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Tokuoka Y, Yamada TG, Mashiko D, Ikeda Z, Hiroi NF, Kobayashi TJ, Yamagata K, Funahashi A. 3D convolutional neural networks-based segmentation to acquire quantitative criteria of the nucleus during mouse embryogenesis. NPJ Syst Biol Appl 2020; 6:32. [PMID: 33082352 PMCID: PMC7575569 DOI: 10.1038/s41540-020-00152-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 09/11/2020] [Indexed: 12/13/2022] Open
Abstract
During embryogenesis, cells repeatedly divide and dynamically change their positions in three-dimensional (3D) space. A robust and accurate algorithm to acquire the 3D positions of the cells would help to reveal the mechanisms of embryogenesis. To acquire quantitative criteria of embryogenesis from time-series 3D microscopic images, image processing algorithms such as segmentation have been applied. Because the cells in embryos are considerably crowded, an algorithm to segment individual cells in detail and accurately is needed. To quantify the nuclear region of every cell from a time-series 3D fluorescence microscopic image of living cells, we developed QCANet, a convolutional neural network-based segmentation algorithm for 3D fluorescence bioimages. We demonstrated that QCANet outperformed 3D Mask R-CNN, which is currently considered as the best algorithm of instance segmentation. We showed that QCANet can be applied not only to developing mouse embryos but also to developing embryos of two other model species. Using QCANet, we were able to extract several quantitative criteria of embryogenesis from 11 early mouse embryos. We showed that the extracted criteria could be used to evaluate the differences between individual embryos. This study contributes to the development of fundamental approaches for assessing embryogenesis on the basis of extracted quantitative criteria.
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Affiliation(s)
- Yuta Tokuoka
- Department of Biosciences and Informatics, Keio University, Kanagawa, 223-8522, Japan
| | - Takahiro G Yamada
- Department of Biosciences and Informatics, Keio University, Kanagawa, 223-8522, Japan
| | - Daisuke Mashiko
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, 649-6493, Japan
| | - Zenki Ikeda
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, 649-6493, Japan
| | - Noriko F Hiroi
- Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Yamaguchi, 756-0884, Japan
| | - Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan
| | - Kazuo Yamagata
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, 649-6493, Japan
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio University, Kanagawa, 223-8522, Japan.
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Toyoshima Y, Tokunaga T, Hirose O, Kanamori M, Teramoto T, Jang MS, Kuge S, Ishihara T, Yoshida R, Iino Y. Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space. PLoS Comput Biol 2016; 12:e1004970. [PMID: 27271939 PMCID: PMC4894571 DOI: 10.1371/journal.pcbi.1004970] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 05/03/2016] [Indexed: 11/18/2022] Open
Abstract
To measure the activity of neurons using whole-brain activity imaging, precise detection of each neuron or its nucleus is required. In the head region of the nematode C. elegans, the neuronal cell bodies are distributed densely in three-dimensional (3D) space. However, no existing computational methods of image analysis can separate them with sufficient accuracy. Here we propose a highly accurate segmentation method based on the curvatures of the iso-intensity surfaces. To obtain accurate positions of nuclei, we also developed a new procedure for least squares fitting with a Gaussian mixture model. Combining these methods enables accurate detection of densely distributed cell nuclei in a 3D space. The proposed method was implemented as a graphical user interface program that allows visualization and correction of the results of automatic detection. Additionally, the proposed method was applied to time-lapse 3D calcium imaging data, and most of the nuclei in the images were successfully tracked and measured.
