visium (Spatial Transcriptomics Inc)
86
Structured Review
Spatial Transcriptomics Inc
visium
![Interactive R-shiny web app created by the Run_Interactive function and visualization of QC metrics created by the Run_Visualization function for data quality assessment. ( a ) Visualization of Slide-seq mouse brain sample Puck_200115_08. The Run_Interactive function offers flexible options for selecting a ROI through four intuitive buttons. The ‘Add Selection’ button allows users to add spatial coordinates along with corresponding metadata, such as UMI count and spatial barcode sequences, each time an ROI is selected. The ‘Clear Last Selection’ button removes the most recently selected ROI from the current selection list. The ‘Reset All Selections’ button resets both the spatial heatmap and clustering plot, providing a clean slate for a new selection. Finally, the ‘Save All Selected ROI’ button saves the finalized selection as ‘selected_ROI’ object in the user’s R global environment, streamlining data management and export. In this example, the selection of cluster 7, highlighted in purple on the t-SNE plot, is found to mostly correspond to the choroid plexus region in the spatial UMI count plot. ( b ) Barplot showing spatial barcode demultiplexing information between 10× <t>Visium</t> probe-based (left) and polyA-based (right) protocols to <t>assess</t> <t>sequencing</t> accuracy. ( c ) Stacked bar plots showing the mapping rate, separated into reads that map to exons, introns, and those that are ambiguously mapped or map elsewhere in the genome (ordered by exon mapping rate) between 10× Visium probe-based (left) and polyA-based (right) protocols. ( d ) UMI duplication plot between a probe-based sample (left) with a higher UMI duplication number than a polyA-based one (right). A distribution skewed toward lower duplication values indicates higher library complexity and minimal redundancy, suggesting that the sequencing depth is well-matched to the diversity of the transcriptome. In contrast, a pronounced tail toward higher duplication values suggests substantial over-sequencing or PCR amplification biases, as many reads may originate from the same underlying transcript molecule. (e) UMI count distribution between sample 709 with two protocols, the first and last two are plotted as distribution of raw UMI count per spot and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $\log _{10}$\end{document} UMI count per gene respectively.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_9247/pmc12639247/pmc12639247__lqaf167fig2.jpg)
Visium, 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/visium/pmc12639247-0-16-0
Average 86 stars, based on 1 article reviews
Visium, 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/visium/pmc12639247-0-16-0
Average 86 stars, based on 1 article reviews
visium - by Bioz Stars,
2026-10
86/100 stars
Images
1) Product Images from "stPipe: a flexible and streamlined R/Bioconductor pipeline for preprocessing sequencing-based spatial transcriptomics data"
Article Title: stPipe: a flexible and streamlined R/Bioconductor pipeline for preprocessing sequencing-based spatial transcriptomics data
Journal: NAR Genomics and Bioinformatics
doi: 10.1093/nargab/lqaf167
Figure Legend Snippet: Interactive R-shiny web app created by the Run_Interactive function and visualization of QC metrics created by the Run_Visualization function for data quality assessment. ( a ) Visualization of Slide-seq mouse brain sample Puck_200115_08. The Run_Interactive function offers flexible options for selecting a ROI through four intuitive buttons. The ‘Add Selection’ button allows users to add spatial coordinates along with corresponding metadata, such as UMI count and spatial barcode sequences, each time an ROI is selected. The ‘Clear Last Selection’ button removes the most recently selected ROI from the current selection list. The ‘Reset All Selections’ button resets both the spatial heatmap and clustering plot, providing a clean slate for a new selection. Finally, the ‘Save All Selected ROI’ button saves the finalized selection as ‘selected_ROI’ object in the user’s R global environment, streamlining data management and export. In this example, the selection of cluster 7, highlighted in purple on the t-SNE plot, is found to mostly correspond to the choroid plexus region in the spatial UMI count plot. ( b ) Barplot showing spatial barcode demultiplexing information between 10× Visium probe-based (left) and polyA-based (right) protocols to assess sequencing accuracy. ( c ) Stacked bar plots showing the mapping rate, separated into reads that map to exons, introns, and those that are ambiguously mapped or map elsewhere in the genome (ordered by exon mapping rate) between 10× Visium probe-based (left) and polyA-based (right) protocols. ( d ) UMI duplication plot between a probe-based sample (left) with a higher UMI duplication number than a polyA-based one (right). A distribution skewed toward lower duplication values indicates higher library complexity and minimal redundancy, suggesting that the sequencing depth is well-matched to the diversity of the transcriptome. In contrast, a pronounced tail toward higher duplication values suggests substantial over-sequencing or PCR amplification biases, as many reads may originate from the same underlying transcript molecule. (e) UMI count distribution between sample 709 with two protocols, the first and last two are plotted as distribution of raw UMI count per spot and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $\log _{10}$\end{document} UMI count per gene respectively.
Techniques Used: Selection, Sequencing, Amplification
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