The Duke Mouse Brain Atlas: MRI and light sheet microscopy stereotaxic atlas of the mouse brain
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Atlases of the brain are critical resources that make it possible to share data in a common reference frame. Unexpectedly, there is no three-dimensional (3D) stereotaxic atlas of the mouse brain that provides whole brain coverage at macro to single-cell levels. Diffusion tensor images from five perfusion-fixed (in skull) specimens were acquired at 15 micrometers, the highest resolution ever reported. Diffusion tensor imaging yields multiple 3D volumes, each of which highlights unique cytoarchitecture. The averages were mapped into micro–computed tomography of the mouse skull to create external landmarks (bregma and lambda). Light sheet images of the same brains were coregistered, providing cell maps in the same stereotaxic space. The Allen Reference Atlas was registered to the volume to correct the geometric distortion in that atlas and bring it into the stereotaxic space. The resulting multiscalar (13 terabytes) atlas provides a common spatial framework to anneal data across molecular, structural, and functional studies of mice.
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The use of sophisticated multiangle methods enhances contrast and precision of delineations, explaining positive results.
“2. the use of sophisticated multiangle methods that enhance contrast and precision of delineations31;”
From Magnetic resonance microscopy maps widespread effects of Alzheimer’s disease on brain structures and behavior in mice (2026) · cites this paper as [31]
The Results sections on diffusion tensor data and the average MRH atlas report that more angular samples help resolve crossing fibers and that multiple MRI contrasts improve recognition of cytoarchitectural boundaries. Figure 2 also attributes improved image contrast and clearer borders to precision registration and averaging. The paper does not attribute both improved contrast and more precise delineation to a single multiangle method. (LLM, conf=0.82)
Experimental — accuracy not yet measuredLight-sheet stereology gained accuracy because the diffeomorphic alignment used corrects for tissue distortions during whole-brain tissue clearing.
“Light-sheet stereology also gained accuracy because the diffeomorphic alignment that we use corrects for tissue distortions that occur during whole-brain tissue clearing31.”
From Magnetic resonance microscopy maps widespread effects of Alzheimer’s disease on brain structures and behavior in mice (2026) · cites this paper as [31]
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Humbel, M., Tanner, C., Deyhle, H., Alarcón, M. G., Bausch, B., Kuo, W., Pleskač, P., Panahifar, A., Gasilov, S., Engelhardt, B., et al. (2026) · World Congress on Medical Physics and Biomedical Engineering, September 7 - 12, 2009, Munich, Germany · doi:10.1007/978-3-032-37736-4_34
- Authors
- Mansour, H., Azrak, R., Cook, J. J., Hornburg, K. J., Qi, Y., Tian, Y., Williams, R. W., Yeh, F.-C., White, L. E., & Johnson, G. A.
- Affiliations
- Duke University (US)
- University of Tennessee Health Science Center (US)
- University of Pittsburgh (US)
- Corresponding author
- Johnson, G. Allan
- ORCID
- Venue
- Science Advances
- Published
- 2025-05-02
- Volume
- 11
- Issue
- 18
- Pages
- eadq8089-eadq8089
- ISSN
- 2375-2548 (ISSN-L)
- PMC
- PMC12042906
- OpenAlex
- W4409982806
- Cited by
- 11
- References
- 62
- Citations by year
- 2026: 9 · 2025: 2
- FWCI
- 6.34
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by-nc
- Locations
- Science Advances (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- National Institute on Aging (R01AG070913)
- National Institute of Neurological Disorders and Stroke (R01NS120954)
- Topics
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced Neuroimaging Techniques and Applications
- Life Sciences › Neuroscience › Cognitive Neuroscience › Functional Brain Connectivity Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Cell Image Analysis Techniques
- Keywords
- mouse brain atlas, stereotactic atlas, diffusion tensor imaging, light-sheet microscopy, micro-computed tomography, brain cytoarchitecture
- MeSH terms
- Animals, Atlases as Topic, Brain, Magnetic Resonance Imaging, Microscopy, Stereotaxic Techniques, Imaging, Three-Dimensional, Mice, X-Ray Microtomography, Diffusion Tensor Imaging
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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