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visium platform (Spatial Transcriptomics Inc)

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Spatial Transcriptomics Inc visium platform

(A) <t>Visium</t> SRT data of breast cancer annotated by pathologists consists of IDC (invasive ductal carcinoma), DCIS (ductal carcinoma in situ), LCIS (lobular carcinoma in situ), tumor edge, and healthy region. (B) Spatial domains identified <t>by</t> <t>stACN</t> (left), stLearn (middle), and stACN-Con (right). (C) Heatmap of Pearson correlation coefficient among domains (domain=13). (D) Visualization of topological structure of spatial domains for breast cancer data in cell affinity graph learned by stACN, where thickness of edges is proportional to edge weights. (E) Distribution density estimation of cells in IDC, DCIS/LCIS and Healthy domain in terms of the learned cell features, where x-axis denotes cell features, and Kolmogorov-Smirnov test is for significance (left), and Distributions of degree, betweennessand eigenvector of cells in IDC, DCIS/LCIS and Healthy domains identified by stACN (right), where p-value is calculated with Student’s t-test. (F) UMAP visualization of spatial domains identified by stACN (left) and stLearn (right), where dashed circle denotes mixed domains. (G) Hierarchical structure of domain 3 and 14 in SRT data (left), and topological structure of subnetwork induced by domain 3 and 14 in cell affinity graph (right). (H) Spatial distribution of expression of GSTM3 and TFF1 with regional annotation (left), and Violin plots of gene expression (right).

Visium Platform, supplied by Spatial Transcriptomics Inc, 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/visium+spatial+transcriptomics+sequencing+data/pmc12799013-59-21-13?v=Spatial+Transcriptomics+Inc
Average 86 stars, based on 1 article reviews

visium platform - by Bioz Stars, 2026-08

86/100 stars

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1) Product Images from "Network models for bridging denoising and identifying spatial domains of spatially resolved transcriptomics"

Article Title: Network models for bridging denoising and identifying spatial domains of spatially resolved transcriptomics

Journal: PLOS Computational Biology

doi: 10.1371/journal.pcbi.1013867

(A) Visium SRT data of breast cancer annotated by pathologists consists of IDC (invasive ductal carcinoma), DCIS (ductal carcinoma in situ), LCIS (lobular carcinoma in situ), tumor edge, and healthy region. (B) Spatial domains identified by stACN (left), stLearn (middle), and stACN-Con (right). (C) Heatmap of Pearson correlation coefficient among domains (domain=13). (D) Visualization of topological structure of spatial domains for breast cancer data in cell affinity graph learned by stACN, where thickness of edges is proportional to edge weights. (E) Distribution density estimation of cells in IDC, DCIS/LCIS and Healthy domain in terms of the learned cell features, where x-axis denotes cell features, and Kolmogorov-Smirnov test is for significance (left), and Distributions of degree, betweennessand eigenvector of cells in IDC, DCIS/LCIS and Healthy domains identified by stACN (right), where p-value is calculated with Student’s t-test. (F) UMAP visualization of spatial domains identified by stACN (left) and stLearn (right), where dashed circle denotes mixed domains. (G) Hierarchical structure of domain 3 and 14 in SRT data (left), and topological structure of subnetwork induced by domain 3 and 14 in cell affinity graph (right). (H) Spatial distribution of expression of GSTM3 and TFF1 with regional annotation (left), and Violin plots of gene expression (right).

Figure Legend Snippet: (A) Visium SRT data of breast cancer annotated by pathologists consists of IDC (invasive ductal carcinoma), DCIS (ductal carcinoma in situ), LCIS (lobular carcinoma in situ), tumor edge, and healthy region. (B) Spatial domains identified by stACN (left), stLearn (middle), and stACN-Con (right). (C) Heatmap of Pearson correlation coefficient among domains (domain=13). (D) Visualization of topological structure of spatial domains for breast cancer data in cell affinity graph learned by stACN, where thickness of edges is proportional to edge weights. (E) Distribution density estimation of cells in IDC, DCIS/LCIS and Healthy domain in terms of the learned cell features, where x-axis denotes cell features, and Kolmogorov-Smirnov test is for significance (left), and Distributions of degree, betweennessand eigenvector of cells in IDC, DCIS/LCIS and Healthy domains identified by stACN (right), where p-value is calculated with Student’s t-test. (F) UMAP visualization of spatial domains identified by stACN (left) and stLearn (right), where dashed circle denotes mixed domains. (G) Hierarchical structure of domain 3 and 14 in SRT data (left), and topological structure of subnetwork induced by domain 3 and 14 in cell affinity graph (right). (H) Spatial distribution of expression of GSTM3 and TFF1 with regional annotation (left), and Violin plots of gene expression (right).

