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10X Genomics st visium 10x genomics

( A ) Molecular cell type–based neuroanatomy of the goldfish telencephalon. Top: Color scheme shown above for GABAergic and glutamatergic cell types (dendrogram). Center: Eight coronal goldfish sections (goldfish 1), sampled for <t>Visium</t> ST, overlaid with a weighted color map that integrates all goldfish telencephalon cell types. Bottom: Regional parcellation based on color map differences above, each color indicates a different region, and suggested nomenclature annotated by similarity region names according to Northcutt . D , area dorsalis; V , area ventralis; Dc , large-celled subdivision of Dm ; Vsst , ventral Sst; Ppa , nucleus preopticus parvocellularis anterioris; a, anterior; p, posterior; d, dorsal; v, ventral; m, medial; l, lateral. ( B ) Heatmaps of SD (normalized per row) along lateral-medial (left) and dorsal-ventral (right) axes for top axial pattern genes, for goldfish 1 and 2; dots indicate spatial enrichment according to axial color scheme shown above; gray without dot, no enrichment. Right: Summary of axial score per gene (mean of enriched sections). ( C ) Expression of 14 axial-patterned genes across the goldfish telencephalon. Gray, low; red, high.

St Visium 10x Genomics, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/array-based+spatial+transcriptomics+visium+10x/st+technology+visium/pmc10619943-51-0-2
Average 86 stars, based on 1 article reviews

st visium 10x genomics - by Bioz Stars, 2026-09

86/100 stars

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1) Product Images from "A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types"

Article Title: A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types

Journal: Science Advances

doi: 10.1126/sciadv.adh7693

Figure Legend Snippet: ( A ) Molecular cell type–based neuroanatomy of the goldfish telencephalon. Top: Color scheme shown above for GABAergic and glutamatergic cell types (dendrogram). Center: Eight coronal goldfish sections (goldfish 1), sampled for Visium ST, overlaid with a weighted color map that integrates all goldfish telencephalon cell types. Bottom: Regional parcellation based on color map differences above, each color indicates a different region, and suggested nomenclature annotated by similarity region names according to Northcutt . D , area dorsalis; V , area ventralis; Dc , large-celled subdivision of Dm ; Vsst , ventral Sst; Ppa , nucleus preopticus parvocellularis anterioris; a, anterior; p, posterior; d, dorsal; v, ventral; m, medial; l, lateral. ( B ) Heatmaps of SD (normalized per row) along lateral-medial (left) and dorsal-ventral (right) axes for top axial pattern genes, for goldfish 1 and 2; dots indicate spatial enrichment according to axial color scheme shown above; gray without dot, no enrichment. Right: Summary of axial score per gene (mean of enriched sections). ( C ) Expression of 14 axial-patterned genes across the goldfish telencephalon. Gray, low; red, high.

Techniques Used: Expressing

( A ) t -SNE visualization of GABAergic neurons in the goldfish forebrain. Each dot represents a cell, colored by cell type assignment. Right: Expression of three branch-organizing genes. ( B ) All GABA types arranged in dendrogram order (GABA1 to GABA40), with top marker gene expression visualized as heatmap (white, high; black, low). Middle: Violin plots, where each dot represents a single cell; maximum expression (UMI) indicated on the right. Bottom: Contribution of four microdissections to each cell type, visualized as pie charts. ( C ) Expression of three branch-organizing genes [as (A)] and, in ST, eight anterior-posterior telencephalon coronal hemisphere sections. ( D ) Examples across the GABAergic dendrogram for spatial correlation of Visium spots: five scRNA-seq cell types (columns) across eight a.-p. coronal sections (rows).

Figure Legend Snippet: ( A ) t -SNE visualization of GABAergic neurons in the goldfish forebrain. Each dot represents a cell, colored by cell type assignment. Right: Expression of three branch-organizing genes. ( B ) All GABA types arranged in dendrogram order (GABA1 to GABA40), with top marker gene expression visualized as heatmap (white, high; black, low). Middle: Violin plots, where each dot represents a single cell; maximum expression (UMI) indicated on the right. Bottom: Contribution of four microdissections to each cell type, visualized as pie charts. ( C ) Expression of three branch-organizing genes [as (A)] and, in ST, eight anterior-posterior telencephalon coronal hemisphere sections. ( D ) Examples across the GABAergic dendrogram for spatial correlation of Visium spots: five scRNA-seq cell types (columns) across eight a.-p. coronal sections (rows).

Techniques Used: Expressing, Marker, Gene Expression

( A ) t -SNE visualization of glutamatergic neurons in the goldfish forebrain. Each dot represents a cell, colored by cell type. ( B ) All glutamatergic types, in dendrogram order (GLUT1 to GLUT48), with top marker gene expression visualized as heatmap (white, high; black, low). Middle: Violin plots, where each dot represents a single cell; maximum expression (UMI) indicated on the right. Bottom: Contribution of four microdissections to each cluster, visualized as pie charts. ( C ) Expression of two branch-organizing genes, NR2F2 and CNR1, visualized on t -SNE [as (A)] and, in ST, eight anterior-posterior telencephalon coronal hemisphere sections. ( D ) Examples across the glutamatergic dendrogram for spatial correlation of Visium spots: four scRNA-seq cell types (columns) across eight anterior-posterior coronal sections (rows).

