ArticleScientific reports2018
Voxel-wise comparisons of cellular microstructure and diffusion-MRI in mouse hippocampus using 3D Bridging of Optically-clear histology with Neuroimaging Data (3D-BOND).
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 64 citations in OpenAlex.
- Graph-Based White Matter Tractometry: Methods, Applications, and the Path to Validation.Neuroinformatics · 2026Review
- Validating the standard model of diffusion MRI in white matter with numerical substrates.Imaging neuroscience (Cambridge, Mass.) · 2026Article
- Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 3-Ex vivo imaging: Data processing, comparisons with microscopy, and tractography.Magnetic resonance in medicine · 2025Review
- Association Between Shift Working and Brain Morphometric Changes in Workers: A Voxel-wise Comparison.Safety and health at work · 2025Article
- Diffusion MRI of the Hippocampus.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2024Review
- Structural projections to the nucleus accumbens link to impulsive components of human risk preference.Imaging neuroscience (Cambridge, Mass.) · 2024Article
- Mapping mesoscale connectivity within the human hippocampus.NeuroImage · 2023Article
- Mapping the macrostructure and microstructure of the in vivo human hippocampus using diffusion MRI.Human brain mapping · 2023Article
- A Novel Needle Mouse Model of Vascular Cognitive Impairment and Dementia.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2023Article
- Ex vivo 100 μm isotropic diffusion MRI-based tractography of connectivity changes in the end-stage R6/2 mouse model of Huntington's disease.Neuroprotection (Chichester, England) · 2023Article
- Using light and X-ray scattering to untangle complex neuronal orientations and validate diffusion MRI.eLife · 2023Article
- Integrating multimodality magnetic resonance imaging to the Allen Mouse Brain Common Coordinate Framework.NMR in biomedicine · 2023Article
- giRAff: an automated atlas segmentation tool adapted to single histological slices.Frontiers in neuroscience · 2023Article
- Montelukast reduces grey matter abnormalities and functional deficits in a mouse model of inflammation-induced encephalopathy of prematurity.Journal of neuroinflammation · 2022Article
- Hippocampal dentate gyrus integrity revealed with ultrahigh resolution diffusion imaging predicts memory performance in older adults.Hippocampus · 2022Article
- Association of War Zone-Related Stress With Alterations in Limbic Gray Matter Microstructure.JAMA network open · 2022Article
- Review
- Brain tract structure predicts relapse to stimulant drug use.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- VascuViz: a multimodality and multiscale imaging and visualization pipeline for vascular systems biology.Nature methods · 2022Article
- Article
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
A key challenge in medical imaging is determining a precise correspondence between image properties and tissue microstructure. This comparison is hindered by disparate scales and resolutions between medical imaging and histology. We present a new technique, 3D Bridging of Optically-clear histology with Neuroimaging Data (3D-BOND), for registering medical images with 3D histology to overcome these limitations. Ex vivo 120 × 120 × 200 μm resolution diffusion-MRI (dMRI) data was acquired at 7 T from adult C57Bl/6 mouse hippocampus. Tissue was then optically cleared using CLARITY and stained with cellular markers and confocal microscopy used to produce high-resolution images of the 3D-tissue microstructure. For each sample, a dense array of hippocampal landmarks was used to drive registration between upsampled dMRI data and the corresponding confocal images. The cell population in each MRI voxel was determined within hippocampal subregions and compared to MRI-derived metrics. 3D-BOND provided robust voxel-wise, cellular correlates of dMRI data. CA1 pyramidal and dentate gyrus granular layers had significantly different mean diffusivity (p > 0.001), which was related to microstructural features. Overall, mean and radial diffusivity correlated with cell and axon density and fractional anisotropy with astrocyte density, while apparent fibre density correlated negatively with axon density. Astrocytes, axons and blood vessels correlated to tensor orientation.
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Registered trials
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