Techniques Used: In Situ, Expressing, Gene Expression

(A) H&E images of mouse anterior and posterior brain datasets of 10 × Visium, which are horizontally aligned (left). The zoomed in region consists of cornu ammonis(CA) and dentate gyrus(DG) domain. The corresponding anatomical Allen Mouse Brain Atlas (right). (B) Spatial domains identified by stACN (left) and STAGATE (right), where CA and DG across different slices. (C) 3D coordinates of MERFISH data for mouse hypothalamic preoptic region with slice 4, 9, and 14 (left), and spatial domains identified by stACN for each slice (right). (D) Visualization of SRT data for mouse breast cancer, where slice S1 and S3 are from different batches (first two columns), visualization of slice S1 and S3 with and without removing batch effect (the third column), and spatial domains identified by stACN with and without removing batch effect (last two columns), respectively.

Figure Legend Snippet: (A) H&E images of mouse anterior and posterior brain datasets of 10 × Visium, which are horizontally aligned (left). The zoomed in region consists of cornu ammonis(CA) and dentate gyrus(DG) domain. The corresponding anatomical Allen Mouse Brain Atlas (right). (B) Spatial domains identified by stACN (left) and STAGATE (right), where CA and DG across different slices. (C) 3D coordinates of MERFISH data for mouse hypothalamic preoptic region with slice 4, 9, and 14 (left), and spatial domains identified by stACN for each slice (right). (D) Visualization of SRT data for mouse breast cancer, where slice S1 and S3 are from different batches (first two columns), visualization of slice S1 and S3 with and without removing batch effect (the third column), and spatial domains identified by stACN with and without removing batch effect (last two columns), respectively.

Techniques Used:

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Spatial Transcriptomics in horizontally sectioned E14.5 mouse diaphragm identifies distinct tissues and muscle domains (A) Schematic representation of embryonic mouse diaphragm in which relevant anatomical regions are indicated. NMJ: Neuromuscular junction, MTJ: Myotendinous junction. (B) SpatialFeaturePlots demonstrating expression levels and distributions of representative genes for muscle, NMJ, MTJ and tendon. (C) SpatialDimPlot demonstrating the distribution of all the identified clusters within the diaphragm tissue. (D) Spatial distribution of representative Seurat clusters differentiating genetically specific domains in developing mouse diaphragm. (E) Uniform Manifold Approximation and Projection (UMAP) diagram of identified clusters of spatial RNA sequencing with muscle and endothelial clusters at the left and tendon and erythrocyte clusters at right. (F) FeaturePlots showing expression of muscle ( Ttn , Myh3 , Myh8 ), crural diaphragm ( Crlf1 ), NMJ ( Chrna1 , Chrng , Musk, Etv5 ), MTJ ( Col22a1 , Ankrd1 , Rxrg , Csrp3 ) and tendon ( Col12a1 , Antxr1, Tnmd , Tnc ) markers displayed by UMAP.

Journal: iScience

Article Title: Spatial transcriptomics in embryonic mouse diaphragm muscle reveals regional gradients and subdomains of developmental gene expression

doi: 10.1016/j.isci.2024.110018

Figure Lengend Snippet: Spatial Transcriptomics in horizontally sectioned E14.5 mouse diaphragm identifies distinct tissues and muscle domains (A) Schematic representation of embryonic mouse diaphragm in which relevant anatomical regions are indicated. NMJ: Neuromuscular junction, MTJ: Myotendinous junction. (B) SpatialFeaturePlots demonstrating expression levels and distributions of representative genes for muscle, NMJ, MTJ and tendon. (C) SpatialDimPlot demonstrating the distribution of all the identified clusters within the diaphragm tissue. (D) Spatial distribution of representative Seurat clusters differentiating genetically specific domains in developing mouse diaphragm. (E) Uniform Manifold Approximation and Projection (UMAP) diagram of identified clusters of spatial RNA sequencing with muscle and endothelial clusters at the left and tendon and erythrocyte clusters at right. (F) FeaturePlots showing expression of muscle ( Ttn , Myh3 , Myh8 ), crural diaphragm ( Crlf1 ), NMJ ( Chrna1 , Chrng , Musk, Etv5 ), MTJ ( Col22a1 , Ankrd1 , Rxrg , Csrp3 ) and tendon ( Col12a1 , Antxr1, Tnmd , Tnc ) markers displayed by UMAP.

