1
|
Guan G, Li Z, Ma Y, Ye P, Cao J, Wong MK, Ho VWS, Chan LY, Yan H, Tang C, Zhao Z. Cell lineage-resolved embryonic morphological map reveals signaling associated with cell fate and size asymmetry. Nat Commun 2025; 16:3700. [PMID: 40251161 PMCID: PMC12008310 DOI: 10.1038/s41467-025-58878-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Accepted: 04/04/2025] [Indexed: 04/20/2025] Open
Abstract
How cells change shape is crucial for the development of tissues, organs and embryos. However, studying these shape changes in detail is challenging. Here we present a comprehensive real-time cellular map that covers over 95% of the cells formed during Caenorhabditis elegans embryogenesis, featuring nearly 400,000 3D cell regions. This map includes information on each cell's identity, lineage, fate, shape, volume, surface area, contact area, and gene expression profiles, all accessible through our user-friendly software and website. Our map allows for detailed analysis of key developmental processes, including dorsal intercalation, intestinal formation, and muscle assembly. We show how Notch and Wnt signaling pathways, along with mechanical forces from cell interactions, regulate cell fate decisions and size asymmetries. Our findings suggest that repeated Notch signaling drives size disparities in the large excretory cell, which functions like a kidney. This work sets the stage for in-depth studies of the mechanisms controlling cell fate differentiation and morphogenesis.
Collapse
Affiliation(s)
- Guoye Guan
- Center for Quantitative Biology, Peking University, Beijing, China
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zelin Li
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong SAR, China
- Centre for Intelligent Multidimensional Data Analysis, Hong Kong Science Park, Hong Kong SAR, China
| | - Yiming Ma
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Pohao Ye
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Jianfeng Cao
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong SAR, China
- Centre for Intelligent Multidimensional Data Analysis, Hong Kong Science Park, Hong Kong SAR, China
- School of Biomedical Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen, China
| | - Ming-Kin Wong
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Vincy Wing Sze Ho
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
- Department of Surgery, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lu-Yan Chan
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
- Department of Surgery, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hong Yan
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong SAR, China.
- Centre for Intelligent Multidimensional Data Analysis, Hong Kong Science Park, Hong Kong SAR, China.
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- School of Physics, Peking University, Beijing, China.
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China.
| |
Collapse
|
2
|
Zhou FY, Marin Z, Yapp C, Zou Q, Nanes BA, Daetwyler S, Jamieson AR, Islam MT, Jenkins E, Gihana GM, Lin J, Borges HM, Chang BJ, Weems A, Morrison SJ, Sorger PK, Fiolka R, Dean KM, Danuser G. Universal consensus 3D segmentation of cells from 2D segmented stacks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.05.03.592249. [PMID: 38766074 PMCID: PMC11100681 DOI: 10.1101/2024.05.03.592249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Cell segmentation is the foundation of a wide range of microscopy-based biological studies. Deep learning has revolutionized 2D cell segmentation, enabling generalized solutions across cell types and imaging modalities. This has been driven by the ease of scaling up image acquisition, annotation, and computation. However, 3D cell segmentation, requiring dense annotation of 2D slices still poses significant challenges. Manual labeling of 3D cells to train broadly applicable segmentation models is prohibitive. Even in high-contrast images annotation is ambiguous and time-consuming. Here we develop a theory and toolbox, u-Segment3D, for 2D-to-3D segmentation, compatible with any 2D method generating pixel-based instance cell masks. u-Segment3D translates and enhances 2D instance segmentations to a 3D consensus instance segmentation without training data, as demonstrated on 11 real-life datasets, >70,000 cells, spanning single cells, cell aggregates, and tissue. Moreover, u-Segment3D is competitive with native 3D segmentation, even exceeding when cells are crowded and have complex morphologies.
Collapse
Affiliation(s)
- Felix Y. Zhou
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zach Marin
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Max Perutz Labs, Department of Structural and Computational Biology, University of Vienna, Vienna, Austria
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, 02115, USA
| | - Qiongjing Zou
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Benjamin A. Nanes
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Dermatology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Stephan Daetwyler
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andrew R. Jamieson
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Md Torikul Islam
- Children’s Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Edward Jenkins
- Kennedy Institute of Rheumatology, University of Oxford, OX3 7FY UK
| | - Gabriel M. Gihana
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jinlong Lin
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hazel M. Borges
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bo-Jui Chang
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andrew Weems
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sean J. Morrison
- Children’s Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Peter K. Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Reto Fiolka
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kevin M. Dean
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| |
Collapse
|
3
|
Israel U, Marks M, Dilip R, Li Q, Yu C, Laubscher E, Iqbal A, Pradhan E, Ates A, Abt M, Brown C, Pao E, Li S, Pearson-Goulart A, Perona P, Gkioxari G, Barnowski R, Yue Y, Van Valen D. CellSAM: A Foundation Model for Cell Segmentation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2023.11.17.567630. [PMID: 38045277 PMCID: PMC10690226 DOI: 10.1101/2023.11.17.567630] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Cells are a fundamental unit of biological organization, and identifying them in imaging data - cell segmentation - is a critical task for various cellular imaging experiments. While deep learning methods have led to substantial progress on this problem, most models are specialist models that work well for specific domains but cannot be applied across domains or scale well with large amounts of data. In this work, we present CellSAM, a universal model for cell segmentation that generalizes across diverse cellular imaging data. CellSAM builds on top of the Segment Anything Model (SAM) by developing a prompt engineering approach for mask generation. We train an object detector, CellFinder, to automatically detect cells and prompt SAM to generate segmentations. We show that this approach allows a single model to achieve human-level performance for segmenting images of mammalian cells, yeast, and bacteria collected across various imaging modalities. We show that CellSAM has strong zero-shot performance and can be improved with a few examples via few-shot learning. Additionally, we demonstrate how CellSAM can be applied across diverse bioimage analysis workflows. A deployed version of CellSAM is available at https://cellsam.deepcell.org/.
