In vivo localization of cortical areas using a 3D computerized atlas of the marmoset brain

Risser, Laurent; Sadoun, Amirouche; Mescam, Muriel; Strelnikov, Kuzma; Lebreton, Sandra; Boucher, Samuel; Girard, Pascal; Vayssière, Nathalie; Rosa, Marcello G. P.; Fonta, Caroline

doi:10.1007/s00429-019-01869-x

Cited by 12 publications

(11 citation statements)

References 68 publications

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“…Are the brain hemispheres used to generate the template sufficient to accurately reflect the variability of the marmoset cerebral cortex? Other population based templates relied on a comparable (Hikishima et al, 2011) or smaller (Risser et al, 2019) numbers of individuals of similar sex and age, but did not incorporate histological validation of the area boundaries. Further, the morphological averaging was performed with a higher number of iterations (20) than recommended (Janke et al, 2015), which allowed to better emphasize cytoarchitectonic features and transitions between individual brain structures.…”

Section: Methodological Considerationsmentioning

confidence: 99%

“…Future registration to in vivo MRI-based templates (e.g. the IMPEC template; Risser et al, 2019) will also allow correction for possible distortions related to the histological processing, further increasing the precision of surgical approaches.…”

Section: Atlas Interoperability and Future Developmentsmentioning

confidence: 99%

“…All of these templates have adopted the scheme of parcellation first proposed by Paxinos et al (2012). More recently, a population template based on 3T MR images of 13 individuals was introduced (Risser et al, 2019), but it was also based on the registration of the same specimen studied by Paxinos et al (2012) to multiple brains. As discussed recently , there is a significant variation in the cortex between individuals, which results in potential errors in the assignment of voxels to areas in studies involving the integration of data from multiple individuals.…”

Section: Introductionmentioning

confidence: 99%

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Histology-based average template of the marmoset cortex with probabilistic localization of cytoarchitectural areas

Majka

Bednarek

Chan

et al. 2020

Preprint

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Highlights• A 3D template of the marmoset cortex representing the average of 20 individuals.• The template is based on Nissl stain and preserves information about cortical layers.• Probabilistic mapping of areas, cortical thickness, and layer intensity profiles.• Includes spatial transformations to other marmoset brain atlases. AbbreviationsFor a list of areas and their abbreviations see Table S2. AbstractThe rapid adoption of marmosets in neuroscience has created a demand for three dimensional (3D) atlases of the brain of this species to facilitate data integration in a common reference space. We report on a new open access template of the marmoset cortex (the Nencki-Monash, or NM template), representing a morphological average of 20 brains of young adult individuals, obtained by 3D reconstructions generated from Nissl-stained serial sections. The method used to generate the tem plate takes into account morphological features of the individual brains, as well as the borders of clearly defined cytoarchitectural areas. This has resulted in a resource which allows direct estimates of the most likely coordinates of each cortical area, as well as quantification of the margins of error involved in assigning voxels to areas, and preserves quantitative information about the laminar structure of the cortex. We provide spatial transformations between the NM and other available marmoset brain templates, thus enabling integration with magnetic resonance imaging (MRI) and tracer-based connectivity data. The NM template combines some of the main advantages of histology-based atlases (e.g. information about the cytoarchitectural structure) with features more commonly associated with MRI-based templates (isotropic nature of the dataset, and probabilistic analyses). The underlying workflow may be found useful in the future development of brain atlases that incorporate information about the variability of areas in species for which it may be impractical to ensure homogeneity of the sample in terms of age, sex and genetic background.

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Section: Methodological Considerationsmentioning

confidence: 99%

Section: Atlas Interoperability and Future Developmentsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Histology-based average template of the marmoset cortex with probabilistic localization of cytoarchitectural areas

Majka

Bednarek

Chan

et al. 2020

Preprint

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“…The segmentation of brain images is done following two main steps. First, a diffeomorphic registration of the marmoset brain template, previously developed in [13], to the image is performed using a module integrated in 3D slicer [14]. The registration process preserves the brain topology and outputs three probability maps of the GM, WM and CSF considered as prior information.…”

Section: Image Acquisition and Segmentationmentioning

confidence: 99%

Brain Segmentation from Super-Resolved Magnetic Resonance Images

Bazzi

Rodríguez-Callejas

Fonta

et al. 2019

2019 Fifth International Conference on Advances in Biomedical Engineering (ICABME)

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The objective of this work is to investigate the ability of a 2D super resolution (SR) technique in 3D restoration and enhancement of brain magnetic resonance images to facilitate the study of cerebral aging bio-markers. The SR method exploits the joint properties of the system point spread function and sub-sampling operators to derive a fast algorithm. Brain images of the common marmoset, Callithrix jacchus, acquired at different ages are used in this study. The evaluation of the final outcome of our method is done by computing the intracranial volume from the segmentation of the brain compartments: gray matter, white matter and cerebrospinal fluid. Results show that the deblurring of the images improves the segmentation process with respect to the ground truth. However, super resolution leads to the best quantification of the intracranial volume when compared to the deblurred and the original images. Therefore, despite its sub-optimality, the 2D SR method provides reliable results for improving the quality of the images used in the study of aging in terms of precision of reconstruction and computational time.

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“…DTI has become an important tool to study the anatomy of animal brains in vivo , for example, the mouse brain (Aggarwal et al, 2010 ; Harsan et al, 2010 ; Nouls et al, 2018 ), the rat brain (Gyengesi et al, 2014 ; Figini et al, 2015 ), the canine brain (Wu et al, 2011 ), or the primate brain (Feng et al, 2017 ; Risser et al, 2019 ). The non-invasive nature of MRI/DTI enables longitudinal studies of transgenic disease models (Haber et al, 2017 ; Petrella et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Diffusion Tensor Imaging-Based Studies at the Group-Level Applied to Animal Models of Neurodegenerative Diseases

et al. 2020

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The understanding of human and non-human microstructural brain alterations in the course of neurodegenerative diseases has substantially improved by the non-invasive magnetic resonance imaging (MRI) technique of diffusion tensor imaging (DTI). Animal models (including disease or knockout models) allow for a variety of experimental manipulations, which are not applicable to humans. Thus, the DTI approach provides a promising tool for cross-species cross-sectional and longitudinal investigations of the neurobiological targets and mechanisms of neurodegeneration. This overview with a systematic review focuses on the principles of DTI analysis as used in studies at the group level in living preclinical models of neurodegeneration. The translational aspect from in-vivo animal models toward (clinical) applications in humans is covered as well as the DTI-based research of the non-human brains' microstructure, the methodological aspects in data processing and analysis, and data interpretation at different abstraction levels. The aim of integrating DTI in multiparametric or multimodal imaging protocols will allow the interrogation of DTI data in terms of directional flow of information and may identify the microstructural underpinnings of neurodegeneration-related patterns.

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In vivo localization of cortical areas using a 3D computerized atlas of the marmoset brain

Cited by 12 publications

References 68 publications

Histology-based average template of the marmoset cortex with probabilistic localization of cytoarchitectural areas

Histology-based average template of the marmoset cortex with probabilistic localization of cytoarchitectural areas

Brain Segmentation from Super-Resolved Magnetic Resonance Images

Diffusion Tensor Imaging-Based Studies at the Group-Level Applied to Animal Models of Neurodegenerative Diseases

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