Article Snippet: Visium Spatial Transcriptomics sequencing data were aligned using the default SpaceRanger (2.0.1) pipeline for FFPE slides in a Singularity Container running Ubuntu 22.04 on a high-performance cluster (Medical University of Innsbruck).

Techniques: Expressing, RNA Sequencing

Spatial Transcriptomics reveals distinct myogenic processes in the muscle center and periphery in E14.5 mouse diaphragm (A) SpatialFeaturePlots demonstrating expression levels and distributions of myogenic differentiation markers. (B) VlnPlots of expression levels of genes in clusters identified as muscle center, default muscle, and muscle periphery show an overall increase or decrease in expression of genes involved in muscle development from the center to the periphery. Y axis indicates expression levels. (C) Cnetplots showing GO terms in biological processes (red nodes) and their associated genes (blue nodes) for the upregulated genes in clusters annotated as muscle center compared to muscle periphery (top) or muscle periphery compared to muscle center (bottom). (D) Dotplots of expression of genes involved in myogenesis displaying a declining (right) or increasing (left) gradient in clusters from the muscle center, over default muscle (muscle middle), to the muscle periphery.

Journal: iScience

Article Title: Spatial transcriptomics in embryonic mouse diaphragm muscle reveals regional gradients and subdomains of developmental gene expression

doi: 10.1016/j.isci.2024.110018

Figure Lengend Snippet: Spatial Transcriptomics reveals distinct myogenic processes in the muscle center and periphery in E14.5 mouse diaphragm (A) SpatialFeaturePlots demonstrating expression levels and distributions of myogenic differentiation markers. (B) VlnPlots of expression levels of genes in clusters identified as muscle center, default muscle, and muscle periphery show an overall increase or decrease in expression of genes involved in muscle development from the center to the periphery. Y axis indicates expression levels. (C) Cnetplots showing GO terms in biological processes (red nodes) and their associated genes (blue nodes) for the upregulated genes in clusters annotated as muscle center compared to muscle periphery (top) or muscle periphery compared to muscle center (bottom). (D) Dotplots of expression of genes involved in myogenesis displaying a declining (right) or increasing (left) gradient in clusters from the muscle center, over default muscle (muscle middle), to the muscle periphery.

Techniques: Expressing

Spatial Transcriptomics in horizontally sectioned E18.5 mouse diaphragm identifies specific functional muscle domains and fiber types (A) SpatialFeaturePlots demonstrating expression levels and distributions of NMJ genes ( Chrna1 , Musk , Etv5 , Ache , Chrng, Chrne ), neonatal ( Myh8 ) and embryonic ( Myh3 ) myosin heavy chains, developmental troponin Tnnt2 , and ventral diaphragm markers ( Myog , Flnc , Csrp3 ). (B) Spatial distribution of Seurat clusters of distinct muscle and tendon domains. (C) UMAP representation of identified clusters of spatial RNA sequencing indicates spatially and functionally divergent differentiation of diaphragm muscle. (D) FeaturePlots demonstrating expression of muscle ( Ttn , Myh3 , Myh8 ), type I muscle ( Myh7, Myl2, Myl3 ), type IIb muscle ( Myh4 , Pvalb , Mybpc2 ), NMJ ( Chrna1 , Musk , Etv5 ), MTJ ( Col22a1 , Ankrd1 , Uchl1 ) and tendon ( Tnmd , Col11a1 , Scx ) markers displayed by UMAP.

