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High-resolution hybrid micro-CT imaging pipeline for mouse brain region segmentation and volumetric morphometry.

Publication ,  Journal Article
Nadkarni, R; Han, ZY; Anderson, RJ; Allphin, AJ; Clark, DP; Badea, A; Badea, CT
Published in: PLoS One
2024

BACKGROUND: Brain region segmentation and morphometry in humanized apolipoprotein E (APOE) mouse models with a human NOS2 background (HN) contribute to Alzheimer's disease (AD) research by demonstrating how various risk factors affect the brain. Photon-counting detector (PCD) micro-CT provides faster scan times than MRI, with superior contrast and spatial resolution to energy-integrating detector (EID) micro-CT. This paper presents a pipeline for mouse brain imaging, segmentation, and morphometry from PCD micro-CT. METHODS: We used brains of 26 mice from 3 genotypes (APOE22HN, APOE33HN, APOE44HN). The pipeline included PCD and EID micro-CT scanning, hybrid (PCD and EID) iterative reconstruction, and brain region segmentation using the Small Animal Multivariate Brain Analysis (SAMBA) tool. We applied SAMBA to transfer brain region labels from our new PCD CT atlas to individual PCD brains via diffeomorphic registration. Region-based and voxel-based analyses were used for comparisons by genotype and sex. RESULTS: Together, PCD and EID scanning take ~5 hours to produce images with a voxel size of 22 μm, which is faster than MRI protocols for mouse brain morphometry with voxel size above 40 μm. Hybrid iterative reconstruction generates PCD images with minimal artifacts and higher spatial resolution and contrast than EID images. Our PCD atlas is qualitatively and quantitatively similar to the prior MRI atlas and successfully transfers labels to PCD brains in SAMBA. Male and female mice had significant volume differences in 26 regions, including parts of the entorhinal cortex and cingulate cortex. APOE22HN brains were larger than APOE44HN brains in clusters from the hippocampus, a region where atrophy is associated with AD. CONCLUSIONS: This work establishes a pipeline for mouse brain analysis using PCD CT, from staining to imaging and labeling brain images. Our results validate the effectiveness of the approach, setting a foundation for research on AD mouse models while reducing scanning durations.

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Published In

PLoS One

DOI

EISSN

1932-6203

Publication Date

2024

Volume

19

Issue

5

Start / End Page

e0303288

Location

United States

Related Subject Headings

  • X-Ray Microtomography
  • Mice, Transgenic
  • Mice
  • Male
  • Image Processing, Computer-Assisted
  • Humans
  • General Science & Technology
  • Female
  • Brain
  • Apolipoproteins E
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Nadkarni, R., Han, Z. Y., Anderson, R. J., Allphin, A. J., Clark, D. P., Badea, A., & Badea, C. T. (2024). High-resolution hybrid micro-CT imaging pipeline for mouse brain region segmentation and volumetric morphometry. PLoS One, 19(5), e0303288. https://doi.org/10.1371/journal.pone.0303288
Nadkarni, Rohan, Zay Yar Han, Robert J. Anderson, Alex J. Allphin, Darin P. Clark, Alexandra Badea, and Cristian T. Badea. “High-resolution hybrid micro-CT imaging pipeline for mouse brain region segmentation and volumetric morphometry.PLoS One 19, no. 5 (2024): e0303288. https://doi.org/10.1371/journal.pone.0303288.
Nadkarni R, Han ZY, Anderson RJ, Allphin AJ, Clark DP, Badea A, et al. High-resolution hybrid micro-CT imaging pipeline for mouse brain region segmentation and volumetric morphometry. PLoS One. 2024;19(5):e0303288.
Nadkarni, Rohan, et al. “High-resolution hybrid micro-CT imaging pipeline for mouse brain region segmentation and volumetric morphometry.PLoS One, vol. 19, no. 5, 2024, p. e0303288. Pubmed, doi:10.1371/journal.pone.0303288.
Nadkarni R, Han ZY, Anderson RJ, Allphin AJ, Clark DP, Badea A, Badea CT. High-resolution hybrid micro-CT imaging pipeline for mouse brain region segmentation and volumetric morphometry. PLoS One. 2024;19(5):e0303288.

Published In

PLoS One

DOI

EISSN

1932-6203

Publication Date

2024

Volume

19

Issue

5

Start / End Page

e0303288

Location

United States

Related Subject Headings

  • X-Ray Microtomography
  • Mice, Transgenic
  • Mice
  • Male
  • Image Processing, Computer-Assisted
  • Humans
  • General Science & Technology
  • Female
  • Brain
  • Apolipoproteins E