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a Schematic of semi-supervised <t>data</t> acquisition and cortical tissue characteristics, exhibiting the laminar structure (layers L1–L6). scRNA-seq data were obtained from layer-enriched dissections (mono- or multi-layer), with layer-specific annotations. Spatial data were obtained from the frontal cortex. b Comparison of cell mapping results across methods in <t>mouse</t> <t>brain</t> tissue. Astro astrocyte, Endo endothelial cell, IT intratelencephalic, CT corticothalamic, NP near-projecting, PT pyramidal tract; L2/3 IT, L4, L5 IT, L5 PT, L6 CT, L6 IT, and L6b are subclasses of Glutamatergic neurons; Lamp5 , Pvalb , Sncg , Sst , and Vip types are subclasses of GABAergic neurons. c Mapping accuracy across methods. In real world, unlike the simulated datasets, cells within the same cluster may have similar identities due to the recognition of clusters. Thus, the accuracy of cell mapping here includes replicates without considering the rate of cell loss. Mono-layer, only statistics on cells dissected from single layers. Multi-layer, statistics on cells dissected from both single and multiple layers. d , e Heatmaps of cell-type enrichment scores across layers for smFISH ( d ) and cell mapping results ( e ), cell-type ordered by CMAP results. Enrichment score is defined as the fold change in cell density within a layer relative to the entire cortex. f Schematic of the mapping strategy for proximal primitive streak cells from an E7.0 mouse embryo onto Geo-seq data. g Comparison of cell mapping results in Geo-seq data. h Schematic of sample collection for Slide-seq and single-cell datasets. ExE, Extraembryonic ectoderm; Troph, Differentiated trophoblasts. i Comparison of cell mapping results in Slide-seq sample. j Bar plots displaying the number of extraembryonic cells: Left, in single-cell data; Right, in mapping results. k Boxplots of Moran’s I values for 30 spatially variable genes in Slide-seq (ground truth) and reconstructed data. Box plots display the median (center line), the first and third quartiles (box limits), and whiskers indicating the minimum and maximum values within 1.5 times the interquartile range. P values were calculated using a two-sided Wilcoxon rank-sum test. Source data are provided as a Source Data file.
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a Schematic of semi-supervised <t>data</t> acquisition and cortical tissue characteristics, exhibiting the laminar structure (layers L1–L6). scRNA-seq data were obtained from layer-enriched dissections (mono- or multi-layer), with layer-specific annotations. Spatial data were obtained from the frontal cortex. b Comparison of cell mapping results across methods in <t>mouse</t> <t>brain</t> tissue. Astro astrocyte, Endo endothelial cell, IT intratelencephalic, CT corticothalamic, NP near-projecting, PT pyramidal tract; L2/3 IT, L4, L5 IT, L5 PT, L6 CT, L6 IT, and L6b are subclasses of Glutamatergic neurons; Lamp5 , Pvalb , Sncg , Sst , and Vip types are subclasses of GABAergic neurons. c Mapping accuracy across methods. In real world, unlike the simulated datasets, cells within the same cluster may have similar identities due to the recognition of clusters. Thus, the accuracy of cell mapping here includes replicates without considering the rate of cell loss. Mono-layer, only statistics on cells dissected from single layers. Multi-layer, statistics on cells dissected from both single and multiple layers. d , e Heatmaps of cell-type enrichment scores across layers for smFISH ( d ) and cell mapping results ( e ), cell-type ordered by CMAP results. Enrichment score is defined as the fold change in cell density within a layer relative to the entire cortex. f Schematic of the mapping strategy for proximal primitive streak cells from an E7.0 mouse embryo onto Geo-seq data. g Comparison of cell mapping results in Geo-seq data. h Schematic of sample collection for Slide-seq and single-cell datasets. ExE, Extraembryonic ectoderm; Troph, Differentiated trophoblasts. i Comparison of cell mapping results in Slide-seq sample. j Bar plots displaying the number of extraembryonic cells: Left, in single-cell data; Right, in mapping results. k Boxplots of Moran’s I values for 30 spatially variable genes in Slide-seq (ground truth) and reconstructed data. Box plots display the median (center line), the first and third quartiles (box limits), and whiskers indicating the minimum and maximum values within 1.5 times the interquartile range. P values were calculated using a two-sided Wilcoxon rank-sum test. Source data are provided as a Source Data file.
