Multiscale 3D phenotyping of human cerebral organoids
Brain organoids grown from human pluripotent stem cells self-organize into cytoarchitectures resembling the developing human brain. These three-dimensional models offer an unprecedented opportunity to study human brain development and dysfunction. Characterization currently sacrifices spatial inform...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Springer Science and Business Media LLC
2021
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| Online Access: | https://hdl.handle.net/1721.1/136109 |
| _version_ | 1826213765660540928 |
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| author | Albanese, Alexandre Swaney, Justin M Yun, Dae Hee Evans, Nicholas B Antonucci, Jenna M Velasco, Silvia Sohn, Chang Ho Arlotta, Paola Gehrke, Lee Chung, Kwanghun |
| author2 | Massachusetts Institute of Technology. Institute for Medical Engineering & Science |
| author_facet | Massachusetts Institute of Technology. Institute for Medical Engineering & Science Albanese, Alexandre Swaney, Justin M Yun, Dae Hee Evans, Nicholas B Antonucci, Jenna M Velasco, Silvia Sohn, Chang Ho Arlotta, Paola Gehrke, Lee Chung, Kwanghun |
| author_sort | Albanese, Alexandre |
| collection | MIT |
| description | Brain organoids grown from human pluripotent stem cells self-organize into cytoarchitectures resembling the developing human brain. These three-dimensional models offer an unprecedented opportunity to study human brain development and dysfunction. Characterization currently sacrifices spatial information for single-cell or histological analysis leaving whole-tissue analysis mostly unexplored. Here, we present the SCOUT pipeline for automated multiscale comparative analysis of intact cerebral organoids. Our integrated technology platform can rapidly clear, label, and image intact organoids. Algorithmic- and convolutional neural network-based image analysis extract hundreds of features characterizing molecular, cellular, spatial, cytoarchitectural, and organoid-wide properties from fluorescence microscopy datasets. Comprehensive analysis of 46 intact organoids and ~ 100 million cells reveals quantitative multiscale “phenotypes" for organoid development, culture protocols and Zika virus infection. SCOUT provides a much-needed framework for comparative analysis of emerging 3D in vitro models using fluorescence microscopy. |
| first_indexed | 2024-09-23T15:54:28Z |
| format | Article |
| id | mit-1721.1/136109 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T15:54:28Z |
| publishDate | 2021 |
| publisher | Springer Science and Business Media LLC |
| record_format | dspace |
| spelling | mit-1721.1/1361092024-03-19T13:40:40Z Multiscale 3D phenotyping of human cerebral organoids Albanese, Alexandre Swaney, Justin M Yun, Dae Hee Evans, Nicholas B Antonucci, Jenna M Velasco, Silvia Sohn, Chang Ho Arlotta, Paola Gehrke, Lee Chung, Kwanghun Massachusetts Institute of Technology. Institute for Medical Engineering & Science Picower Institute for Learning and Memory Massachusetts Institute of Technology. Department of Chemical Engineering Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences Harvard University--MIT Division of Health Sciences and Technology Brain organoids grown from human pluripotent stem cells self-organize into cytoarchitectures resembling the developing human brain. These three-dimensional models offer an unprecedented opportunity to study human brain development and dysfunction. Characterization currently sacrifices spatial information for single-cell or histological analysis leaving whole-tissue analysis mostly unexplored. Here, we present the SCOUT pipeline for automated multiscale comparative analysis of intact cerebral organoids. Our integrated technology platform can rapidly clear, label, and image intact organoids. Algorithmic- and convolutional neural network-based image analysis extract hundreds of features characterizing molecular, cellular, spatial, cytoarchitectural, and organoid-wide properties from fluorescence microscopy datasets. Comprehensive analysis of 46 intact organoids and ~ 100 million cells reveals quantitative multiscale “phenotypes" for organoid development, culture protocols and Zika virus infection. SCOUT provides a much-needed framework for comparative analysis of emerging 3D in vitro models using fluorescence microscopy. 2021-10-27T20:30:51Z 2021-10-27T20:30:51Z 2020 2021-06-08T18:16:30Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/136109 en 10.1038/s41598-020-78130-7 Scientific Reports Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf Springer Science and Business Media LLC Scientific Reports |
| spellingShingle | Albanese, Alexandre Swaney, Justin M Yun, Dae Hee Evans, Nicholas B Antonucci, Jenna M Velasco, Silvia Sohn, Chang Ho Arlotta, Paola Gehrke, Lee Chung, Kwanghun Multiscale 3D phenotyping of human cerebral organoids |
| title | Multiscale 3D phenotyping of human cerebral organoids |
| title_full | Multiscale 3D phenotyping of human cerebral organoids |
| title_fullStr | Multiscale 3D phenotyping of human cerebral organoids |
| title_full_unstemmed | Multiscale 3D phenotyping of human cerebral organoids |
| title_short | Multiscale 3D phenotyping of human cerebral organoids |
| title_sort | multiscale 3d phenotyping of human cerebral organoids |
| url | https://hdl.handle.net/1721.1/136109 |
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