Journal: iScience

Article Title: Spatial transcriptomics in embryonic mouse diaphragm muscle reveals regional gradients and subdomains of developmental gene expression

doi: 10.1016/j.isci.2024.110018

Figure Lengend Snippet: Spatial Transcriptomics in horizontally sectioned E18.5 mouse diaphragm identifies specific functional muscle domains and fiber types (A) SpatialFeaturePlots demonstrating expression levels and distributions of NMJ genes ( Chrna1 , Musk , Etv5 , Ache , Chrng, Chrne ), neonatal ( Myh8 ) and embryonic ( Myh3 ) myosin heavy chains, developmental troponin Tnnt2 , and ventral diaphragm markers ( Myog , Flnc , Csrp3 ). (B) Spatial distribution of Seurat clusters of distinct muscle and tendon domains. (C) UMAP representation of identified clusters of spatial RNA sequencing indicates spatially and functionally divergent differentiation of diaphragm muscle. (D) FeaturePlots demonstrating expression of muscle ( Ttn , Myh3 , Myh8 ), type I muscle ( Myh7, Myl2, Myl3 ), type IIb muscle ( Myh4 , Pvalb , Mybpc2 ), NMJ ( Chrna1 , Musk , Etv5 ), MTJ ( Col22a1 , Ankrd1 , Uchl1 ) and tendon ( Tnmd , Col11a1 , Scx ) markers displayed by UMAP.

Techniques: Functional Assay, Expressing, RNA Sequencing

Spatial transcriptomics reveals aberrant regulation of myogenic genes in Ca V 1.1 −/− mice (A) FeaturePlots showing expression of Ttn (muscle), Chrna1 and Musk (NMJ) displayed by UMAP in control and Ca V 1.1 −/− integrated dataset at E14.5 (left) and E18.5 (right). (B) Violin plots showing expression of representative genes differentially expressed in control and Ca V 1.1 −/− samples at E14.5 and E18.5. Y axis indicates expression level. (C) FeaturePlots of module scores of muscle differentiation markers displayed by UMAP in E18.5 control and Ca V 1.1 −/− integrated dataset show increased expression of early markers (top) and a decreased expression of late markers (bottom) in Ca V 1.1 −/− muscles. (D) Venn diagrams of top 200 DEGs genes and GO terms for these genes between E14.5 control and E18.5 control and between E18.5 Ca V 1.1 −/− and E18.5 control muscles indicate more shared genes and GO terms for upregulated genes in E18.5 Ca V 1.1 −/− with E14.5 control muscle and for downregulated genes in E18.5 Ca V 1.1 −/− with E18.5 control muscle. (E) FeaturePlots showing expression of Klf5 and Tead4 displayed by UMAP in control and Ca V 1.1 −/− integrated dataset at E14.5 (left) and E18.5 (right). (F) Violin plots of Klf5 and Tead4 expression in muscle clusters of E14.5 and E18.5 control and Ca V 1.1 −/− spatial datasets. Y axis indicates expression level.

Journal: iScience

Article Title: Spatial transcriptomics in embryonic mouse diaphragm muscle reveals regional gradients and subdomains of developmental gene expression

doi: 10.1016/j.isci.2024.110018

Figure Lengend Snippet: Spatial transcriptomics reveals aberrant regulation of myogenic genes in Ca V 1.1 −/− mice (A) FeaturePlots showing expression of Ttn (muscle), Chrna1 and Musk (NMJ) displayed by UMAP in control and Ca V 1.1 −/− integrated dataset at E14.5 (left) and E18.5 (right). (B) Violin plots showing expression of representative genes differentially expressed in control and Ca V 1.1 −/− samples at E14.5 and E18.5. Y axis indicates expression level. (C) FeaturePlots of module scores of muscle differentiation markers displayed by UMAP in E18.5 control and Ca V 1.1 −/− integrated dataset show increased expression of early markers (top) and a decreased expression of late markers (bottom) in Ca V 1.1 −/− muscles. (D) Venn diagrams of top 200 DEGs genes and GO terms for these genes between E14.5 control and E18.5 control and between E18.5 Ca V 1.1 −/− and E18.5 control muscles indicate more shared genes and GO terms for upregulated genes in E18.5 Ca V 1.1 −/− with E14.5 control muscle and for downregulated genes in E18.5 Ca V 1.1 −/− with E18.5 control muscle. (E) FeaturePlots showing expression of Klf5 and Tead4 displayed by UMAP in control and Ca V 1.1 −/− integrated dataset at E14.5 (left) and E18.5 (right). (F) Violin plots of Klf5 and Tead4 expression in muscle clusters of E14.5 and E18.5 control and Ca V 1.1 −/− spatial datasets. Y axis indicates expression level.

Techniques: Expressing, Control, Muscles

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