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mouse coronal brain data set from the 10x visium platform  (10X Genomics)
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a Schematic of semi-supervised <t>data</t> acquisition and cortical tissue characteristics, exhibiting the laminar structure (layers L1–L6). scRNA-seq data were obtained from layer-enriched dissections (mono- or multi-layer), with layer-specific annotations. Spatial data were obtained from the frontal cortex. b Comparison of cell mapping results across methods in <t>mouse</t> <t>brain</t> tissue. Astro astrocyte, Endo endothelial cell, IT intratelencephalic, CT corticothalamic, NP near-projecting, PT pyramidal tract; L2/3 IT, L4, L5 IT, L5 PT, L6 CT, L6 IT, and L6b are subclasses of Glutamatergic neurons; Lamp5 , Pvalb , Sncg , Sst , and Vip types are subclasses of GABAergic neurons. c Mapping accuracy across methods. In real world, unlike the simulated datasets, cells within the same cluster may have similar identities due to the recognition of clusters. Thus, the accuracy of cell mapping here includes replicates without considering the rate of cell loss. Mono-layer, only statistics on cells dissected from single layers. Multi-layer, statistics on cells dissected from both single and multiple layers. d , e Heatmaps of cell-type enrichment scores across layers for smFISH ( d ) and cell mapping results ( e ), cell-type ordered by CMAP results. Enrichment score is defined as the fold change in cell density within a layer relative to the entire cortex. f Schematic of the mapping strategy for proximal primitive streak cells from an E7.0 mouse embryo onto Geo-seq data. g Comparison of cell mapping results in Geo-seq data. h Schematic of sample collection for Slide-seq and single-cell datasets. ExE, Extraembryonic ectoderm; Troph, Differentiated trophoblasts. i Comparison of cell mapping results in Slide-seq sample. j Bar plots displaying the number of extraembryonic cells: Left, in single-cell data; Right, in mapping results. k Boxplots of Moran’s I values for 30 spatially variable genes in Slide-seq (ground truth) and reconstructed data. Box plots display the median (center line), the first and third quartiles (box limits), and whiskers indicating the minimum and maximum values within 1.5 times the interquartile range. P values were calculated using a two-sided Wilcoxon rank-sum test. Source data are provided as a Source Data file.
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mouse brain scrna-seq data  (10X Genomics)
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a Schematic of semi-supervised <t>data</t> acquisition and cortical tissue characteristics, exhibiting the laminar structure (layers L1–L6). scRNA-seq data were obtained from layer-enriched dissections (mono- or multi-layer), with layer-specific annotations. Spatial data were obtained from the frontal cortex. b Comparison of cell mapping results across methods in <t>mouse</t> <t>brain</t> tissue. Astro astrocyte, Endo endothelial cell, IT intratelencephalic, CT corticothalamic, NP near-projecting, PT pyramidal tract; L2/3 IT, L4, L5 IT, L5 PT, L6 CT, L6 IT, and L6b are subclasses of Glutamatergic neurons; Lamp5 , Pvalb , Sncg , Sst , and Vip types are subclasses of GABAergic neurons. c Mapping accuracy across methods. In real world, unlike the simulated datasets, cells within the same cluster may have similar identities due to the recognition of clusters. Thus, the accuracy of cell mapping here includes replicates without considering the rate of cell loss. Mono-layer, only statistics on cells dissected from single layers. Multi-layer, statistics on cells dissected from both single and multiple layers. d , e Heatmaps of cell-type enrichment scores across layers for smFISH ( d ) and cell mapping results ( e ), cell-type ordered by CMAP results. Enrichment score is defined as the fold change in cell density within a layer relative to the entire cortex. f Schematic of the mapping strategy for proximal primitive streak cells from an E7.0 mouse embryo onto Geo-seq data. g Comparison of cell mapping results in Geo-seq data. h Schematic of sample collection for Slide-seq and single-cell datasets. ExE, Extraembryonic ectoderm; Troph, Differentiated trophoblasts. i Comparison of cell mapping results in Slide-seq sample. j Bar plots displaying the number of extraembryonic cells: Left, in single-cell data; Right, in mapping results. k Boxplots of Moran’s I values for 30 spatially variable genes in Slide-seq (ground truth) and reconstructed data. Box plots display the median (center line), the first and third quartiles (box limits), and whiskers indicating the minimum and maximum values within 1.5 times the interquartile range. P values were calculated using a two-sided Wilcoxon rank-sum test. Source data are provided as a Source Data file.
