visium mouse brain section coronal  (10X Genomics)

Journal: Cell Reports Methods

Article Title: Multiscale domain identification for spatial transcriptomics via persistent homology

doi: 10.1016/j.crmeth.2026.101376

Figure Lengend Snippet: PHD-MS identifies stable brain structures in a Visium mouse brain (A) An annotated coronal section from Allen Brain Atlas as the ground truth. (B) NeST coexpression hotspots of the Visium mouse brain data. NeST identifies 5 relevant layers of structure, color coded by layer (bottom), matched to the annotated regions of Allen Atlas (right). (C) Nested PHD-MS domains with layer labels, color coded with matched regions in Allen Atlas. Top layer represents the domain at its broadest scale, including low-coreness spots. Middle layer includes medium-coreness spots, and core layer forms the domain’s stable core.

Article Snippet: Visium mouse brain section (coronal) , 10x Genomics , https://squidpy.readthedocs.io/en/stable/api/squidpy.datasets.visium_hne_adata.html#squidpy.datasets.visium_hne_adata.

Techniques:

Journal: bioRxiv

Article Title: Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem

doi: 10.1101/2023.11.26.568752

Figure Lengend Snippet: A-C) Multi-scale analysis. A) Pictogram depicting the hierarchy of multiple biological scales. B) Sankeyplot showing the hierarchical relationships between different spatial units in Giotto Suite. C) Overlay of multi-scale annotations of a MERFISH dataset; depicting nuclear (magenta) and cytoplasmic (cyan) enriched transcripts for all genes in GSEA terms related to “programmed cell death” and “COPII-coated ER to Golgi transport vesicle”, respectively. The nuclear boundary is defined with a yellow border, and the cell body is filled in with dark green. D-F) Registration and segmentation. D) Pictogram showing multi-modal co-registration from serial tissue sections. E) Aligned Xenium (Black), Visium (Orange), and immunofluorescence (Red and Green) spatial datasets from a single breast cancer sample (10X Genomics). F) Overlay of HER2 protein (rasterized intensity, blue gradient) and ERBB2 transcripts (points, red) after co-registration, inset shows zoomed-in region. G-H ) Multi-modal data analysis. G) Pictogram depicting multi-modal data analysis from two different modalities obtained from the same tissue slice. H) Integrated clustering results (RNA + Protein) from the 10X Genomics CytAassist Visium Human Tonsil dataset. I-L) Scalable data analysis. I) Pictograms depicting on-disk backends, parallelization, and projection to improve scalability within Giotto Suite. J) Stereo-seq datasets processed at bin1 and analyzed through multiple levels of hexagon aggregation, the inset depicts a zoomed-in subset and visualization of niche clustering on Leiden annotations and associated selected transcripts with random jitter. K-L) Tiling and pseudo-spatial data creation K) Schematic pictograms for different tiling options and tunable parameters. L) Spatial deconvolution plot showing the percentage of individual brain cell types for the pseudo-visium dataset generated from the stereo-seq subset in J.

Article Snippet: 10X Genomics Visium Mouse Brain Section (Coronal) dataset.

Techniques: Immunofluorescence, Generated

Journal: bioRxiv

Article Title: Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem

doi: 10.1101/2023.11.26.568752

Figure Lengend Snippet: A ) A schematic workflow of the co-registration step for the 10X Genomics Xenium pre-release breast cancer dataset. B ) Rasterized CD20 intensity data (left) and rasterized MS4A1 transcript counts (right). Pearson’s r is shown. C ) Rasterized HER2 intensity data (left) and rasterized ERBB2 transcript counts (right). Pearson’s r is shown. Rank of correlation scores between overlapping genes expressed in Visium and registered Xenium data. D) LOESS regression (solid curves) of log expression against ranked correlation scores from (D) . F-G ) Spatial feature expression plots for registered Xenium and Visium data for genes FASN ( F ) and HDC ( G ).

Article Snippet: 10X Genomics Visium Mouse Brain Section (Coronal) dataset.

Techniques: Expressing