Cell density quantification of high resolution Nissl images of the juvenile rat brain
Nissl histology underpins our understanding of brain anatomy and architecture. Despite its importance, no high-resolution datasets are currently available in the literature for 14-day-old rats. To remedy this issue and demonstrate the utility of such a dataset, we have acquired over 2000 high-resolu...
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| Language: | English |
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Frontiers Media S.A.
2024-12-01
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| Series: | Frontiers in Neuroanatomy |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fnana.2024.1463632/full |
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| author | Julie Meystre Jean Jacquemier Olivier Burri Csaba Zsolnai Nicolas Frank João Prado Vieira Ying Shi Ying Shi Rodrigo Perin Daniel Keller Henry Markram Henry Markram |
| author_facet | Julie Meystre Jean Jacquemier Olivier Burri Csaba Zsolnai Nicolas Frank João Prado Vieira Ying Shi Ying Shi Rodrigo Perin Daniel Keller Henry Markram Henry Markram |
| author_sort | Julie Meystre |
| collection | DOAJ |
| description | Nissl histology underpins our understanding of brain anatomy and architecture. Despite its importance, no high-resolution datasets are currently available in the literature for 14-day-old rats. To remedy this issue and demonstrate the utility of such a dataset, we have acquired over 2000 high-resolution images (0.346 μm per pixel) from eight juvenile rat brains stained with cresyl violet. To analyze this dataset, we developed a semi-automated pipeline using open-source software to perform cell density quantification in the primary somatosensory hindlimb (S1HL) cortical column. In addition, we performed cortical layer annotations both manually and using a machine learning model to expand the number of annotated samples. After training the model, we applied it to 262 images of the S1HL, retroactively assigning segmented cells to specific cortical layers, enabling cell density quantification per layer rather than just for entire brain regions. The pipeline improved the efficiency and reliability of cell density quantification while accurately assigning cortical layer boundaries. Furthermore, the method is adaptable to different brain regions and cell morphologies. The full dataset, annotations, and analysis tools are made publicly available for further research and applications. |
| format | Article |
| id | doaj-art-e1b3522208334207b46dfb0ac3902e45 |
| institution | OA Journals |
| issn | 1662-5129 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Neuroanatomy |
| spelling | doaj-art-e1b3522208334207b46dfb0ac3902e452025-08-20T02:36:58ZengFrontiers Media S.A.Frontiers in Neuroanatomy1662-51292024-12-011810.3389/fnana.2024.14636321463632Cell density quantification of high resolution Nissl images of the juvenile rat brainJulie Meystre0Jean Jacquemier1Olivier Burri2Csaba Zsolnai3Nicolas Frank4João Prado Vieira5Ying Shi6Ying Shi7Rodrigo Perin8Daniel Keller9Henry Markram10Henry Markram11Laboratory of Neural Microcircuitry, École Polytechnique Fédérale de Lausanne, Lausanne, SwitzerlandBlue Brain Project, École Polytechnique Fédérale de Lausanne, Genève, SwitzerlandBioimaging and Optics Platform, École Polytechnique Fédérale de Lausanne, Lausanne, SwitzerlandBlue Brain Project, École Polytechnique Fédérale de Lausanne, Genève, SwitzerlandBlue Brain Project, École Polytechnique Fédérale de Lausanne, Genève, SwitzerlandLaboratory of Neural Microcircuitry, École Polytechnique Fédérale de Lausanne, Lausanne, SwitzerlandLaboratory of Neural Microcircuitry, École Polytechnique Fédérale de Lausanne, Lausanne, SwitzerlandBlue Brain Project, École Polytechnique Fédérale de Lausanne, Genève, SwitzerlandLaboratory of Neural Microcircuitry, École Polytechnique Fédérale de Lausanne, Lausanne, SwitzerlandBlue Brain Project, École Polytechnique Fédérale de Lausanne, Genève, SwitzerlandLaboratory of Neural Microcircuitry, École Polytechnique Fédérale de Lausanne, Lausanne, SwitzerlandBlue Brain Project, École Polytechnique Fédérale de Lausanne, Genève, SwitzerlandNissl histology underpins our understanding of brain anatomy and architecture. Despite its importance, no high-resolution datasets are currently available in the literature for 14-day-old rats. To remedy this issue and demonstrate the utility of such a dataset, we have acquired over 2000 high-resolution images (0.346 μm per pixel) from eight juvenile rat brains stained with cresyl violet. To analyze this dataset, we developed a semi-automated pipeline using open-source software to perform cell density quantification in the primary somatosensory hindlimb (S1HL) cortical column. In addition, we performed cortical layer annotations both manually and using a machine learning model to expand the number of annotated samples. After training the model, we applied it to 262 images of the S1HL, retroactively assigning segmented cells to specific cortical layers, enabling cell density quantification per layer rather than just for entire brain regions. The pipeline improved the efficiency and reliability of cell density quantification while accurately assigning cortical layer boundaries. Furthermore, the method is adaptable to different brain regions and cell morphologies. The full dataset, annotations, and analysis tools are made publicly available for further research and applications.https://www.frontiersin.org/articles/10.3389/fnana.2024.1463632/fullrodentsomatosensory hindlimbcell densitystereologycortical layeringCellpose |
| spellingShingle | Julie Meystre Jean Jacquemier Olivier Burri Csaba Zsolnai Nicolas Frank João Prado Vieira Ying Shi Ying Shi Rodrigo Perin Daniel Keller Henry Markram Henry Markram Cell density quantification of high resolution Nissl images of the juvenile rat brain Frontiers in Neuroanatomy rodent somatosensory hindlimb cell density stereology cortical layering Cellpose |
| title | Cell density quantification of high resolution Nissl images of the juvenile rat brain |
| title_full | Cell density quantification of high resolution Nissl images of the juvenile rat brain |
| title_fullStr | Cell density quantification of high resolution Nissl images of the juvenile rat brain |
| title_full_unstemmed | Cell density quantification of high resolution Nissl images of the juvenile rat brain |
| title_short | Cell density quantification of high resolution Nissl images of the juvenile rat brain |
| title_sort | cell density quantification of high resolution nissl images of the juvenile rat brain |
| topic | rodent somatosensory hindlimb cell density stereology cortical layering Cellpose |
| url | https://www.frontiersin.org/articles/10.3389/fnana.2024.1463632/full |
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