whole brain sections  (3DHistech ltd)

Journal: Communications Biology

Article Title: The xIV-LDDMM toolkit of image-varifold based technologies for mapping 3D images and spatial-omics across scales

doi: 10.1038/s42003-025-08800-7

Figure Lengend Snippet: a Shows minimization in varifold norm achieved with 180 degree rotation of atlas to target when homogeneous regions (colors in atlas, black/white probability distributions) in atlas and target are aligned. b Shows CCFv3 section 837/1320 (anterior to posterior). c Shows transformed CCFv3 section with colors indicating determinant of the Jacobian reflective of areas of expansion (red) and contraction (blue). d Shows BARseq measured cells with designated cell type. e Shows predicted cell type with highest probability per each transformed CCFv3 partition.

Article Snippet: Serial whole-brain BARseq sections are available at Mendeley data (10.17632/byp7p32gpx) .

Techniques: Transformation Assay

Journal: Communications Biology

Article Title: The xIV-LDDMM toolkit of image-varifold based technologies for mapping 3D images and spatial-omics across scales

doi: 10.1038/s42003-025-08800-7

Figure Lengend Snippet: a – f Show estimated support weights in transforming whole brain CCFv3 to MERFISH and BARseq data. a – c Show initial alignment of CCFv3 to parallel sections of a MERFISH or b BARseq whole brain or c hemi-brain data, with initial support weights in atlas set to 1 (red). d – f Show transformed CCFv3 optimally aligned to molecular/cellular sections, with estimated support weights per particle. White arrows indicate smooth transition zone from within support (weight of 1) to outside support (weight of 0). Both CCFv3 and molecular/cellular targets depicted as 200 um approximations, with total particles numbering 68k (CCFv3), 95k (MERFISH), 163k (BARseq whole brain), 62k (BARseq hemi-brain). g – j Show initial intersecting slice through CCFv3 aligning to single g , h MERFISH or i , j BARseq section of data. k – n Show intersecting slice after alignment.

Article Snippet: Serial whole-brain BARseq sections are available at Mendeley data (10.17632/byp7p32gpx) .

Techniques: Transformation Assay

Journal: Communications Biology

Article Title: The xIV-LDDMM toolkit of image-varifold based technologies for mapping 3D images and spatial-omics across scales

doi: 10.1038/s42003-025-08800-7

Figure Lengend Snippet: a , b Show initial alignment of CCFv3 to BARseq sections (black dots) for a mouse 1 and b mouse 2. c , d Show physically transformed CCFv3 to coordinates of target BARseq sections, with determinant of the Jacobian showing areas of expansion (red) and contraction (blue). e , f Show intersecting sections of deformed CCFv3 (white arrow) overlaid with corresponding BARseq section (black dots) from each hemi-brain. g – l Show intersecting sections of deformed CCFv3 with ontology regions in grayscale and cell type delineations for BARseq sections overlaid in color, with g , h taken at white arrow and i-l more posteriorly (yellow bracket in c , d ). m , n Show fraction of correctly aligned cells within each hemi-brain per each of four layer delineations (L2/3, L4, L5, L6) to corresponding CCFv3 region within 500-μm invervals along caudal-rostral axis. Total number of cells within each of four layer delineations given in Supplementary Data . o Shows average fraction for 7 hemi-brains of correctly aligned cells with manual alignment (data per hemi-brain provided in Supplementary Table ) versus fractions achieved with xIV-LDDMM for the two hemi-brains shown.

Article Snippet: Serial whole-brain BARseq sections are available at Mendeley data (10.17632/byp7p32gpx) .

Techniques: Transformation Assay

Journal: Communications Biology

Article Title: The xIV-LDDMM toolkit of image-varifold based technologies for mapping 3D images and spatial-omics across scales

doi: 10.1038/s42003-025-08800-7

Figure Lengend Snippet: a Shows a single section with 16 selected gene measurements totaling 48 M transcripts. b – d Show the gene with highest probability per particle at 50 μm,100 μm, 200 μm approximations with 82k, 21k and 6k particles, respectively. e – h Show probabilities at each scale of the single Slc17a7 gene. i – l Show a single slice of BARseq cell-segmented data with 104K cells at highest resolution and at 50 μ, 100 μ, and 200 μ approximations with 54k, 18k and 5k cells, respectively. Each cell is colored with the highest probability cell type. m Shows 1 mm × 1.25 mm window of full resolution gene detections for 16 genes (in a ), and n shows detections only of Alcam and Nnat. o Shows detections in n overlaid with particles whose estimated feature distributions carry the highest probability of expression for Alcam (yellow) and Nnat (pink) in optimally estimated positions along the curvilinear boundary of tissue.

Article Snippet: Serial whole-brain BARseq sections are available at Mendeley data (10.17632/byp7p32gpx) .

