giRAff: an automated atlas segmentation tool adapted to single histological slices
Conventional histology of the brain remains the gold standard in the analysis of animal models. In most biological studies, standard protocols usually involve producing a limited number of histological slices to be analyzed. These slices are often selected into a specific anatomical region of intere...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2024-01-01
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| Series: | Frontiers in Neuroscience |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fnins.2023.1230814/full |
| _version_ | 1797357812266827776 |
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| author | Sébastien Piluso Sébastien Piluso Nicolas Souedet Caroline Jan Anne-Sophie Hérard Cédric Clouchoux Thierry Delzescaux |
| author_facet | Sébastien Piluso Sébastien Piluso Nicolas Souedet Caroline Jan Anne-Sophie Hérard Cédric Clouchoux Thierry Delzescaux |
| author_sort | Sébastien Piluso |
| collection | DOAJ |
| description | Conventional histology of the brain remains the gold standard in the analysis of animal models. In most biological studies, standard protocols usually involve producing a limited number of histological slices to be analyzed. These slices are often selected into a specific anatomical region of interest or around a specific pathological lesion. Due to the lack of automated solutions to analyze such single slices, neurobiologists perform the segmentation of anatomical regions manually most of the time. Because the task is long, tedious, and operator-dependent, we propose an automated atlas segmentation method called giRAff, which combines rigid and affine registrations and is suitable for conventional histological protocols involving any number of single slices from a given mouse brain. In particular, the method has been tested on several routine experimental protocols involving different anatomical regions of different sizes and for several brains. For a given set of single slices, the method can automatically identify the corresponding slices in the mouse Allen atlas template with good accuracy and segmentations comparable to those of an expert. This versatile and generic method allows the segmentation of any single slice without additional anatomical context in about 1 min. Basically, our proposed giRAff method is an easy-to-use, rapid, and automated atlas segmentation tool compliant with a wide variety of standard histological protocols. |
| first_indexed | 2024-03-08T14:50:43Z |
| format | Article |
| id | doaj.art-e4db8167e9884f7f9920c06452106f23 |
| institution | Directory Open Access Journal |
| issn | 1662-453X |
| language | English |
| last_indexed | 2024-03-08T14:50:43Z |
| publishDate | 2024-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Neuroscience |
| spelling | doaj.art-e4db8167e9884f7f9920c06452106f232024-01-11T04:29:58ZengFrontiers Media S.A.Frontiers in Neuroscience1662-453X2024-01-011710.3389/fnins.2023.12308141230814giRAff: an automated atlas segmentation tool adapted to single histological slicesSébastien Piluso0Sébastien Piluso1Nicolas Souedet2Caroline Jan3Anne-Sophie Hérard4Cédric Clouchoux5Thierry Delzescaux6Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, FranceWITSEE, Paris, FranceUniversité Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, FranceUniversité Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, FranceUniversité Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, FranceWITSEE, Paris, FranceUniversité Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, FranceConventional histology of the brain remains the gold standard in the analysis of animal models. In most biological studies, standard protocols usually involve producing a limited number of histological slices to be analyzed. These slices are often selected into a specific anatomical region of interest or around a specific pathological lesion. Due to the lack of automated solutions to analyze such single slices, neurobiologists perform the segmentation of anatomical regions manually most of the time. Because the task is long, tedious, and operator-dependent, we propose an automated atlas segmentation method called giRAff, which combines rigid and affine registrations and is suitable for conventional histological protocols involving any number of single slices from a given mouse brain. In particular, the method has been tested on several routine experimental protocols involving different anatomical regions of different sizes and for several brains. For a given set of single slices, the method can automatically identify the corresponding slices in the mouse Allen atlas template with good accuracy and segmentations comparable to those of an expert. This versatile and generic method allows the segmentation of any single slice without additional anatomical context in about 1 min. Basically, our proposed giRAff method is an easy-to-use, rapid, and automated atlas segmentation tool compliant with a wide variety of standard histological protocols.https://www.frontiersin.org/articles/10.3389/fnins.2023.1230814/fullatlas segmentationimage registrationhistologybrainmouse |
| spellingShingle | Sébastien Piluso Sébastien Piluso Nicolas Souedet Caroline Jan Anne-Sophie Hérard Cédric Clouchoux Thierry Delzescaux giRAff: an automated atlas segmentation tool adapted to single histological slices Frontiers in Neuroscience atlas segmentation image registration histology brain mouse |
| title | giRAff: an automated atlas segmentation tool adapted to single histological slices |
| title_full | giRAff: an automated atlas segmentation tool adapted to single histological slices |
| title_fullStr | giRAff: an automated atlas segmentation tool adapted to single histological slices |
| title_full_unstemmed | giRAff: an automated atlas segmentation tool adapted to single histological slices |
| title_short | giRAff: an automated atlas segmentation tool adapted to single histological slices |
| title_sort | giraff an automated atlas segmentation tool adapted to single histological slices |
| topic | atlas segmentation image registration histology brain mouse |
| url | https://www.frontiersin.org/articles/10.3389/fnins.2023.1230814/full |
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