ArticleJournal of experimental & clinical cancer research : CR2025
Comparing Xenium 5K and Visium HD data from identical tissue slide at a pathological perspective.
Article in Journal of experimental & clinical cancer research : CR, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 12 papers, 1 of them a synthesis that pooled it.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Enhancing RNA Capture Efficiency in Spatial Transcriptomics: A Review of Innovative Technologies and Strategies.International journal of molecular sciences · 2025Pooled it
- Correction: Comparing Xenium 5K and Visium HD data from identical tissue slide at a pathological perspective.Journal of experimental & clinical cancer research : CR · 2026Article
- Single-cell and spatial transcriptomics identify SPP1 + trophoblast necroptosis as a potential contributor to late-onset preeclampsia via SPP1-CD44-mediated interaction with macrophages.Journal of translational medicine · 2026Article
- Beyond the Cell Atlas: Functional Communities as the Essential Pathologic Units Driving Kidney Disease.Journal of the American Society of Nephrology : JASN · 2026Review
- Beyond silencing: integrative multi-omics and spatial profiling unravel the systems-level role of piRNAs in HBV-driven Hepatocarcinogenesis.Molecular biology reports · 2026Review
- Review
- Global scientific growth and thematic development of spatial transcriptomics in oncology research.Discover oncology · 2026Article
- SpatialFusion: A lightweight multimodal foundation model for pathway-informed spatial niche mapping.bioRxiv : the preprint server for biology · 2026Article
- Spatial Transcriptomics of Early Tooth Morphogenesis in Formalin-fixed Paraffin-embedded Mouse Embryonic Tissue.Journal of visualized experiments : JoVE · 2026Article
- Spatial AI in cancer: mapping immune evasion topology through multi-modal omics and deep learning.Frontiers in oncology · 2026Review
- From Histology to High-Resolution Mapping: The Rise of Spatial Omics in Immunology.European journal of immunology · 2025Review
- Single-Cell and Spatial Transcriptomics in Renal Injury and Fibrosis Research.Kidney diseases (Basel, Switzerland)Review
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
Abstract
Recent advancements in spatial transcriptomics have been largely triggered by two high-resolution technologies: Visium-HD and Xenium in-situ. While sequencing-based Visium HD features a refined bin size of 2 µm and transcriptome wide coverage, Xenium in-situ is a targeted imaging-based detection technology with sub-micron resolution. Herein we use a publicly available lung dataset which contains Visium-HD and Xenium-5K data generated on identical tissue slides to make a bona-fide technical comparison aligned with thorough pathological annotations. Whilst Visium-HD offers a broader gene coverage for detection and likely detects more tumor subclones, Xenium-5K achieves comparable results when robust clustering algorithms are applied. Importantly, from the pathological point of view, the single-cell segmentation accuracy is essential when analyzing irregularly shaped cells, where Xenium may be in favor. At the opposite side, although Xenium-5K based cell segmentation to delineate immune cells, normal lung, and vasculature at cell resolution is decent, it relies on fluorescent signals for transcript detection, which is challenging in heavily pigmented tissues such as melanoma or dust-laden alveolar macrophages, an application scenario for which Visium HD may stand out. From this perspective, pathological derived factors are the prior consideration for selecting an appropriate ST approach under difference research settings including cancer.
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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.