Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
The Xenium In Situ platform is a new spatial transcriptomics product commercialized by 10x Genomics, capable of mapping hundreds of genes in situ at subcellular resolution. Given the multitude of commercially available spatial transcriptomics technologies, recommendations in choice of platform and analysis guidelines are increasingly important. Herein, we explore 25 Xenium datasets generated from multiple tissues and species, comparing scalability, resolution, data quality, capacities and limitations with eight other spatially resolved transcriptomics technologies and commercial platforms. In addition, we benchmark the performance of multiple open-source computational tools, when applied to Xenium datasets, in tasks including preprocessing, cell segmentation, selection of spatially variable features and domain identification. This study serves as an independent analysis of the performance of Xenium, and provides best practices and recommendations for analysis of such datasets.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11978515 | PMC |
| http://dx.doi.org/10.1038/s41592-025-02617-2 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Single cell spatial transcriptomics links Wnt signaling disruption to extracellular matrix development in a cleft palate model.
Sci Rep
August 2025
Section on Craniofacial Genetic Disorders, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA.
Despite advances in understanding the morphological disruptions that lead to defects in palate formation, the precise perturbations within the signaling microenvironment of palatal clefts remain poorly understood. To explore in greater depth the genomic basis of palatal clefts, we designed and implemented the first single cell spatial RNA-sequencing study in a cleft palate model, utilizing the Pax9 murine model at multiple developmental timepoints, which exhibits a consistent cleft palate defect. Visium HD, an emerging platform for true single-cell resolution spatially resolved transcriptomics, was employed using custom bins of 2 × 2 μm spatial gene expression data.
View Article and Find Full Text PDFEn face Cryosectioning of Mouse Retina for High-dimensional Spatial Molecular Analysis.
J Vis Exp
July 2025
Department of Physiology and Biophysics, University of Colorado Anschutz Medical Center;
The complex laminar structure of the retina presents significant challenges for comprehensive spatial molecular mapping. Current techniques for investigating tissue architecture and molecular interactions are limited by technical constraints that compromise spatial relationships or restrict molecular profiling. Existing methods like cross-sectioning, whole mount preparations, chemical or mechanical dissociations, and thick en face sections either disrupt tissue integrity, lose critical spatial context, or most often, are simply incompatible with high-dimensional spatial sequencing platforms.
View Article and Find Full Text PDFComparing Xenium 5K and Visium HD data from identical tissue slide at a pathological perspective.
J Exp Clin Cancer Res
July 2025
Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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.
View Article and Find Full Text PDFDefining Keypoints to Align H&E Images and Xenium DAPI-Stained Images Automatically.
Cells
June 2025
Department of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
10X Xenium is an in situ spatial transcriptomics platform that enables single-cell and subcellular-level gene expression analysis. In Xenium data analysis, defining matched keypoints to align H&E and spatial transcriptomic images is critical for cross-referencing sequencing and histology. Currently, it is labor-intensive for domain experts to manually place keypoints to perform image registration in the Xenium Explorer software.
View Article and Find Full Text PDFAnalysis of Hyperexpanded T Cell Clones in SARS-CoV-2 Vaccine-Associated Liver Injury by Spatial Proteomics and Transcriptomics.
Liver Int
July 2025
Institute of Pathology, University Hospital of Basel, University of Basel, Basel, Switzerland.
Background And Aims: SARS-CoV-2 vaccine-associated liver injury (SVALI) is a rare event and its pathophysiology remains unclear. Previous studies have found an oligoclonal CD8+ T cell infiltrate and SARS-CoV-2 spike antigen-specific T cells in the liver of patients with SVALI. Therefore, we aimed to characterise the immune infiltrate in a liver explant from a patient with severe SVALI.
View Article and Find Full Text PDF