Spatiotemporal 3D image registration for mesoscale studies of brain development

Shuvaev, Sergey, Lazutkin, Alexander, Kiryanov, Roman, Anokhin, Konstantin, Enikolopov, Grigori, Koulakov, Alexei A (March 2022) Spatiotemporal 3D image registration for mesoscale studies of brain development. Scientific Reports, 12 (1). p. 3648. ISSN 2045-2322

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DOI: 10.1038/s41598-022-06871-8


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.

Item Type: Paper
Subjects: bioinformatics
Investigative techniques and equipment
bioinformatics > computational biology > algorithms
organism description > animal
organs, tissues, organelles, cell types and functions > organs types and functions > brain
bioinformatics > computational biology
Investigative techniques and equipment > imaging
Investigative techniques and equipment > magnetic resonance imaging
organism description > animal > mammal
organism description > animal > mammal > rodent > mouse
organism description > animal > developmental stage > neurodevelopment
organs, tissues, organelles, cell types and functions > organs types and functions
organs, tissues, organelles, cell types and functions
organism description > animal > mammal > rodent
Investigative techniques and equipment > Whole Brain Circuit Mapping
CSHL Authors:
Communities: CSHL labs > Koulakov lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 7 March 2022
Date Deposited: 10 Mar 2022 14:19
Last Modified: 17 Jan 2024 15:13
PMCID: PMC8901792

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