Automatic segmentation of the olfactory bulb

Detalhes bibliográficos
Autor(a) principal: Desser, Dmitriy
Data de Publicação: 2021
Outros Autores: Assunção, Francisca, Yan, Xiaoguang, Alves, Victor, Fernandes, Henrique M., Hummel, Thomas
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/1822/74763
Resumo: The olfactory bulb (OB) has an essential role in the human olfactory pathway. A change in olfactory function is associated with a change of OB volume. It has been shown to predict the prognosis of olfactory loss and its volume is a biomarker for various neurodegenerative diseases, such as Alzheimer’s disease. Thus far, obtaining an OB volume for research purposes has been performed by manual segmentation alone; a very time-consuming and highly rater-biased process. As such, this process dramatically reduces the ability to produce fair and reliable comparisons between studies, as well as the processing of large datasets. Our study aims to solve this by proposing a novel methodological framework for the unbiased measurement of OB volume. In this paper, we present a fully automated tool that successfully performs such a task, accurately and quickly. In order to develop a stable and versatile algorithm and to train the neural network, we used four datasets consisting of whole-brain T1 and high-resolution T2 MRI scans, as well as the corresponding clinical information of the subject’s smelling ability. One dataset contained data of patients suffering from anosmia or hyposmia (N = 79), and the other three datasets contained data of healthy controls (N = 91). First, the manual segmentation labels of the OBs were created by two experienced raters, independently and blinded. The algorithm consisted of the following four different steps: (1) multimodal data co-registration of whole-brain T1 images and T2 images, (2) template-based localization of OBs, (3) bounding box construction, and lastly, (4) segmentation of the OB using a 3D-U-Net. The results from the automated segmentation algorithm were tested on previously unseen data, achieving a mean dice coefficient (DC) of 0.77 ± 0.05, which is remarkably convergent with the inter-rater DC of 0.79 ± 0.08 estimated for the same cohort. Additionally, the symmetric surface distance (ASSD) was 0.43 ± 0.10. Furthermore, the segmentations produced using our algorithm were manually rated by an independent blinded rater and have reached an equivalent rating score of 5.95 ± 0.87 compared to a rating score of 6.23 ± 0.87 for the first rater’s segmentation and 5.92 ± 0.81 for the second rater’s manual segmentation. Taken together, these results support the success of our tool in producing automatic fast (3–5 min per subject) and reliable segmentations of the OB, with virtually matching accuracy with the current gold standard technique for OB segmentation. In conclusion, we present a newly developed ready-to-use tool that can perform the segmentation of OBs based on multimodal data consisting of T1 whole-brain images and T2 coronal high-resolution images. The accuracy of the segmentations predicted by the algorithm matches the manual segmentations made by two well-experienced raters. This method holds potential for immediate implementation in clinical practice. Furthermore, its ability to perform quick and accurate processing of large datasets may provide a valuable contribution to advancing our knowledge of the olfactory system, in health and disease. Specifically, our framework may integrate the use of olfactory bulb volume (OBV) measurements for the diagnosis and treatment of olfactory loss and improve the prognosis and treatment options of olfactory dysfunctions.
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spelling Automatic segmentation of the olfactory bulbOlfactory bulbOlfactory lossDeep learningSegmentationScience & TechnologyThe olfactory bulb (OB) has an essential role in the human olfactory pathway. A change in olfactory function is associated with a change of OB volume. It has been shown to predict the prognosis of olfactory loss and its volume is a biomarker for various neurodegenerative diseases, such as Alzheimer’s disease. Thus far, obtaining an OB volume for research purposes has been performed by manual segmentation alone; a very time-consuming and highly rater-biased process. As such, this process dramatically reduces the ability to produce fair and reliable comparisons between studies, as well as the processing of large datasets. Our study aims to solve this by proposing a novel methodological framework for the unbiased measurement of OB volume. In this paper, we present a fully automated tool that successfully performs such a task, accurately and quickly. In order to develop a stable and versatile algorithm and to train the neural network, we used four datasets consisting of whole-brain T1 and high-resolution T2 MRI scans, as well as the corresponding clinical information of the subject’s smelling ability. One dataset contained data of patients suffering from anosmia or hyposmia (N = 79), and the other three datasets contained data of healthy controls (N = 91). First, the manual segmentation labels of the OBs were created by two experienced raters, independently and blinded. The algorithm consisted of the following four different steps: (1) multimodal data co-registration of whole-brain T1 images and T2 images, (2) template-based localization of OBs, (3) bounding box construction, and lastly, (4) segmentation of the OB using a 3D-U-Net. The results from the automated segmentation algorithm were tested on previously unseen data, achieving a mean dice coefficient (DC) of 0.77 ± 0.05, which is remarkably convergent with the inter-rater DC of 0.79 ± 0.08 estimated for the same cohort. Additionally, the symmetric surface distance (ASSD) was 0.43 ± 0.10. Furthermore, the segmentations produced using our algorithm were manually rated by an independent blinded rater and have reached an equivalent rating score of 5.95 ± 0.87 compared to a rating score of 6.23 ± 0.87 for the first rater’s segmentation and 5.92 ± 0.81 for the second rater’s manual segmentation. Taken together, these results support the success of our tool in producing automatic fast (3–5 min per subject) and reliable segmentations of the OB, with virtually matching accuracy with the current gold standard technique for OB segmentation. In conclusion, we present a newly developed ready-to-use tool that can perform the segmentation of OBs based on multimodal data consisting of T1 whole-brain images and T2 coronal high-resolution images. The accuracy of the segmentations predicted by the algorithm matches the manual segmentations made by two well-experienced raters. This method holds potential for immediate implementation in clinical practice. Furthermore, its ability to perform quick and accurate processing of large datasets may provide a valuable contribution to advancing our knowledge of the olfactory system, in health and disease. Specifically, our framework may integrate the use of olfactory bulb volume (OBV) measurements for the diagnosis and treatment of olfactory loss and improve the prognosis and treatment options of olfactory dysfunctions.