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: Nature Communications

Article Title: Fate mapping of peripherally-derived macrophages after traumatic brain injury in mice reveals a long-lasting population with a distinct transcriptomic signature

doi: 10.1038/s41467-025-63952-8

Figure Lengend Snippet: a Experimental design - Ccr2-creER T2 ::Ai14D mice were injured using the controlled cortical impact TBI model and brain samples were collected at 7 and 30 days post injury (dpi) and at 8 months post TBI injury (mpi). Pericontusional regions (top quarter of a coronal brain section) were acquired as 20x z-stacked tiled images. Cavitation images were acquired at 3 different coordinates from Bregma: −1.34 mm (Anterior), −1.81 mm (Central) and −2.54 mm (Posterior). Nissl (left) and anatomical annotations (right) from the Allen Mouse Brain Atlas and Allen Reference Atlas – Mouse Brain. Allen Mouse Brain Atlas, mouse.brain-map.org and atlas.brain-map.org . Anatomical annotations from the Allen Reference Atlas – Mouse Brain, https://atlas.brain-map.org/ . b Representative images of pericontusional regions of Ccr2-creER T2 ::Ai14D mice at different time points. c Representative example of machine learning-based surface rendering (Imaris 10.2.0) at different time points. d % of tdTomato+ cells that express Iba1. e % of tdTomato+ cells that express Iba1 and P2ry12. f Volume (µm 3 ) of tdTomato+Iba1+ cells across the 3 selected coronal sections. g Volume (µm 3 ) of tdTomato+Iba1+P2ry12+ cells across the 3 selected coronal sections. Violin plots depict the distribution of samples. 7dpi n = 2 males, 1 female; 30dpi n = 3 males, 4 females; 8mpi n = 2 males, 2 females. (One-way ANOVA and two-sided unpaired Student’s t -test, statistical difference are denoted in the graphs). h Experimental design - Ccr2-creER T2 ::Ai14D mice were injured using the controlled cortical impact TBI model and phagocytosis capacity was measured at 7 and 30dpi. Fluorescent beads (2μm diameter) were injected in the ipsilateral hippocampus, and brains were collected 3 days after for IF analysis. i 3D rendering of MDM engulfing one bead and K-means segmentation overlay. j Representative confocal image of MDMs (tdTomato, red) engulfing injected beads (blue) in the pericontusional area. Nuclei are visualized in green. k % of tdTomato+ macrophages that engulfed one or more fluorescent beads was quantified for each acquired image. Each dot is the average of 2/4 images acquired for each animal. Individual animals are plotted (7dpi n = 4 males, 4 females; 30dpi n = 5 males, 5 females). Data are expressed as the mean of the examined variable ± SEM. (Two-sided unpaired Student’s t -test). Source data are provided as a Source Data file. Created in BioRender. Krukowski, K. (2025) https://BioRender.com/uoqnpdv .

Article Snippet: To determine if infiltrated tdTomato+ cells were differentiating into microglia, we analyzed the colocalization of tdTomato+ cells with ionized calcium-binding adapter molecule1 (Iba1) (a pan-myeloid cells marker) and the purinergic receptor P2ry12 (a microglia specific marker) across the top quarter of the mouse brain coronal section (pericontusional region) using Imaris, a microscopy image analysis software (Fig. ).

Techniques: Injection

Journal: Nature Communications

Article Title: Cooperative integration of spatially resolved multi-omics data with COSMOS

doi: 10.1038/s41467-024-55204-y

Figure Lengend Snippet: a Annotation of P56 mouse brain coronal sections from the Allen Brain Atlas. b Manual annotation of tissue from P22 mouse brain coronal sections in Zhang et al., overlaid on the image from a . c Comparison of domain segmentation results from five algorithms. Note that SpaMultiVAE was excluded as it is not designed for ATAC-RNA multi-omics data analysis. d Distribution of modality weights for RNA and ATAC in COSMOS analysis. e UMAP visualizations of integrated embeddings produced by SpatialGlue and COSMOS. f Pseudo-spatiotemporal maps (pSM) generated by SpatialGlue and COSMOS. ( g) Gene Ontology Biological Process (GOBP) analysis of genes associated with pseudo-time. h Gene expression profiles for the top 15 positive and 15 negative pSM-associated genes. i Spatial mapping of gene expressions for brain development genes negatively ( Nexn, Bcl11b, Mbp ) and positively ( Nfix, Mef2c, Cux2 ) correlated with pseudo-time, as identified by COSMOS. The full names of the abbreviations of brain regions are: nucleus accumbens (ACB), caudoputamen (CP), lateral ventricle (VL), genu of corpus callosum (ccg) and anterior commissure olfactory limb (aco). Source data are provided as a Source Data file.

Article Snippet: The reference of mouse brain ATAC-RNA data is obtained from a P56 mouse brain coronal section from Allen Mouse Brain Atlas (Allen Institute for Brain Science: https://mouse.brain-map.org/static/atlas ).

Techniques: Comparison, Biomarker Discovery, Produced, Generated, Gene Expression