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(a) Spatial visualization comparing k-means clustering of niche representations from methods (Mievformer, NicheCompass, CellCharter, Banksy, GraphST, STAGATE, ENVI, Spatial, PCA). cell type annotations (left). (b) Heatmap showing the Pearson correlation between eight evaluation metrics (CAS, SCAS, NEA, DREC, NCB-GCS, NCB-CAS, NCB-NASW, NCB-MLAMI) and ground-truth Niche ARI across varying simulation parameters. (c) Horizontal bar graphs showing dual recovery (DREC) metrics across methods and five datasets: Xenium GBM, Xenium Lung, Xenium Pancreas, Mouse Brain Stereo-seq, and Mouse Brain <t>Visium</t> <t>HD.</t>
Visium Hd Mouse Brain Data, 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/result/visium hd mouse brain data/product/10X Genomics
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visium hd mouse brain data - by Bioz Stars, 2026-05
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merscope mouse brain data  (Vizgen Inc)
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(a) Spatial visualization comparing k-means clustering of niche representations from methods (Mievformer, NicheCompass, CellCharter, Banksy, GraphST, STAGATE, ENVI, Spatial, PCA). cell type annotations (left). (b) Heatmap showing the Pearson correlation between eight evaluation metrics (CAS, SCAS, NEA, DREC, NCB-GCS, NCB-CAS, NCB-NASW, NCB-MLAMI) and ground-truth Niche ARI across varying simulation parameters. (c) Horizontal bar graphs showing dual recovery (DREC) metrics across methods and five datasets: Xenium GBM, Xenium Lung, Xenium Pancreas, Mouse Brain Stereo-seq, and Mouse Brain <t>Visium</t> <t>HD.</t>
Merscope Mouse Brain Data, supplied by Vizgen 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/result/merscope mouse brain data/product/Vizgen Inc
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(a) Spatial visualization comparing k-means clustering of niche representations from methods (Mievformer, NicheCompass, CellCharter, Banksy, GraphST, STAGATE, ENVI, Spatial, PCA). cell type annotations (left). (b) Heatmap showing the Pearson correlation between eight evaluation metrics (CAS, SCAS, NEA, DREC, NCB-GCS, NCB-CAS, NCB-NASW, NCB-MLAMI) and ground-truth Niche ARI across varying simulation parameters. (c) Horizontal bar graphs showing dual recovery (DREC) metrics across methods and five datasets: Xenium GBM, Xenium Lung, Xenium Pancreas, Mouse Brain Stereo-seq, and Mouse Brain <t>Visium</t> <t>HD.</t>
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(a) Spatial visualization comparing k-means clustering of niche representations from methods (Mievformer, NicheCompass, CellCharter, Banksy, GraphST, STAGATE, ENVI, Spatial, PCA). cell type annotations (left). (b) Heatmap showing the Pearson correlation between eight evaluation metrics (CAS, SCAS, NEA, DREC, NCB-GCS, NCB-CAS, NCB-NASW, NCB-MLAMI) and ground-truth Niche ARI across varying simulation parameters. (c) Horizontal bar graphs showing dual recovery (DREC) metrics across methods and five datasets: Xenium GBM, Xenium Lung, Xenium Pancreas, Mouse Brain Stereo-seq, and Mouse Brain <t>Visium</t> <t>HD.</t>
10x Embryonic E18 Mouse Brain Data, 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/result/10x embryonic e18 mouse brain data/product/10X Genomics
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10x embryonic e18 mouse brain data - by Bioz Stars, 2026-05
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bin 60 stereo seq mouse brain data  (Dropbox Inc)
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(a) Spatial visualization comparing k-means clustering of niche representations from methods (Mievformer, NicheCompass, CellCharter, Banksy, GraphST, STAGATE, ENVI, Spatial, PCA). cell type annotations (left). (b) Heatmap showing the Pearson correlation between eight evaluation metrics (CAS, SCAS, NEA, DREC, NCB-GCS, NCB-CAS, NCB-NASW, NCB-MLAMI) and ground-truth Niche ARI across varying simulation parameters. (c) Horizontal bar graphs showing dual recovery (DREC) metrics across methods and five datasets: Xenium GBM, Xenium Lung, Xenium Pancreas, Mouse Brain Stereo-seq, and Mouse Brain <t>Visium</t> <t>HD.</t>