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3t brain raw data  (Siemens AG)
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a Schematic of semi-supervised <t>data</t> acquisition and cortical tissue characteristics, exhibiting the laminar structure (layers L1–L6). scRNA-seq data were obtained from layer-enriched dissections (mono- or multi-layer), with layer-specific annotations. Spatial data were obtained from the frontal cortex. b Comparison of cell mapping results across methods in <t>mouse</t> <t>brain</t> tissue. Astro astrocyte, Endo endothelial cell, IT intratelencephalic, CT corticothalamic, NP near-projecting, PT pyramidal tract; L2/3 IT, L4, L5 IT, L5 PT, L6 CT, L6 IT, and L6b are subclasses of Glutamatergic neurons; Lamp5 , Pvalb , Sncg , Sst , and Vip types are subclasses of GABAergic neurons. c Mapping accuracy across methods. In real world, unlike the simulated datasets, cells within the same cluster may have similar identities due to the recognition of clusters. Thus, the accuracy of cell mapping here includes replicates without considering the rate of cell loss. Mono-layer, only statistics on cells dissected from single layers. Multi-layer, statistics on cells dissected from both single and multiple layers. d , e Heatmaps of cell-type enrichment scores across layers for smFISH ( d ) and cell mapping results ( e ), cell-type ordered by CMAP results. Enrichment score is defined as the fold change in cell density within a layer relative to the entire cortex. f Schematic of the mapping strategy for proximal primitive streak cells from an E7.0 mouse embryo onto Geo-seq data. g Comparison of cell mapping results in Geo-seq data. h Schematic of sample collection for Slide-seq and single-cell datasets. ExE, Extraembryonic ectoderm; Troph, Differentiated trophoblasts. i Comparison of cell mapping results in Slide-seq sample. j Bar plots displaying the number of extraembryonic cells: Left, in single-cell data; Right, in mapping results. k Boxplots of Moran’s I values for 30 spatially variable genes in Slide-seq (ground truth) and reconstructed data. Box plots display the median (center line), the first and third quartiles (box limits), and whiskers indicating the minimum and maximum values within 1.5 times the interquartile range. P values were calculated using a two-sided Wilcoxon rank-sum test. Source data are provided as a Source Data file.