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Affiliation(s)
- Yu Toyoshima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Terumasa Tokunaga
- Department of Systems Design and Informatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka-shi, Fukuoka, Japan
- The Institute of Statistical Mathematics, Research Organization of Information and Systems, Tachikawa, Tokyo, Japan
| | - Osamu Hirose
- Faculty of Electrical and Computer Engineering, Institute of Science and Engineering, Kanazawa University, Kakuma, Kanazawa, Japan
| | - Manami Kanamori
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takayuki Teramoto
- Department of Biology, Faculty of Sciences, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Moon Sun Jang
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Sayuri Kuge
- Department of Biology, Faculty of Sciences, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Takeshi Ishihara
- Department of Biology, Faculty of Sciences, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Ryo Yoshida
- The Institute of Statistical Mathematics, Research Organization of Information and Systems, Tachikawa, Tokyo, Japan
| | - Yuichi Iino
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- CREST, Japan Science and Technology Corporation, Bunkyo-ku, Tokyo, Japan
- * E-mail:
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Mathew B, Schmitz A, Muñoz-Descalzo S, Ansari N, Pampaloni F, Stelzer EHK, Fischer SC. Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition. BMC Bioinformatics 2015; 16:187. [PMID: 26049713 PMCID: PMC4458345 DOI: 10.1186/s12859-015-0617-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 05/18/2015] [Indexed: 12/02/2022] Open
Abstract
Background Due to the large amount of data produced by advanced microscopy, automated image analysis is crucial in modern biology. Most applications require reliable cell nuclei segmentation. However, in many biological specimens cell nuclei are densely packed and appear to touch one another in the images. Therefore, a major difficulty of three-dimensional cell nuclei segmentation is the decomposition of cell nuclei that apparently touch each other. Current methods are highly adapted to a certain biological specimen or a specific microscope. They do not ensure similarly accurate segmentation performance, i.e. their robustness for different datasets is not guaranteed. Hence, these methods require elaborate adjustments to each dataset. Results We present an advanced three-dimensional cell nuclei segmentation algorithm that is accurate and robust. Our approach combines local adaptive pre-processing with decomposition based on Lines-of-Sight (LoS) to separate apparently touching cell nuclei into approximately convex parts. We demonstrate the superior performance of our algorithm using data from different specimens recorded with different microscopes. The three-dimensional images were recorded with confocal and light sheet-based fluorescence microscopes. The specimens are an early mouse embryo and two different cellular spheroids. We compared the segmentation accuracy of our algorithm with ground truth data for the test images and results from state-of-the-art methods. The analysis shows that our method is accurate throughout all test datasets (mean F-measure: 91 %) whereas the other methods each failed for at least one dataset (F-measure ≤ 69 %). Furthermore, nuclei volume measurements are improved for LoS decomposition. The state-of-the-art methods required laborious adjustments of parameter values to achieve these results. Our LoS algorithm did not require parameter value adjustments. The accurate performance was achieved with one fixed set of parameter values. Conclusion We developed a novel and fully automated three-dimensional cell nuclei segmentation method incorporating LoS decomposition. LoS are easily accessible features that ensure correct splitting of apparently touching cell nuclei independent of their shape, size or intensity. Our method showed superior performance compared to state-of-the-art methods, performing accurately for a variety of test images. Hence, our LoS approach can be readily applied to quantitative evaluation in drug testing, developmental and cell biology. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0617-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- B Mathew
- Buchmann Institute for Molecular Life Sciences (BMLS), Fachbereich Biowissenschaften (FB15, IZN), Goethe Universität Frankfurt am Main, Max-von-Laue-Straße 15, 60438, Frankfurt am Main, Germany.
| | - A Schmitz
- Buchmann Institute for Molecular Life Sciences (BMLS), Fachbereich Biowissenschaften (FB15, IZN), Goethe Universität Frankfurt am Main, Max-von-Laue-Straße 15, 60438, Frankfurt am Main, Germany.
| | - S Muñoz-Descalzo
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.
| | - N Ansari
- Buchmann Institute for Molecular Life Sciences (BMLS), Fachbereich Biowissenschaften (FB15, IZN), Goethe Universität Frankfurt am Main, Max-von-Laue-Straße 15, 60438, Frankfurt am Main, Germany.
| | - F Pampaloni
- Buchmann Institute for Molecular Life Sciences (BMLS), Fachbereich Biowissenschaften (FB15, IZN), Goethe Universität Frankfurt am Main, Max-von-Laue-Straße 15, 60438, Frankfurt am Main, Germany.
| | - E H K Stelzer
- Buchmann Institute for Molecular Life Sciences (BMLS), Fachbereich Biowissenschaften (FB15, IZN), Goethe Universität Frankfurt am Main, Max-von-Laue-Straße 15, 60438, Frankfurt am Main, Germany.
| | - S C Fischer
- Buchmann Institute for Molecular Life Sciences (BMLS), Fachbereich Biowissenschaften (FB15, IZN), Goethe Universität Frankfurt am Main, Max-von-Laue-Straße 15, 60438, Frankfurt am Main, Germany.
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