prediction and spatial transcriptomics reconstruction.Briefings in bioinformatics · 2026Article
102 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRecent advancements in in situ gene expression technologies constitute a new and rapidly evolving field of transcriptomics. With the recent launch of the 10x Genomics Visium platform, such methods have started to become widely adopted. The experimental protocol is conducted on individual tissue sections collected from a larger tissue sample. The two-dimensional nature of this data requires multiple consecutive sections to be collected from the sample in order to construct a comprehensive three-dimensional map of the tissue. However, there is currently no software available that lets the user process the images, align stacked experiments, and finally visualize them together in 3D to create a holistic view of the tissue.
resultsWe have developed an R package named STUtility that takes 10x Genomics Visium data as input and provides features to perform standardized data transformations, alignment of multiple tissue sections, regional annotation, and visualizations of the combined data in a 3D model framework.
conclusionsSTUtility lets the user process, analyze and visualize multiple samples of spatially resolved RNA sequencing and image data from the 10x Genomics Visium platform. The package builds on the Seurat framework and uses familiar APIs and well-proven analysis methods. An introduction to the software package is available at https://ludvigla.github.io/STUtility_web_site/ .
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Registered trials
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.