ArticleBioinformatics (Oxford, England)2020
TissUUmaps: interactive visualization of large-scale spatial gene expression and tissue morphology data.
Article in Bioinformatics (Oxford, England), 2020. 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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18 citing papers in PubMed, 44 citations in OpenAlex.
- SpatialVista as a unified ecosystem for high-performance visualization and exploration of 3D spatial transcriptomics data.Nature genetics · 2026Article
- Multimodal spatial omics: From data acquisition to computational integration.Patterns (New York, N.Y.) · 2026Review
- Streamlining Multiplexed Tissue Image Analysis with PIPΣX: An Integrated Automated Pipeline for Image Processing and EXploration for Diverse Tissue Types.bioRxiv : the preprint server for biology · 2025Article
- Spatial transcriptomics in the adulteLife · 2025Article
- NIPMAP: niche-phenotype mapping of multiplex histology data by community ecology.Nature communications · 2023Article
- Spatial-Live: A lightweight and versatile tool for single cell spatial-omics data visualization.bioRxiv : the preprint server for biology · 2023Article
- Computational textural mapping harmonises sampling variation and reveals multidimensional histopathological fingerprints.British journal of cancer · 2023Article
- A Multi-Stain Breast Cancer Histological Whole-Slide-Image Data Set from Routine Diagnostics.Scientific data · 2023Article
- Molecular and immune signatures, and pathological trajectories of fatal COVID-19 lungs defined by in situ spatial single-cell transcriptome analysis.Journal of medical virology · 2023Article
- Article
- A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.Nature cell biology · 2023Article
- Moving beyond the desktop: prospects for practical bioimage analysis via the web.Frontiers in bioinformatics · 2023Article
- De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks.PLoS computational biology · 2022Article
- Spatial components of molecular tissue biology.Nature biotechnology · 2022Review
- Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer.Cancers · 2021Article
- Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps.BMC bioinformatics · 2021Article
- Spage2vec: Unsupervised representation of localized spatial gene expression signatures.The FEBS journal · 2021Article
- Automated identification of the mouse brain's spatial compartments from in situ sequencing data.BMC biology · 2020Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationVisual assessment of scanned tissue samples and associated molecular markers, such as gene expression, requires easy interactive inspection at multiple resolutions. This requires smart handling of image pyramids and efficient distribution of different types of data across several levels of detail.
resultsWe present TissUUmaps, enabling fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUmaps can be used both as a web service or locally in any computer, and regions of interest as well as local statistics can be extracted and shared among users. AVAILABILITY AND IMPLEMENTATION: TissUUmaps is available on github at github.com/wahlby-lab/TissUUmaps. Several demos and video tutorials are available at http://tissuumaps.research.it.uu.se/howto.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.