(undefined)Multidisciplinary Digital Publishing Institute (MDPI)Universidade do MinhoDesser, DmitriyAssunção, FranciscaYan, XiaoguangAlves, VictorFernandes, Henrique M.Hummel, Thomas2021-08-282021-08-28T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/74763engDesser, D.; Assunção, F.; Yan, X.; Alves, V.; Fernandes, H.M.; Hummel, T. Automatic Segmentation of the Olfactory Bulb. Brain Sci. 2021, 11, 1141. https://doi.org/10.3390/brainsci110911412076342510.3390/brainsci11091141https://www.mdpi.com/2076-3425/11/9/1141info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:52:13Zoai:repositorium.sdum.uminho.pt:1822/74763Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:51:17.971890Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Automatic segmentation of the olfactory bulb
title Automatic segmentation of the olfactory bulb
spellingShingle Automatic segmentation of the olfactory bulb
Desser, Dmitriy
Olfactory bulb
Olfactory loss
Deep learning
Segmentation
Science & Technology
title_short Automatic segmentation of the olfactory bulb
title_full Automatic segmentation of the olfactory bulb
title_fullStr Automatic segmentation of the olfactory bulb
title_full_unstemmed Automatic segmentation of the olfactory bulb
title_sort Automatic segmentation of the olfactory bulb
author Desser, Dmitriy
author_facet Desser, Dmitriy
Assunção, Francisca
Yan, Xiaoguang
Alves, Victor
Fernandes, Henrique M.
Hummel, Thomas
author_role author
author2 Assunção, Francisca
Yan, Xiaoguang
Alves, Victor
Fernandes, Henrique M.
Hummel, Thomas
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade do Minho
dc.contributor.author.fl_str_mv Desser, Dmitriy
Assunção, Francisca
Yan, Xiaoguang
Alves, Victor
Fernandes, Henrique M.
Hummel, Thomas
dc.subject.por.fl_str_mv Olfactory bulb
Olfactory loss
Deep learning
Segmentation
Science & Technology
topic Olfactory bulb
Olfactory loss
Deep learning
Segmentation
Science & Technology
description The olfactory bulb (OB) has an essential role in the human olfactory pathway. A change in olfactory function is associated with a change of OB volume. It has been shown to predict the prognosis of olfactory loss and its volume is a biomarker for various neurodegenerative diseases, such as Alzheimer’s disease. Thus far, obtaining an OB volume for research purposes has been performed by manual segmentation alone; a very time-consuming and highly rater-biased process. As such, this process dramatically reduces the ability to produce fair and reliable comparisons between studies, as well as the processing of large datasets. Our study aims to solve this by proposing a novel methodological framework for the unbiased measurement of OB volume. In this paper, we present a fully automated tool that successfully performs such a task, accurately and quickly. In order to develop a stable and versatile algorithm and to train the neural network, we used four datasets consisting of whole-brain T1 and high-resolution T2 MRI scans, as well as the corresponding clinical information of the subject’s smelling ability. One dataset contained data of patients suffering from anosmia or hyposmia (N = 79), and the other three datasets contained data of healthy controls (N = 91). First, the manual segmentation labels of the OBs were created by two experienced raters, independently and blinded. The algorithm consisted of the following four different steps: (1) multimodal data co-registration of whole-brain T1 images and T2 images, (2) template-based localization of OBs, (3) bounding box construction, and lastly, (4) segmentation of the OB using a 3D-U-Net. The results from the automated segmentation algorithm were tested on previously unseen data, achieving a mean dice coefficient (DC) of 0.77 ± 0.05, which is remarkably convergent with the inter-rater DC of 0.79 ± 0.08 estimated for the same cohort. Additionally, the symmetric surface distance (ASSD) was 0.43 ± 0.10. Furthermore, the segmentations produced using our algorithm were manually rated by an independent blinded rater and have reached an equivalent rating score of 5.95 ± 0.87 compared to a rating score of 6.23 ± 0.87 for the first rater’s segmentation and 5.92 ± 0.81 for the second rater’s manual segmentation. Taken together, these results support the success of our tool in producing automatic fast (3–5 min per subject) and reliable segmentations of the OB, with virtually matching accuracy with the current gold standard technique for OB segmentation. In conclusion, we present a newly developed ready-to-use tool that can perform the segmentation of OBs based on multimodal data consisting of T1 whole-brain images and T2 coronal high-resolution images. The accuracy of the segmentations predicted by the algorithm matches the manual segmentations made by two well-experienced raters. This method holds potential for immediate implementation in clinical practice. Furthermore, its ability to perform quick and accurate processing of large datasets may provide a valuable contribution to advancing our knowledge of the olfactory system, in health and disease. Specifically, our framework may integrate the use of olfactory bulb volume (OBV) measurements for the diagnosis and treatment of olfactory loss and improve the prognosis and treatment options of olfactory dysfunctions.
publishDate 2021
dc.date.none.fl_str_mv 2021-08-28
2021-08-28T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
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status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/1822/74763
url http://hdl.handle.net/1822/74763
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Desser, D.; Assunção, F.; Yan, X.; Alves, V.; Fernandes, H.M.; Hummel, T. Automatic Segmentation of the Olfactory Bulb. Brain Sci. 2021, 11, 1141. https://doi.org/10.3390/brainsci11091141
20763425
10.3390/brainsci11091141
https://www.mdpi.com/2076-3425/11/9/1141
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dc.publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute (MDPI)
publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute (MDPI)
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