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https://www.bioz.com/result/bin 60 stereo seq mouse brain data/product/Dropbox Inc
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bin 60 stereo seq mouse brain data - by Bioz Stars, 2026-05
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brain region data  (Human Protein Atlas)
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(a) Spatial visualization comparing k-means clustering of niche representations from methods (Mievformer, NicheCompass, CellCharter, Banksy, GraphST, STAGATE, ENVI, Spatial, PCA). cell type annotations (left). (b) Heatmap showing the Pearson correlation between eight evaluation metrics (CAS, SCAS, NEA, DREC, NCB-GCS, NCB-CAS, NCB-NASW, NCB-MLAMI) and ground-truth Niche ARI across varying simulation parameters. (c) Horizontal bar graphs showing dual recovery (DREC) metrics across methods and five datasets: Xenium GBM, Xenium Lung, Xenium Pancreas, Mouse Brain Stereo-seq, and Mouse Brain <t>Visium</t> <t>HD.</t>
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https://www.bioz.com/result/brain region data/product/Human Protein Atlas
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mouse brain sagittal posterior visium data  (10X Genomics)
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10X Genomics mouse brain sagittal posterior visium data
a <t>Visium</t> ST data from a slice of the mouse cortex. b The distribution of annotated cell types from the scRNA-seq data on the CellRefiner output. c Segmentation of CellRefiner reconstruction of mouse cortex <t>Visium</t> <t>data,</t> using SpaceFlow, with colors corresponding to clusters. d Ripley’s L for spatial organization on Visium and CellRefiner. e Neighborhood enrichment score on spatial proximity of clusters for CellRefiner output. f ST data from murine lymph node using Visium. Source data are provided as a Source Data file.
Mouse Brain Sagittal Posterior Visium Data, 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/result/mouse brain sagittal posterior visium data/product/10X Genomics
Average 86 stars, based on 1 article reviews
mouse brain sagittal posterior visium data - by Bioz Stars, 2026-05
86/100 stars
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brain mri data  (Kaggle Inc)
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Kaggle Inc brain mri data
a <t>Visium</t> ST data from a slice of the mouse cortex. b The distribution of annotated cell types from the scRNA-seq data on the CellRefiner output. c Segmentation of CellRefiner reconstruction of mouse cortex <t>Visium</t> <t>data,</t> using SpaceFlow, with colors corresponding to clusters. d Ripley’s L for spatial organization on Visium and CellRefiner. e Neighborhood enrichment score on spatial proximity of clusters for CellRefiner output. f ST data from murine lymph node using Visium. Source data are provided as a Source Data file.
Brain Mri Data, supplied by Kaggle Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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structural brain mri data  (Philips Healthcare)
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Philips Healthcare structural brain mri data
a <t>Visium</t> ST data from a slice of the mouse cortex. b The distribution of annotated cell types from the scRNA-seq data on the CellRefiner output. c Segmentation of CellRefiner reconstruction of mouse cortex <t>Visium</t> <t>data,</t> using SpaceFlow, with colors corresponding to clusters. d Ripley’s L for spatial organization on Visium and CellRefiner. e Neighborhood enrichment score on spatial proximity of clusters for CellRefiner output. f ST data from murine lymph node using Visium. Source data are provided as a Source Data file.
Structural Brain Mri Data, supplied by Philips Healthcare, 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/result/structural brain mri data/product/Philips Healthcare
Average 86 stars, based on 1 article reviews
structural brain mri data - by Bioz Stars, 2026-05
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Image Search Results


