Constructing and optimizing 3D atlases from 2D data with application to the developing mouse brain
- University of California, San Francisco, United States
- Agency for Science, Technology and Research, Singapore
Abstract
3D imaging data necessitate 3D reference atlases for accurate quantitative interpretation. Existing computational methods to generate 3D atlases from 2D-derived atlases result in extensive artifacts, while manual curation approaches are labor-intensive. We present a computational approach for 3D atlas construction that substantially reduces artifacts by identifying anatomical boundaries in the underlying imaging data and using these to guide 3D transformation. Anatomical boundaries also allow extension of atlases to complete edge regions. Applying these methods to the eight developmental stages in the Allen Developing Mouse Brain Atlas (ADMBA) led to more comprehensive and accurate atlases. We generated imaging data from fifteen whole mouse brains to validate atlas performance and observed qualitative and quantitative improvement (37% greater alignment between atlas and anatomical boundaries). We provide the pipeline as the MagellanMapper software and the eight 3D reconstructed ADMBA atlases. These resources facilitate whole-organ quantitative analysis between samples and across development.
Data availability
The full 3D generated atlases and wild-type brain images are being deposited with the Human Brain Project EBRAINS data platform. All data analyses are included in the manuscript and supporting files.
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E11.5 3D Edge-Aware Refined Atlas Derived from the Allen Developing Mouse Brain AtlasEBRAINS , 10.25493/H9A3-GFT.
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E13.5 3D Edge-Aware Refined Atlas Derived from the Allen Developing Mouse Brain AtlasEBRAINS , 10.25493/YP9K-YMW.
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E15.5 3D Edge-Aware Refined Atlas Derived from the Allen Developing Mouse Brain AtlasEBRAINS , 10.25493/EXET-XND.
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E18.5 3D Edge-Aware Refined Atlas Derived from the Allen Developing Mouse Brain AtlasEBRAINS , 10.25493/X4ZT-ARE.
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P4 3D Edge-Aware Refined Atlas Derived from the Allen Developing Mouse Brain AtlasEBRAINS , 10.25493/QYP4-5VQ.
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P14 3D Edge-Aware Refined Atlas Derived from the Allen Developing Mouse Brain AtlasEBRAINS , 10.25493/QYP4-5VQ.
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P28 3D Edge-Aware Refined Atlas Derived from the Allen Developing Mouse Brain AtlasEBRAINS , 10.25493/YW1E-6BW.
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P56 3D Edge-Aware Refined Atlas Derived from the Allen Developing Mouse Brain AtlasEBRAINS , 10.25493/MYPD-QB8.
Article and author information
Author details
John LR Rubenstein
Funding
Brain and Behavior Research Foundation (NARSAD Young Investigator Grant)
- Stephan J Sanders
National Institute of Mental Health (U01 MH122681)
- Stephan J Sanders
National Institute of Mental Health (R01 MH109901)
- Stephan J Sanders
National Institute of Neurological Disorders and Stroke (R01 NS099099)
- John LR Rubenstein
The authors declare that the funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: All procedures and animal care were approved and performed in accordance with institutional guidelines from the University of California San Francisco Laboratory Animal Research Center (LARC). All animal handling complied with the approved Institutional Animal Care and Use Committee (IACUC) protocol (AN180174-02) at the University of California San Francisco.
Copyright
© 2021, Young et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Constructing and optimizing 3D atlases from 2D data with application to the developing mouse brain
eLife 10:e61408.
https://doi.org/10.7554/eLife.61408
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