spatial transcriptomics sequencing Search Results


spatial transcriptomics sequencing  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc spatial transcriptomics sequencing
Spatial Transcriptomics Sequencing, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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in situ sequencing panel  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc in situ sequencing panel
In Situ Sequencing Panel, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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rna-rescue spatial transcriptomics (rrst)  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc rna-rescue spatial transcriptomics (rrst)
Rna Rescue Spatial Transcriptomics (Rrst), supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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single-cell rna sequencing  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc single-cell rna sequencing
Single Cell Rna Sequencing, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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next-generation sequencing data  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc next-generation sequencing data
Next Generation Sequencing Data, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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single-nucleus rna-seq  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc single-nucleus rna-seq
Single Nucleus Rna Seq, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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bulk rna sequencing  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc bulk rna sequencing
Bulk Rna Sequencing, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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st 10x genomics xenium 339 gene custom panel  (10X Genomics)
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10X Genomics st 10x genomics xenium 339 gene custom panel
A. Distribution of cell types annotated by nuclei-only and cell-morphology segmentation. Sample annotated by cell type, showing only nuclei which share the same cell type annotations with cell-morphology segmentation. B. IF tile scan conducted post <t>10x</t> Genomics Xenium data acquisition, showing cells stained for glial fibrillary protein (GFAP, green), actin (Phalloidin, magenta) and nuclei (DAPI, cyan). Scale, 1 mm. Inset indicated in red box, used in C. Scale, 50 µm. C. Structural comparison between polygons generated from expansion-based segmentation (top, left), overlaid with IF (bottom, left) and nuclei-only with overlaid cell-morphology segmentation (top, right), overlaid with IF (bottom, right). Scale, 10 µm. D. Comparison of cell area between expansion-based and cell-morphology segmentation strategies, only considering cells identified by both segmentations. The x-axis is the size of cell area as estimated by cell-morphology and the y-axis is the size of cell area estimated by expansion-based segmentation. Points are colored by the average number of nearest neighbors within 15 µm between the two segmentation strategies. E. Comparison of circular ratio between expansion-based and cell-morphology segmentation strategies for matched cells identified by both segmentations. This ratio for a particular cell mask is calculated by dividing the area of the maximum inscribed circle by the area of minimum binding circle. The x-axis is the ratio based on cell-morphology segmentations, and the y-axis is the ratio based on expansion-based segmentations. Cells are colored by the average number of nearest neighbors within 15 µm between the two segmentation strategies.
St 10x Genomics Xenium 339 Gene Custom Panel, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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single cell/nuclei sequencing  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc single cell/nuclei sequencing
A. Distribution of cell types annotated by nuclei-only and cell-morphology segmentation. Sample annotated by cell type, showing only nuclei which share the same cell type annotations with cell-morphology segmentation. B. IF tile scan conducted post <t>10x</t> Genomics Xenium data acquisition, showing cells stained for glial fibrillary protein (GFAP, green), actin (Phalloidin, magenta) and nuclei (DAPI, cyan). Scale, 1 mm. Inset indicated in red box, used in C. Scale, 50 µm. C. Structural comparison between polygons generated from expansion-based segmentation (top, left), overlaid with IF (bottom, left) and nuclei-only with overlaid cell-morphology segmentation (top, right), overlaid with IF (bottom, right). Scale, 10 µm. D. Comparison of cell area between expansion-based and cell-morphology segmentation strategies, only considering cells identified by both segmentations. The x-axis is the size of cell area as estimated by cell-morphology and the y-axis is the size of cell area estimated by expansion-based segmentation. Points are colored by the average number of nearest neighbors within 15 µm between the two segmentation strategies. E. Comparison of circular ratio between expansion-based and cell-morphology segmentation strategies for matched cells identified by both segmentations. This ratio for a particular cell mask is calculated by dividing the area of the maximum inscribed circle by the area of minimum binding circle. The x-axis is the ratio based on cell-morphology segmentations, and the y-axis is the ratio based on expansion-based segmentations. Cells are colored by the average number of nearest neighbors within 15 µm between the two segmentation strategies.
Single Cell/Nuclei Sequencing, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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quantitative transcriptome rna sequencing data  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc quantitative transcriptome rna sequencing data