Techniques: Expressing

Journal: Communications Biology

Article Title: The xIV-LDDMM toolkit of image-varifold based technologies for mapping 3D images and spatial-omics across scales

doi: 10.1038/s42003-025-08800-7

Figure Lengend Snippet: a Shows initial alignment of CCFv3 (grayscale) to whole-brain BARseq sections (color). b shows alignment in BARseq coordinates following diffeomorphic transformation of CCFv3. c , d show intersecting planes of transformed CCFv3 with two BARseq full resolution cellular sections ( n = 80–100k cells per section). Yellow arrows point to areas of correct alignment between designated BARseq cell types and regional CCFv3 delineations. e , f Show zoomed in region of of lateral visual area and primary somatosensory cortex (dotted circles) in tissue sections in ( c , d ) with individual cells overlaying corresponding layers in CCFv3 grayscale delineations. Areas of the dentate gyrus and hippocampus show some misalignment in dorsal-ventral placement. g Shows percentages of correctly aligned cells across 10 sections bilaterally in the area of the primary somatosensory cortex and lateral visual area to corresponding CCFv3 cortical layer designation. Total cells mapped per layer are 23660 (L2/3), 19796 (L4), 11194 (L5), 22928 (L6). h Shows the distance of incorrectly aligned cells to the correct corresponding layer designation, with total number of incorrectly aligned cells per layer as 6345 (L2/3), 6279 (L4), 1975 (L5), 5681 (L6). All computed distances provided in Supplementary Data .

Article Snippet: Serial whole-brain BARseq sections are available at Mendeley data (10.17632/byp7p32gpx) .

Techniques: Transformation Assay

Journal: Advanced Science

Article Title: In Vivo Cytosolic Delivery of Biomolecules into Neurons for Super‐Resolution Imaging and Genome Modification

doi: 10.1002/advs.202501033

Figure Lengend Snippet: Selective neuronal uptake of N1 peptide after systemic administration coupled with FUS‐mediated BBB opening, and intrathecal administration into the spinal cord. A) Schematic timeline illustrating the process of FUS‐mediated BBB opening facilitated by microbubbles, systemic administration of FITC‐N1, and its subsequent specific delivery to the brain parenchyma. B) Mouse brain atlas indicating the trajectory of ultrasound waves from the transducer (blue lines) and the targeted area (cyan ellipse). C) Large field‐of‐view image showing the area labeled with FITC‐N1 following FUS‐mediated BBB opening (FUS‐treated), with the contralateral side (without FUS treatment) serving as the control. D) Zoomed views of the FUS‐treated area and the contralateral control side. E) High‐magnification images (maximum intensity projection) illustrating the neuronal specificity of FITC‐N1 after FUS‐facilitated BBB opening, confirmed by colocalization with the neuronal marker NeuN. F) The percentage of FITC‐N1 + cells colocalized with NeuN + cells relative to the total number of FITC‐N1 + cells. A total of 776 FITC‐N1 + cells were analyzed and data are presented as mean ± s.d., n = 4 animals. G) Schematic representation of intrathecal injection of FITC‐N1 between the lumbar 3 (L3) and lumbar 5 (L5) vertebral levels. H) Upon intrathecal injection, FITC‐N1 diffuses within the cerebrospinal fluid (CSF), leading to its distribution in the brain and penetration into the spinal cord. I) Image of a sagittal spinal cord section labeled with FITC‐N1 after intrathecal injection. J,K) Images (maximum intensity projection) showing the neuronal specificity of FITC‐N1 in the spinal cord after intrathecal injection, confirmed by colocalization of FITC‐N1 + cells and NeuroTrace™ 640/660 + cells. J) was acquired from the gray matter (ROI1) and K) from the white matter (ROI2) in (I). White boxes in (I) do not indicate the actual size of images (J) and (K). L) Quantification of the percentage of FITC‐N1 + cells colocalized with NeuroTrace™ 640/660 + cells relative to the total number of FITC‐N1 + cells. A total of 753 FITC‐N1 + cells were analyzed. Data are presented as mean ± s.d., n = 4 animals. Scale bars: C) 1 mm; I) 0.5 mm; D) 200 µm; E,J,K) 50 µm.

Article Snippet: Whole brain section images were acquired using a VS120 virtual slide microscope (Olympus) equipped with a SOLA‐SE‐II solid‐state white light excitation source.

Techniques: Labeling, Control, Marker, Injection

Journal: Advanced Science

Article Title: In Vivo Cytosolic Delivery of Biomolecules into Neurons for Super‐Resolution Imaging and Genome Modification

doi: 10.1002/advs.202501033

Figure Lengend Snippet: Two‐step entry mechanism of N1 peptide. A) Schematic showing of hyaluronidase injected into the lateral ventricle to deplete hyaluronan within 2 days, followed by administration of FITC‐N1 into the cortex 30 min before mouse sacrifice. B) Hyaluronan loss was observed across a large brain area, confirmed by the reduced HABP staining near the ventricle. The arrow indicates the cortical injection site of FITC‐N1 following hyaluronan depletion. C) Merged image of HABP staining and FITC‐N1 lebeling. D) High‐resolution images showing FITC‐N1 only exists in the extracellular space instead of neurons in the cortex. E) Two‐step targeting mechanism for N1 peptide's cytosolic entry. Initially, N1 peptide binds the hyaluronan (step I). Afterward, the N1 peptide diffuses to the surface and the cytosolic entry was mediated by neuron‐specific transporters or specialized membrane channels (step II). Once inside cytosol, the N1 peptide diffuses throughout the whole cytosol and enters the nucleus.

Article Snippet: Whole brain section images were acquired using a VS120 virtual slide microscope (Olympus) equipped with a SOLA‐SE‐II solid‐state white light excitation source.

Techniques: Injection, Staining, Membrane