Small hand-designed convolutional neural networks outperform transfer learning in automated cell shape detection in confluent tissues
Mechanical cues such as stresses and strains are now recognized as essential regulators in many biological processes like cell division, gene expression or morphogenesis. Studying the interplay between these mechanical cues and biological responses requires experimental tools to measure these cues....
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2023-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9934364/?tool=EBI |
| _version_ | 1797903243655774208 |
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| author | Louis Combe Mélina Durande Hélène Delanoë-Ayari Olivier Cochet-Escartin |
| author_facet | Louis Combe Mélina Durande Hélène Delanoë-Ayari Olivier Cochet-Escartin |
| author_sort | Louis Combe |
| collection | DOAJ |
| description | Mechanical cues such as stresses and strains are now recognized as essential regulators in many biological processes like cell division, gene expression or morphogenesis. Studying the interplay between these mechanical cues and biological responses requires experimental tools to measure these cues. In the context of large scale tissues, this can be achieved by segmenting individual cells to extract their shapes and deformations which in turn inform on their mechanical environment. Historically, this has been done by segmentation methods which are well known to be time consuming and error prone. In this context however, one doesn’t necessarily require a cell-level description and a coarse-grained approach can be more efficient while using tools different from segmentation. The advent of machine learning and deep neural networks has revolutionized the field of image analysis in recent years, including in biomedical research. With the democratization of these techniques, more and more researchers are trying to apply them to their own biological systems. In this paper, we tackle a problem of cell shape measurement thanks to a large annotated dataset. We develop simple Convolutional Neural Networks (CNNs) which we thoroughly optimize in terms of architecture and complexity to question construction rules usually applied. We find that increasing the complexity of the networks rapidly no longer yields improvements in performance and that the number of kernels in each convolutional layer is the most important parameter to achieve good results. In addition, we compare our step-by-step approach with transfer learning and find that our simple, optimized CNNs give better predictions, are faster in training and analysis and don’t require more technical knowledge to be implemented. Overall, we offer a roadmap to develop optimized models and argue that we should limit the complexity of such models. We conclude by illustrating this strategy on a similar problem and dataset. |
| first_indexed | 2024-04-10T09:29:50Z |
| format | Article |
| id | doaj.art-5f0a946ee8f545c5a52237178859a536 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-10T09:29:50Z |
| publishDate | 2023-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-5f0a946ee8f545c5a52237178859a5362023-02-19T05:31:32ZengPublic Library of Science (PLoS)PLoS ONE1932-62032023-01-01182Small hand-designed convolutional neural networks outperform transfer learning in automated cell shape detection in confluent tissuesLouis CombeMélina DurandeHélène Delanoë-AyariOlivier Cochet-EscartinMechanical cues such as stresses and strains are now recognized as essential regulators in many biological processes like cell division, gene expression or morphogenesis. Studying the interplay between these mechanical cues and biological responses requires experimental tools to measure these cues. In the context of large scale tissues, this can be achieved by segmenting individual cells to extract their shapes and deformations which in turn inform on their mechanical environment. Historically, this has been done by segmentation methods which are well known to be time consuming and error prone. In this context however, one doesn’t necessarily require a cell-level description and a coarse-grained approach can be more efficient while using tools different from segmentation. The advent of machine learning and deep neural networks has revolutionized the field of image analysis in recent years, including in biomedical research. With the democratization of these techniques, more and more researchers are trying to apply them to their own biological systems. In this paper, we tackle a problem of cell shape measurement thanks to a large annotated dataset. We develop simple Convolutional Neural Networks (CNNs) which we thoroughly optimize in terms of architecture and complexity to question construction rules usually applied. We find that increasing the complexity of the networks rapidly no longer yields improvements in performance and that the number of kernels in each convolutional layer is the most important parameter to achieve good results. In addition, we compare our step-by-step approach with transfer learning and find that our simple, optimized CNNs give better predictions, are faster in training and analysis and don’t require more technical knowledge to be implemented. Overall, we offer a roadmap to develop optimized models and argue that we should limit the complexity of such models. We conclude by illustrating this strategy on a similar problem and dataset.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9934364/?tool=EBI |
| spellingShingle | Louis Combe Mélina Durande Hélène Delanoë-Ayari Olivier Cochet-Escartin Small hand-designed convolutional neural networks outperform transfer learning in automated cell shape detection in confluent tissues PLoS ONE |
| title | Small hand-designed convolutional neural networks outperform transfer learning in automated cell shape detection in confluent tissues |
| title_full | Small hand-designed convolutional neural networks outperform transfer learning in automated cell shape detection in confluent tissues |
| title_fullStr | Small hand-designed convolutional neural networks outperform transfer learning in automated cell shape detection in confluent tissues |
| title_full_unstemmed | Small hand-designed convolutional neural networks outperform transfer learning in automated cell shape detection in confluent tissues |
| title_short | Small hand-designed convolutional neural networks outperform transfer learning in automated cell shape detection in confluent tissues |
| title_sort | small hand designed convolutional neural networks outperform transfer learning in automated cell shape detection in confluent tissues |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9934364/?tool=EBI |
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