A. Distribution of cell types annotated by nuclei-only and cell-morphology segmentation. Sample annotated by cell type, showing only nuclei which share the same cell type annotations with cell-morphology segmentation. B. IF tile scan conducted post <t>10x</t> Genomics Xenium data acquisition, showing cells stained for glial fibrillary protein (GFAP, green), actin (Phalloidin, magenta) and nuclei (DAPI, cyan). Scale, 1 mm. Inset indicated in red box, used in C. Scale, 50 µm. C. Structural comparison between polygons generated from expansion-based segmentation (top, left), overlaid with IF (bottom, left) and nuclei-only with overlaid cell-morphology segmentation (top, right), overlaid with IF (bottom, right). Scale, 10 µm. D. Comparison of cell area between expansion-based and cell-morphology segmentation strategies, only considering cells identified by both segmentations. The x-axis is the size of cell area as estimated by cell-morphology and the y-axis is the size of cell area estimated by expansion-based segmentation. Points are colored by the average number of nearest neighbors within 15 µm between the two segmentation strategies. E. Comparison of circular ratio between expansion-based and cell-morphology segmentation strategies for matched cells identified by both segmentations. This ratio for a particular cell mask is calculated by dividing the area of the maximum inscribed circle by the area of minimum binding circle. The x-axis is the ratio based on cell-morphology segmentations, and the y-axis is the ratio based on expansion-based segmentations. Cells are colored by the average number of nearest neighbors within 15 µm between the two segmentation strategies.
Quantitative Transcriptome Rna Sequencing Data, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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snrna sequencing  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc snrna sequencing
A. Distribution of cell types annotated by nuclei-only and cell-morphology segmentation. Sample annotated by cell type, showing only nuclei which share the same cell type annotations with cell-morphology segmentation. B. IF tile scan conducted post <t>10x</t> Genomics Xenium data acquisition, showing cells stained for glial fibrillary protein (GFAP, green), actin (Phalloidin, magenta) and nuclei (DAPI, cyan). Scale, 1 mm. Inset indicated in red box, used in C. Scale, 50 µm. C. Structural comparison between polygons generated from expansion-based segmentation (top, left), overlaid with IF (bottom, left) and nuclei-only with overlaid cell-morphology segmentation (top, right), overlaid with IF (bottom, right). Scale, 10 µm. D. Comparison of cell area between expansion-based and cell-morphology segmentation strategies, only considering cells identified by both segmentations. The x-axis is the size of cell area as estimated by cell-morphology and the y-axis is the size of cell area estimated by expansion-based segmentation. Points are colored by the average number of nearest neighbors within 15 µm between the two segmentation strategies. E. Comparison of circular ratio between expansion-based and cell-morphology segmentation strategies for matched cells identified by both segmentations. This ratio for a particular cell mask is calculated by dividing the area of the maximum inscribed circle by the area of minimum binding circle. The x-axis is the ratio based on cell-morphology segmentations, and the y-axis is the ratio based on expansion-based segmentations. Cells are colored by the average number of nearest neighbors within 15 µm between the two segmentation strategies.
Snrna Sequencing, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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geomx spatial transcriptomics sequencing  (Bruker Corporation)
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Bruker Corporation geomx spatial transcriptomics sequencing
A. Distribution of cell types annotated by nuclei-only and cell-morphology segmentation. Sample annotated by cell type, showing only nuclei which share the same cell type annotations with cell-morphology segmentation. B. IF tile scan conducted post <t>10x</t> Genomics Xenium data acquisition, showing cells stained for glial fibrillary protein (GFAP, green), actin (Phalloidin, magenta) and nuclei (DAPI, cyan). Scale, 1 mm. Inset indicated in red box, used in C. Scale, 50 µm. C. Structural comparison between polygons generated from expansion-based segmentation (top, left), overlaid with IF (bottom, left) and nuclei-only with overlaid cell-morphology segmentation (top, right), overlaid with IF (bottom, right). Scale, 10 µm. D. Comparison of cell area between expansion-based and cell-morphology segmentation strategies, only considering cells identified by both segmentations. The x-axis is the size of cell area as estimated by cell-morphology and the y-axis is the size of cell area estimated by expansion-based segmentation. Points are colored by the average number of nearest neighbors within 15 µm between the two segmentation strategies. E. Comparison of circular ratio between expansion-based and cell-morphology segmentation strategies for matched cells identified by both segmentations. This ratio for a particular cell mask is calculated by dividing the area of the maximum inscribed circle by the area of minimum binding circle. The x-axis is the ratio based on cell-morphology segmentations, and the y-axis is the ratio based on expansion-based segmentations. Cells are colored by the average number of nearest neighbors within 15 µm between the two segmentation strategies.
Geomx Spatial Transcriptomics Sequencing, supplied by Bruker Corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


