spatial transcriptomics (st) Search Results


spatial transcriptomics (st) methods  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc spatial transcriptomics (st) methods
Spatial Transcriptomics (St) Methods, 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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spatial transcriptome (st) data gsm6433610  (10X Genomics)
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10X Genomics spatial transcriptome (st) data gsm6433610
Spatial Transcriptome (St) Data Gsm6433610, 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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mouse olfactory bulb dataset  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc mouse olfactory bulb dataset
Mouse Olfactory Bulb Dataset, 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-gears  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc st-gears
St Gears, 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_pipeline  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc st_pipeline
St Pipeline, 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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spot-level st dataset  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc spot-level st dataset
Spot Level St Dataset, 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 array  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc st array
St Array, 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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graph contrastive feature representation method coco-st  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc graph contrastive feature representation method coco-st
Graph Contrastive Feature Representation Method Coco St, 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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st profiles of periodontal tissues  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc st profiles of periodontal tissues
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 Profiles Of Periodontal Tissues, 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 pipeline v1.7.2  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc st pipeline v1.7.2
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 Pipeline V1.7.2, 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 pipeline v1.7.2 - by Bioz Stars, 2026-04
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mouse olfactory bulb data rep11_mob_st  (Spatial Transcriptomics Inc)
90
Spatial Transcriptomics Inc mouse olfactory bulb data rep11_mob_st
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.
Mouse Olfactory Bulb Data Rep11 Mob St, 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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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