Open Access
Scientific Reports, volume 12, issue 1, publication number 3648
Spatiotemporal 3D image registration for mesoscale studies of brain development
Shuvaev Sergey
1, 2
,
Lazutkin Alexander
3, 4
,
Kiryanov Roman
2
,
Anokhin Konstantin
5, 6
,
Enikolopov Grigori
3, 6
,
Koulakov Alexei A.
1
1
Cold Spring Harbor Laboratory, Cold Spring Harbor, USA
|
Publication type: Journal Article
Publication date: 2022-03-07
Multidisciplinary
Abstract
Comparison of brain samples representing different developmental stages often necessitates registering the samples to common coordinates. Although the available software tools are successful in registering 3D images of adult brains, registration of perinatal brains remains challenging due to rapid growth-dependent morphological changes and variations in developmental pace between animals. To address these challenges, we introduce CORGI (Customizable Object Registration for Groups of Images), an algorithm for the registration of perinatal brains. First, we optimized image preprocessing to increase the algorithm’s sensitivity to mismatches in registered images. Second, we developed an attention-gated simulated annealing procedure capable of focusing on the differences between perinatal brains. Third, we applied classical multidimensional scaling (CMDS) to align (“synchronize”) brain samples in time, accounting for individual development paces. We tested CORGI on 28 samples of whole-mounted perinatal mouse brains (P0–P9) and compared its accuracy with other registration algorithms. Our algorithm offers a runtime of several minutes per brain on a laptop and automates such brain registration tasks as mapping brain data to atlases, comparing experimental groups, and monitoring brain development dynamics.
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Shuvaev S. et al. Spatiotemporal 3D image registration for mesoscale studies of brain development // Scientific Reports. 2022. Vol. 12. No. 1. 3648
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Shuvaev S., Lazutkin A., Kiryanov R., Anokhin K., Enikolopov G., Koulakov A. A. Spatiotemporal 3D image registration for mesoscale studies of brain development // Scientific Reports. 2022. Vol. 12. No. 1. 3648
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TY - JOUR
DO - 10.1038/s41598-022-06871-8
UR - https://doi.org/10.1038%2Fs41598-022-06871-8
TI - Spatiotemporal 3D image registration for mesoscale studies of brain development
T2 - Scientific Reports
AU - Shuvaev, Sergey
AU - Lazutkin, Alexander
AU - Kiryanov, Roman
AU - Anokhin, Konstantin
AU - Enikolopov, Grigori
AU - Koulakov, Alexei A.
PY - 2022
DA - 2022/03/07 00:00:00
PB - Springer Nature
IS - 1
VL - 12
SN - 2045-2322
ER -
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@article{2022_Shuvaev,
author = {Sergey Shuvaev and Alexander Lazutkin and Roman Kiryanov and Konstantin Anokhin and Grigori Enikolopov and Alexei A. Koulakov},
title = {Spatiotemporal 3D image registration for mesoscale studies of brain development},
journal = {Scientific Reports},
year = {2022},
volume = {12},
publisher = {Springer Nature},
month = {mar},
url = {https://doi.org/10.1038%2Fs41598-022-06871-8},
number = {1},
doi = {10.1038/s41598-022-06871-8}
}
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