(a) Spatial visualization comparing k-means clustering of niche representations from methods (Mievformer, NicheCompass, CellCharter, Banksy, GraphST, STAGATE, ENVI, Spatial, PCA). cell type annotations (left). (b) Heatmap showing the Pearson correlation between eight evaluation metrics (CAS, SCAS, NEA, DREC, NCB-GCS, NCB-CAS, NCB-NASW, NCB-MLAMI) and ground-truth Niche ARI across varying simulation parameters. (c) Horizontal bar graphs showing dual recovery (DREC) metrics across methods and five datasets: Xenium GBM, Xenium Lung, Xenium Pancreas, Mouse Brain Stereo-seq, and Mouse Brain Visium HD.

Journal: bioRxiv

Article Title: Probabilistic coupling of cellular and microenvironmental heterogeneity by masked self-supervised learning

doi: 10.64898/2026.04.21.719876

Figure Lengend Snippet: (a) Spatial visualization comparing k-means clustering of niche representations from methods (Mievformer, NicheCompass, CellCharter, Banksy, GraphST, STAGATE, ENVI, Spatial, PCA). cell type annotations (left). (b) Heatmap showing the Pearson correlation between eight evaluation metrics (CAS, SCAS, NEA, DREC, NCB-GCS, NCB-CAS, NCB-NASW, NCB-MLAMI) and ground-truth Niche ARI across varying simulation parameters. (c) Horizontal bar graphs showing dual recovery (DREC) metrics across methods and five datasets: Xenium GBM, Xenium Lung, Xenium Pancreas, Mouse Brain Stereo-seq, and Mouse Brain Visium HD.

Article Snippet: The Visium HD Mouse Brain data were obtained from the 10x Genomics public dataset repository ( https://www.10xgenomics.com/datasets ).

Techniques:

a Visium ST data from a slice of the mouse cortex. b The distribution of annotated cell types from the scRNA-seq data on the CellRefiner output. c Segmentation of CellRefiner reconstruction of mouse cortex Visium data, using SpaceFlow, with colors corresponding to clusters. d Ripley’s L for spatial organization on Visium and CellRefiner. e Neighborhood enrichment score on spatial proximity of clusters for CellRefiner output. f ST data from murine lymph node using Visium. Source data are provided as a Source Data file.

Journal: Nature Communications

Article Title: Reconstructing single-cell resolution from spatial transcriptomics with CellRefiner

doi: 10.1038/s41467-026-70090-2

Figure Lengend Snippet: a Visium ST data from a slice of the mouse cortex. b The distribution of annotated cell types from the scRNA-seq data on the CellRefiner output. c Segmentation of CellRefiner reconstruction of mouse cortex Visium data, using SpaceFlow, with colors corresponding to clusters. d Ripley’s L for spatial organization on Visium and CellRefiner. e Neighborhood enrichment score on spatial proximity of clusters for CellRefiner output. f ST data from murine lymph node using Visium. Source data are provided as a Source Data file.

Article Snippet: The mouse brain (sagittal posterior) Visium data is available at the 10X Genomics website ( https://www.10xgenomics.com/resources/datasets/mouse-brain-serial-section-1-sagittal-anterior-1-standard-1-1-0 ).

Techniques:

a The single-cell resolution spatial map of cells reconstructed by CellRefiner using a paired Visium data and scRNA-seq data. The analysis rediscovered several contact-based signaling activities confirmed by prior knowledge, including EPHB, NOTCH, ICAM, and CDH. b CellRefiner also identified several highly active junction-related signaling including EPHA, MPZ, CD39, CD46, DESMOSOME, and JAM. Source data are provided as a Source Data file.

Journal: Nature Communications

Article Title: Reconstructing single-cell resolution from spatial transcriptomics with CellRefiner

doi: 10.1038/s41467-026-70090-2

Figure Lengend Snippet: a The single-cell resolution spatial map of cells reconstructed by CellRefiner using a paired Visium data and scRNA-seq data. The analysis rediscovered several contact-based signaling activities confirmed by prior knowledge, including EPHB, NOTCH, ICAM, and CDH. b CellRefiner also identified several highly active junction-related signaling including EPHA, MPZ, CD39, CD46, DESMOSOME, and JAM. Source data are provided as a Source Data file.

Article Snippet: The mouse brain (sagittal posterior) Visium data is available at the 10X Genomics website ( https://www.10xgenomics.com/resources/datasets/mouse-brain-serial-section-1-sagittal-anterior-1-standard-1-1-0 ).

Techniques: Single Cell