The Spheroid Light Microscopy Image Atlas for morphometrical analysis of three-dimensional cell cultures
Abstract The application of three-dimensional (3D) cell cultures such as spheroids and organoids is growing in popularity both in academia and industry. However, morphology of the 3D architecture remains remarkably understudied. Here, we introduce an open-access Spheroid Light Microscopy Image Atlas...
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Nature Portfolio
2025-02-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-04441-x |
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| author | Eva Blondeel Arne Peirsman Stephanie Vermeulen Filippo Piccinini Felix De Vuyst Diogo Estêvão Sayida Al-Jamei Martina Bedeschi Gastone Castellani Tânia Cruz Sándor Dedeyne Maria José Oliveira Satoru Kawakita Huu Tuan Nguyen Leoni A. Kunz-Schughart Soojung Lee Noemi Marino Patrick Steigemann Shuichi Takayama Anna Tesei Nina Zablowsky Phillip Blondeel Olivier De Wever |
| author_facet | Eva Blondeel Arne Peirsman Stephanie Vermeulen Filippo Piccinini Felix De Vuyst Diogo Estêvão Sayida Al-Jamei Martina Bedeschi Gastone Castellani Tânia Cruz Sándor Dedeyne Maria José Oliveira Satoru Kawakita Huu Tuan Nguyen Leoni A. Kunz-Schughart Soojung Lee Noemi Marino Patrick Steigemann Shuichi Takayama Anna Tesei Nina Zablowsky Phillip Blondeel Olivier De Wever |
| author_sort | Eva Blondeel |
| collection | DOAJ |
| description | Abstract The application of three-dimensional (3D) cell cultures such as spheroids and organoids is growing in popularity both in academia and industry. However, morphology of the 3D architecture remains remarkably understudied. Here, we introduce an open-access Spheroid Light Microscopy Image Atlas (SLiMIA) that can serve as a training set for morphology studies of 3D cell cultures. We provide images with a variety of metadata: 9 microscopes, 47 cell lines, 8 culture media, 4 spheroid formation methods and multiple cell seeding densities; totalling approximately 8,000 images of spheroids. This comprehensive dataset can guide spheroid researchers and promote economizing of resources by advancing 3D cell culture optimization, standardization and implementation by the community at large. Considering the exponentially growing interest in spheroid morphometrical analyses and the emerging technological possibilities to do so, this atlas can be applied to train and develop image segmentation models to deepen our understanding of 3D spheroid morphometry in biomedical research. |
| format | Article |
| id | doaj-art-b50b996866754224b62c45cf9f2ae2a1 |
| institution | DOAJ |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-b50b996866754224b62c45cf9f2ae2a12025-08-20T03:13:11ZengNature PortfolioScientific Data2052-44632025-02-0112111210.1038/s41597-025-04441-xThe Spheroid Light Microscopy Image Atlas for morphometrical analysis of three-dimensional cell culturesEva Blondeel0Arne Peirsman1Stephanie Vermeulen2Filippo Piccinini3Felix De Vuyst4Diogo Estêvão5Sayida Al-Jamei6Martina Bedeschi7Gastone Castellani8Tânia Cruz9Sándor Dedeyne10Maria José Oliveira11Satoru Kawakita12Huu Tuan Nguyen13Leoni A. Kunz-Schughart14Soojung Lee15Noemi Marino16Patrick Steigemann17Shuichi Takayama18Anna Tesei19Nina Zablowsky20Phillip Blondeel21Olivier De Wever22Laboratory of Experimental Cancer Research (LECR), Ghent UniversityLaboratory of Experimental Cancer Research (LECR), Ghent UniversityLaboratory of Experimental Cancer Research (LECR), Ghent UniversityIRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”Laboratory of Experimental Cancer Research (LECR), Ghent UniversityTumour and Microenvironment Interactions group, i3S – Institute for Research & Innovation in Health, Porto UnSiversityOncoRay – National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden and Helmholtz- Zentrum Dresden–RossendorfIRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of BolognaTumour and Microenvironment Interactions group, i3S – Institute for Research & Innovation in Health, Porto UnSiversityLaboratory of Experimental Cancer Research (LECR), Ghent UniversityTumour and Microenvironment Interactions group, i3S – Institute for Research & Innovation in Health, Porto UnSiversityTerasaki Institute for Biomedical Innovation, Los AngelesTerasaki Institute for Biomedical Innovation, Los AngelesOncoRay – National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden and Helmholtz- Zentrum Dresden–RossendorfWallace H. Coulter Department of Biomedical Engineering and Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of TechnologyIRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”Lead Discovery, Nuvisan ICB GmbH, Muellerstr. 178Wallace H. Coulter Department of Biomedical Engineering and Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of TechnologyIRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”Lead Discovery, Nuvisan ICB GmbH, Muellerstr. 178Plastic, Reconstructive and Aesthetic Surgery University Hospital GhentLaboratory of Experimental Cancer Research (LECR), Ghent UniversityAbstract The application of three-dimensional (3D) cell cultures such as spheroids and organoids is growing in popularity both in academia and industry. However, morphology of the 3D architecture remains remarkably understudied. Here, we introduce an open-access Spheroid Light Microscopy Image Atlas (SLiMIA) that can serve as a training set for morphology studies of 3D cell cultures. We provide images with a variety of metadata: 9 microscopes, 47 cell lines, 8 culture media, 4 spheroid formation methods and multiple cell seeding densities; totalling approximately 8,000 images of spheroids. This comprehensive dataset can guide spheroid researchers and promote economizing of resources by advancing 3D cell culture optimization, standardization and implementation by the community at large. Considering the exponentially growing interest in spheroid morphometrical analyses and the emerging technological possibilities to do so, this atlas can be applied to train and develop image segmentation models to deepen our understanding of 3D spheroid morphometry in biomedical research.https://doi.org/10.1038/s41597-025-04441-x |
| spellingShingle | Eva Blondeel Arne Peirsman Stephanie Vermeulen Filippo Piccinini Felix De Vuyst Diogo Estêvão Sayida Al-Jamei Martina Bedeschi Gastone Castellani Tânia Cruz Sándor Dedeyne Maria José Oliveira Satoru Kawakita Huu Tuan Nguyen Leoni A. Kunz-Schughart Soojung Lee Noemi Marino Patrick Steigemann Shuichi Takayama Anna Tesei Nina Zablowsky Phillip Blondeel Olivier De Wever The Spheroid Light Microscopy Image Atlas for morphometrical analysis of three-dimensional cell cultures Scientific Data |
| title | The Spheroid Light Microscopy Image Atlas for morphometrical analysis of three-dimensional cell cultures |
| title_full | The Spheroid Light Microscopy Image Atlas for morphometrical analysis of three-dimensional cell cultures |
| title_fullStr | The Spheroid Light Microscopy Image Atlas for morphometrical analysis of three-dimensional cell cultures |
| title_full_unstemmed | The Spheroid Light Microscopy Image Atlas for morphometrical analysis of three-dimensional cell cultures |
| title_short | The Spheroid Light Microscopy Image Atlas for morphometrical analysis of three-dimensional cell cultures |
| title_sort | spheroid light microscopy image atlas for morphometrical analysis of three dimensional cell cultures |
| url | https://doi.org/10.1038/s41597-025-04441-x |
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