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a Schematic of semi-supervised data acquisition and cortical tissue characteristics, exhibiting the laminar structure (layers L1–L6). scRNA-seq data were obtained from layer-enriched dissections (mono- or multi-layer), with layer-specific annotations. Spatial data were obtained from the frontal cortex. b Comparison of cell mapping results across methods in mouse brain tissue. Astro astrocyte, Endo endothelial cell, IT intratelencephalic, CT corticothalamic, NP near-projecting, PT pyramidal tract; L2/3 IT, L4, L5 IT, L5 PT, L6 CT, L6 IT, and L6b are subclasses of Glutamatergic neurons; Lamp5 , Pvalb , Sncg , Sst , and Vip types are subclasses of GABAergic neurons. c Mapping accuracy across methods. In real world, unlike the simulated datasets, cells within the same cluster may have similar identities due to the recognition of clusters. Thus, the accuracy of cell mapping here includes replicates without considering the rate of cell loss. Mono-layer, only statistics on cells dissected from single layers. Multi-layer, statistics on cells dissected from both single and multiple layers. d , e Heatmaps of cell-type enrichment scores across layers for smFISH ( d ) and cell mapping results ( e ), cell-type ordered by CMAP results. Enrichment score is defined as the fold change in cell density within a layer relative to the entire cortex. f Schematic of the mapping strategy for proximal primitive streak cells from an E7.0 mouse embryo onto Geo-seq data. g Comparison of cell mapping results in Geo-seq data. h Schematic of sample collection for Slide-seq and single-cell datasets. ExE, Extraembryonic ectoderm; Troph, Differentiated trophoblasts. i Comparison of cell mapping results in Slide-seq sample. j Bar plots displaying the number of extraembryonic cells: Left, in single-cell data; Right, in mapping results. k Boxplots of Moran’s I values for 30 spatially variable genes in Slide-seq (ground truth) and reconstructed data. Box plots display the median (center line), the first and third quartiles (box limits), and whiskers indicating the minimum and maximum values within 1.5 times the interquartile range. P values were calculated using a two-sided Wilcoxon rank-sum test. Source data are provided as a Source Data file.

Journal: Nature Communications

Article Title: High-resolution mapping of single cells in spatial context

doi: 10.1038/s41467-025-61667-4

Figure Lengend Snippet: a Schematic of semi-supervised data acquisition and cortical tissue characteristics, exhibiting the laminar structure (layers L1–L6). scRNA-seq data were obtained from layer-enriched dissections (mono- or multi-layer), with layer-specific annotations. Spatial data were obtained from the frontal cortex. b Comparison of cell mapping results across methods in mouse brain tissue. Astro astrocyte, Endo endothelial cell, IT intratelencephalic, CT corticothalamic, NP near-projecting, PT pyramidal tract; L2/3 IT, L4, L5 IT, L5 PT, L6 CT, L6 IT, and L6b are subclasses of Glutamatergic neurons; Lamp5 , Pvalb , Sncg , Sst , and Vip types are subclasses of GABAergic neurons. c Mapping accuracy across methods. In real world, unlike the simulated datasets, cells within the same cluster may have similar identities due to the recognition of clusters. Thus, the accuracy of cell mapping here includes replicates without considering the rate of cell loss. Mono-layer, only statistics on cells dissected from single layers. Multi-layer, statistics on cells dissected from both single and multiple layers. d , e Heatmaps of cell-type enrichment scores across layers for smFISH ( d ) and cell mapping results ( e ), cell-type ordered by CMAP results. Enrichment score is defined as the fold change in cell density within a layer relative to the entire cortex. f Schematic of the mapping strategy for proximal primitive streak cells from an E7.0 mouse embryo onto Geo-seq data. g Comparison of cell mapping results in Geo-seq data. h Schematic of sample collection for Slide-seq and single-cell datasets. ExE, Extraembryonic ectoderm; Troph, Differentiated trophoblasts. i Comparison of cell mapping results in Slide-seq sample. j Bar plots displaying the number of extraembryonic cells: Left, in single-cell data; Right, in mapping results. k Boxplots of Moran’s I values for 30 spatially variable genes in Slide-seq (ground truth) and reconstructed data. Box plots display the median (center line), the first and third quartiles (box limits), and whiskers indicating the minimum and maximum values within 1.5 times the interquartile range. P values were calculated using a two-sided Wilcoxon rank-sum test. Source data are provided as a Source Data file.

Article Snippet: Mouse brain ST data are available from https://www.10xgenomics.com/datasets/mouse-brain-serial-section-1-sagittal-anterior-1-standard-1-0-0 .

Techniques: Comparison