WIKIBrainStem: An online atlas to manually segment the human brainstem at the mesoscopic scale from ultrahigh field MRI
The brainstem is one of the most densely packed areas of the central nervous system in terms of gray, but also white, matter structures and, therefore, is a highly functional hub. It has mainly been studied by the means of histological techniques, which requires several hundreds of slices with a los...
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doaj-10f680ee2e9940d5b375e3040d707ca22021-06-29T04:11:54ZengElsevierNeuroImage1095-95722021-08-01236118080WIKIBrainStem: An online atlas to manually segment the human brainstem at the mesoscopic scale from ultrahigh field MRIFrançois Lechanoine0Timothée Jacquesson1Justine Beaujoin2Barthélemy Serres3Mohammad Mohammadi4Alexia Planty-Bonjour5Frédéric Andersson6Fabrice Poupon7Cyril Poupon8Christophe Destrieux9UMR 1253, iBrain, Université de Tours, Inserm, Tours, France; CHRU de Tours, Tours, FranceCREATIS Laboratory CNRS UMR5220, Inserm U1206, INSA-Lyon, University of Lyon 1, Lyon, FranceBAOBAB, Paris-Saclay University, CNRS, CEA, FranceILIAD3, Université de Tours, Tours, France; LIFAT, EA6300, Université de Tours, Tours, FranceUMR 1253, iBrain, Université de Tours, Inserm, Tours, FranceUMR 1253, iBrain, Université de Tours, Inserm, Tours, France; CHRU de Tours, Tours, FranceUMR 1253, iBrain, Université de Tours, Inserm, Tours, FranceBAOBAB, Paris-Saclay University, CNRS, CEA, FranceBAOBAB, Paris-Saclay University, CNRS, CEA, FranceUMR 1253, iBrain, Université de Tours, Inserm, Tours, France; CHRU de Tours, Tours, France; Corresponding author at: UMR 1253, iBrain, Université de Tours, Inserm, Tours, FranceThe brainstem is one of the most densely packed areas of the central nervous system in terms of gray, but also white, matter structures and, therefore, is a highly functional hub. It has mainly been studied by the means of histological techniques, which requires several hundreds of slices with a loss of the 3D coherence of the whole specimen. Access to the inner structure of the brainstem is possible using Magnetic Resonance Imaging (MRI), but this method has a limited spatial resolution and contrast in vivo. Here, we scanned an ex vivo specimen using an ultra-high field (11.7T) preclinical MRI scanner providing data at a mesoscopic scale for anatomical T2-weighted (100 µm and 185 µm isotropic) and diffusion-weighted imaging (300 µm isotropic). We then proposed a hierarchical segmentation of the inner gray matter of the brainstem and defined a set of rules for each segmented anatomical class. These rules were gathered in a freely accessible web-based application, WIKIBrainStem (https://fibratlas.univ-tours.fr/brainstems/index.html), for 99 structures, from which 13 were subdivided into 29 substructures.This segmentation is, to date, the most detailed one developed from ex vivo MRI of the brainstem. This should be regarded as a tool that will be complemented by future results of alternative methods, such as Optical Coherence Tomography, Polarized Light Imaging or histology… This is a mandatory step prior to segmenting multiple specimens, which will be used to create a probabilistic automated segmentation method of ex vivo, but also in vivo, brainstem and may be used for targeting anatomical structures of interest in managing some degenerative or psychiatric disorders.http://www.sciencedirect.com/science/article/pii/S1053811921003578BrainstemAnatomyExvivo MRIAtlas |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
François Lechanoine Timothée Jacquesson Justine Beaujoin Barthélemy Serres Mohammad Mohammadi Alexia Planty-Bonjour Frédéric Andersson Fabrice Poupon Cyril Poupon Christophe Destrieux |
spellingShingle |
François Lechanoine Timothée Jacquesson Justine Beaujoin Barthélemy Serres Mohammad Mohammadi Alexia Planty-Bonjour Frédéric Andersson Fabrice Poupon Cyril Poupon Christophe Destrieux WIKIBrainStem: An online atlas to manually segment the human brainstem at the mesoscopic scale from ultrahigh field MRI NeuroImage Brainstem Anatomy Exvivo MRI Atlas |
author_facet |
François Lechanoine Timothée Jacquesson Justine Beaujoin Barthélemy Serres Mohammad Mohammadi Alexia Planty-Bonjour Frédéric Andersson Fabrice Poupon Cyril Poupon Christophe Destrieux |
author_sort |
François Lechanoine |
title |
WIKIBrainStem: An online atlas to manually segment the human brainstem at the mesoscopic scale from ultrahigh field MRI |
title_short |
WIKIBrainStem: An online atlas to manually segment the human brainstem at the mesoscopic scale from ultrahigh field MRI |
title_full |
WIKIBrainStem: An online atlas to manually segment the human brainstem at the mesoscopic scale from ultrahigh field MRI |
title_fullStr |
WIKIBrainStem: An online atlas to manually segment the human brainstem at the mesoscopic scale from ultrahigh field MRI |
title_full_unstemmed |
WIKIBrainStem: An online atlas to manually segment the human brainstem at the mesoscopic scale from ultrahigh field MRI |
title_sort |
wikibrainstem: an online atlas to manually segment the human brainstem at the mesoscopic scale from ultrahigh field mri |
publisher |
Elsevier |
series |
NeuroImage |
issn |
1095-9572 |
publishDate |
2021-08-01 |
description |
The brainstem is one of the most densely packed areas of the central nervous system in terms of gray, but also white, matter structures and, therefore, is a highly functional hub. It has mainly been studied by the means of histological techniques, which requires several hundreds of slices with a loss of the 3D coherence of the whole specimen. Access to the inner structure of the brainstem is possible using Magnetic Resonance Imaging (MRI), but this method has a limited spatial resolution and contrast in vivo. Here, we scanned an ex vivo specimen using an ultra-high field (11.7T) preclinical MRI scanner providing data at a mesoscopic scale for anatomical T2-weighted (100 µm and 185 µm isotropic) and diffusion-weighted imaging (300 µm isotropic). We then proposed a hierarchical segmentation of the inner gray matter of the brainstem and defined a set of rules for each segmented anatomical class. These rules were gathered in a freely accessible web-based application, WIKIBrainStem (https://fibratlas.univ-tours.fr/brainstems/index.html), for 99 structures, from which 13 were subdivided into 29 substructures.This segmentation is, to date, the most detailed one developed from ex vivo MRI of the brainstem. This should be regarded as a tool that will be complemented by future results of alternative methods, such as Optical Coherence Tomography, Polarized Light Imaging or histology… This is a mandatory step prior to segmenting multiple specimens, which will be used to create a probabilistic automated segmentation method of ex vivo, but also in vivo, brainstem and may be used for targeting anatomical structures of interest in managing some degenerative or psychiatric disorders. |
topic |
Brainstem Anatomy Exvivo MRI Atlas |
url |
http://www.sciencedirect.com/science/article/pii/S1053811921003578 |
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