A deep learning algorithm for 3D cell detection in whole mouse brain image datasets.
Understanding the function of the nervous system necessitates mapping the spatial distributions of its constituent cells defined by function, anatomy or gene expression. Recently, developments in tissue preparation and microscopy allow cellular populations to be imaged throughout the entire rodent b...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2021-05-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1009074 |
| _version_ | 1818579164360343552 |
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| author | Adam L Tyson Charly V Rousseau Christian J Niedworok Sepiedeh Keshavarzi Chryssanthi Tsitoura Lee Cossell Molly Strom Troy W Margrie |
| author_facet | Adam L Tyson Charly V Rousseau Christian J Niedworok Sepiedeh Keshavarzi Chryssanthi Tsitoura Lee Cossell Molly Strom Troy W Margrie |
| author_sort | Adam L Tyson |
| collection | DOAJ |
| description | Understanding the function of the nervous system necessitates mapping the spatial distributions of its constituent cells defined by function, anatomy or gene expression. Recently, developments in tissue preparation and microscopy allow cellular populations to be imaged throughout the entire rodent brain. However, mapping these neurons manually is prone to bias and is often impractically time consuming. Here we present an open-source algorithm for fully automated 3D detection of neuronal somata in mouse whole-brain microscopy images using standard desktop computer hardware. We demonstrate the applicability and power of our approach by mapping the brain-wide locations of large populations of cells labeled with cytoplasmic fluorescent proteins expressed via retrograde trans-synaptic viral infection. |
| first_indexed | 2024-12-16T06:57:21Z |
| format | Article |
| id | doaj.art-6e786c78174c437ba66de5157f9cbdc1 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-16T06:57:21Z |
| publishDate | 2021-05-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-6e786c78174c437ba66de5157f9cbdc12022-12-21T22:40:15ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582021-05-01175e100907410.1371/journal.pcbi.1009074A deep learning algorithm for 3D cell detection in whole mouse brain image datasets.Adam L TysonCharly V RousseauChristian J NiedworokSepiedeh KeshavarziChryssanthi TsitouraLee CossellMolly StromTroy W MargrieUnderstanding the function of the nervous system necessitates mapping the spatial distributions of its constituent cells defined by function, anatomy or gene expression. Recently, developments in tissue preparation and microscopy allow cellular populations to be imaged throughout the entire rodent brain. However, mapping these neurons manually is prone to bias and is often impractically time consuming. Here we present an open-source algorithm for fully automated 3D detection of neuronal somata in mouse whole-brain microscopy images using standard desktop computer hardware. We demonstrate the applicability and power of our approach by mapping the brain-wide locations of large populations of cells labeled with cytoplasmic fluorescent proteins expressed via retrograde trans-synaptic viral infection.https://doi.org/10.1371/journal.pcbi.1009074 |
| spellingShingle | Adam L Tyson Charly V Rousseau Christian J Niedworok Sepiedeh Keshavarzi Chryssanthi Tsitoura Lee Cossell Molly Strom Troy W Margrie A deep learning algorithm for 3D cell detection in whole mouse brain image datasets. PLoS Computational Biology |
| title | A deep learning algorithm for 3D cell detection in whole mouse brain image datasets. |
| title_full | A deep learning algorithm for 3D cell detection in whole mouse brain image datasets. |
| title_fullStr | A deep learning algorithm for 3D cell detection in whole mouse brain image datasets. |
| title_full_unstemmed | A deep learning algorithm for 3D cell detection in whole mouse brain image datasets. |
| title_short | A deep learning algorithm for 3D cell detection in whole mouse brain image datasets. |
| title_sort | deep learning algorithm for 3d cell detection in whole mouse brain image datasets |
| url | https://doi.org/10.1371/journal.pcbi.1009074 |
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