Figure Legend Snippet: ( A ) t -SNE visualization of glutamatergic neurons in the goldfish forebrain. Each dot represents a cell, colored by cell type. ( B ) All glutamatergic types, in dendrogram order (GLUT1 to GLUT48), with top marker gene expression visualized as heatmap (white, high; black, low). Middle: Violin plots, where each dot represents a single cell; maximum expression (UMI) indicated on the right. Bottom: Contribution of four microdissections to each cluster, visualized as pie charts. ( C ) Expression of two branch-organizing genes, NR2F2 and CNR1, visualized on t -SNE [as (A)] and, in ST, eight anterior-posterior telencephalon coronal hemisphere sections. ( D ) Examples across the glutamatergic dendrogram for spatial correlation of Visium spots: four scRNA-seq cell types (columns) across eight anterior-posterior coronal sections (rows).

Techniques Used: Marker, Gene Expression, Expressing

( A and B ) t -SNE visualizing comparative species analysis between goldfish and zebrafish telencephalon, with cell types highlighted per species; (A) goldfish and (B) zebrafish. Per cell class, both species’ datasets are integrated (Harmony), followed by DBSCAN clustering. ( C ) Per cell type comparison, scored using KNN classifier. ( D ) Expression of CBLN1, PENK , and SST in the integrated teleostean dataset; dots (cells) colored by species origin. ( E ) Validation of gene expression detected in ST using HCR-FISH. Top row: Corresponding section overviews of genes detected in Visium (left) and HCR (right), where each spot represents a segmented fluorescent cell, colored by normalized expression. Bottom row: Raw fluorescent signal in zoom-ins, as indicated in overview sections.

Figure Legend Snippet: ( A and B ) t -SNE visualizing comparative species analysis between goldfish and zebrafish telencephalon, with cell types highlighted per species; (A) goldfish and (B) zebrafish. Per cell class, both species’ datasets are integrated (Harmony), followed by DBSCAN clustering. ( C ) Per cell type comparison, scored using KNN classifier. ( D ) Expression of CBLN1, PENK , and SST in the integrated teleostean dataset; dots (cells) colored by species origin. ( E ) Validation of gene expression detected in ST using HCR-FISH. Top row: Corresponding section overviews of genes detected in Visium (left) and HCR (right), where each spot represents a segmented fluorescent cell, colored by normalized expression. Bottom row: Raw fluorescent signal in zoom-ins, as indicated in overview sections.

Techniques Used: Comparison, Expressing, Biomarker Discovery, Gene Expression

Sequencing:

Article Title: Spatial multi-omics reveals the potential involvement of SPP1 + fibroblasts in determining metabolic heterogeneity and promoting metastatic growth of colorectal cancer liver metastasis.
Article Snippet: 1Department of Clinical Laboratory, Sir Run Run Shaw Hospital of Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China; 2Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center of Chinese People’s Liberation Army (PLA) General Hospital, Beijing 100853, P.R.. China; 3Department of Gastroenterology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China; 4Institute of Respiratory Diseases, Department of Basic Medicine, Xiamen Medical College, Xiamen 361023, Fujian, China; 5Organiod Platform of Medical Laboratory Science, Department of Basic Medicine, Xiamen Medical College, Xiamen 361023, Fujian, China; 6Department of Gynecological Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou Zhejiang, China; 7Department of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China; 8Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province,

Article Title: Inhibiting EZH2 complements steroid effects in Duchenne muscular dystrophy.
Article Snippet: .. Sequencing reads from Visium ST (10x Genomics) experiments were first preprocessed with Space Ranger v1.3.1 and mapped to the human reference genome (GRCh38). ..

other:

Article Title: Spatial transcriptomics identifies SPARC as a prognostic marker in interstitial lung diseases.
Article Snippet: Spatial coexpression network analysis uncovered the molecular landscape within the fibrotic lesion associated with poor prognosis We performed ST analysis (Visium, 10x Genomics) on five lung cryobiopsy specimens from patients with various ILDs, ensuring preserved histology and morphology with DV200 values >50% (Figure 1A).

Olfactory:

Article Title: SpaCross deciphers spatial structures and corrects batch effects in multi-slice spatially resolved transcriptomics
Article Snippet: .. All data sets used in this article are publicly available: (1) Human dorsolateral prefrontal cortex data captured using 10X Visium technology can be downloaded from http://research.libd.org/spatialLIBD/ . (2) Human breast cancer data obtained with 10x Visium technology can be downloaded from https://www.10xgenomics.com/datasets/human-breast-cancer-block-a-section-1-1-standard-1-1-0 . (3) Mouse olfactory bulb tissue data generated by the Stereo-seq and Slide-seqV2 platforms can be accessed from https://github.com/JinmiaoChenLab/SEDR_analyses/tree/master/data and https://singlecell.broadinstitute.org/single_cell/study/SCP815 , respectively. (4) The spatial transcriptomic data of the mouse embryo obtained with Stereo-seq technology can be downloaded from https://db.cngb.org/stomics/mosta/ . (5) The mouse primary visual cortex (V1) STARmap dataset is available at https://www.starmapresources.com/data . (6) The mouse brain somatosensory cortex osmFISH dataset can be downloaded from http://linnarssonlab.org/osmFISH . (7) The mouse hypothalamus dataset from MERFISH can be downloaded from 10.5061/dryad.8t8s248. (8) The mouse whole brain dataset profiled by the ST platform can be downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE147747 . ..

Generated:

Single Cell:

Article Title: Glia Are Bussin': How Single-Cell and Spatial Transcriptomics Enlighten the Role of Neuroglia in Spinal Cord Injury and Regeneration.
Article Snippet: .. The major drawback of 10X Genomics' Traditional Visium technology is that it lacks single- cell resolution as the 55- μm capture spots pool the RNA from 1 to 10 cells per spot, depending on cell size. ..

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