A. Distribution of cell types annotated by nuclei-only and cell-morphology segmentation. Sample annotated by cell type, showing only nuclei which share the same cell type annotations with cell-morphology segmentation. B. IF tile scan conducted post 10x Genomics Xenium data acquisition, showing cells stained for glial fibrillary protein (GFAP, green), actin (Phalloidin, magenta) and nuclei (DAPI, cyan). Scale, 1 mm. Inset indicated in red box, used in C. Scale, 50 µm. C. Structural comparison between polygons generated from expansion-based segmentation (top, left), overlaid with IF (bottom, left) and nuclei-only with overlaid cell-morphology segmentation (top, right), overlaid with IF (bottom, right). Scale, 10 µm. D. Comparison of cell area between expansion-based and cell-morphology segmentation strategies, only considering cells identified by both segmentations. The x-axis is the size of cell area as estimated by cell-morphology and the y-axis is the size of cell area estimated by expansion-based segmentation. Points are colored by the average number of nearest neighbors within 15 µm between the two segmentation strategies. E. Comparison of circular ratio between expansion-based and cell-morphology segmentation strategies for matched cells identified by both segmentations. This ratio for a particular cell mask is calculated by dividing the area of the maximum inscribed circle by the area of minimum binding circle. The x-axis is the ratio based on cell-morphology segmentations, and the y-axis is the ratio based on expansion-based segmentations. Cells are colored by the average number of nearest neighbors within 15 µm between the two segmentation strategies.

Journal: bioRxiv

Article Title: An integrative spatial multi-omic workflow for unified analysis of tumor tissue

doi: 10.1101/2024.10.15.618574

Figure Lengend Snippet: A. Distribution of cell types annotated by nuclei-only and cell-morphology segmentation. Sample annotated by cell type, showing only nuclei which share the same cell type annotations with cell-morphology segmentation. B. IF tile scan conducted post 10x Genomics Xenium data acquisition, showing cells stained for glial fibrillary protein (GFAP, green), actin (Phalloidin, magenta) and nuclei (DAPI, cyan). Scale, 1 mm. Inset indicated in red box, used in C. Scale, 50 µm. C. Structural comparison between polygons generated from expansion-based segmentation (top, left), overlaid with IF (bottom, left) and nuclei-only with overlaid cell-morphology segmentation (top, right), overlaid with IF (bottom, right). Scale, 10 µm. D. Comparison of cell area between expansion-based and cell-morphology segmentation strategies, only considering cells identified by both segmentations. The x-axis is the size of cell area as estimated by cell-morphology and the y-axis is the size of cell area estimated by expansion-based segmentation. Points are colored by the average number of nearest neighbors within 15 µm between the two segmentation strategies. E. Comparison of circular ratio between expansion-based and cell-morphology segmentation strategies for matched cells identified by both segmentations. This ratio for a particular cell mask is calculated by dividing the area of the maximum inscribed circle by the area of minimum binding circle. The x-axis is the ratio based on cell-morphology segmentations, and the y-axis is the ratio based on expansion-based segmentations. Cells are colored by the average number of nearest neighbors within 15 µm between the two segmentation strategies.

Article Snippet: Here, we address these challenges and present Spatial Multi-omics Integration (SMINT), a unified analysis framework for the effective analysis of ST (10x Genomics Xenium, 339 gene custom panel) and SM (MALDI-IMS) data generated from sequential sections of surgically resected low-grade glioma.

Techniques: Staining, Comparison, Generated, Binding Assay