Collapse
Affiliation(s)
- Uriah Israel
- Division of Biology and Biological Engineering, Caltech
- Division of Computing and Mathematical Science, Caltech
| | - Markus Marks
- Division of Engineering and Applied Science, Caltech
- Division of Computing and Mathematical Science, Caltech
| | - Rohit Dilip
- Division of Computing and Mathematical Science, Caltech
| | - Qilin Li
- Division of Engineering and Applied Science, Caltech
| | - Changhua Yu
- Division of Biology and Biological Engineering, Caltech
| | | | - Ahamed Iqbal
- Division of Biology and Biological Engineering, Caltech
| | - Elora Pradhan
- Division of Biology and Biological Engineering, Caltech
| | - Ada Ates
- Division of Biology and Biological Engineering, Caltech
| | - Martin Abt
- Division of Biology and Biological Engineering, Caltech
| | - Caitlin Brown
- Division of Biology and Biological Engineering, Caltech
| | - Edward Pao
- Division of Biology and Biological Engineering, Caltech
| | - Shenyi Li
- Division of Biology and Biological Engineering, Caltech
| | | | - Pietro Perona
- Division of Engineering and Applied Science, Caltech
- Division of Computing and Mathematical Science, Caltech
| | | | | | - Yisong Yue
- Division of Computing and Mathematical Science, Caltech
| | - David Van Valen
- Division of Biology and Biological Engineering, Caltech
- Howard Hughes Medical Institute
| |
Collapse
|
4
|
Guo M, Wu Y, Hobson CM, Su Y, Qian S, Krueger E, Christensen R, Kroeschell G, Bui J, Chaw M, Zhang L, Liu J, Hou X, Han X, Lu Z, Ma X, Zhovmer A, Combs C, Moyle M, Yemini E, Liu H, Liu Z, Benedetto A, La Riviere P, Colón-Ramos D, Shroff H. Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy. Nat Commun 2025; 16:313. [PMID: 39747824 PMCID: PMC11697233 DOI: 10.1038/s41467-024-55267-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Accepted: 12/06/2024] [Indexed: 01/04/2025] Open
Abstract
Optical aberrations hinder fluorescence microscopy of thick samples, reducing image signal, contrast, and resolution. Here we introduce a deep learning-based strategy for aberration compensation, improving image quality without slowing image acquisition, applying additional dose, or introducing more optics. Our method (i) introduces synthetic aberrations to images acquired on the shallow side of image stacks, making them resemble those acquired deeper into the volume and (ii) trains neural networks to reverse the effect of these aberrations. We use simulations and experiments to show that applying the trained 'de-aberration' networks outperforms alternative methods, providing restoration on par with adaptive optics techniques; and subsequently apply the networks to diverse datasets captured with confocal, light-sheet, multi-photon, and super-resolution microscopy. In all cases, the improved quality of the restored data facilitates qualitative image inspection and improves downstream image quantitation, including orientational analysis of blood vessels in mouse tissue and improved membrane and nuclear segmentation in C. elegans embryos.
Collapse
Affiliation(s)
- Min Guo
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China.
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA.
| | - Yicong Wu
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
- Nanodelivery Systems and Devices Branch, Cancer Imaging Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Chad M Hobson
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Shuhao Qian
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Eric Krueger
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Ryan Christensen
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Grant Kroeschell
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Johnny Bui
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Matthew Chaw
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Lixia Zhang
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Jiamin Liu
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Xuekai Hou
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Xiaofei Han
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Zhiye Lu
- Laboratory of Molecular Cardiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xuefei Ma
- Laboratory of Molecular Cardiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alexander Zhovmer
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Christian Combs
- NHLBI Light Microscopy Facility, National Institutes of Health, Bethesda, MD, USA
| | - Mark Moyle
- Department of Biology, Brigham Young University-Idaho, Rexburg, ID, USA
| | - Eviatar Yemini
- Department of Neurobiology, UMass Chan Medical School, Worcester, MA, USA
| | - Huafeng Liu
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Zhiyi Liu
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Alexandre Benedetto
- Faculty of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster, UK
| | - Patrick La Riviere
- Department of Radiology, University of Chicago, Chicago, IL, USA
- MBL Fellows Program, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Daniel Colón-Ramos
- MBL Fellows Program, Marine Biological Laboratory, Woods Hole, MA, USA
- Wu Tsai Institute, Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
- MBL Fellows Program, Marine Biological Laboratory, Woods Hole, MA, USA
| |
Collapse
|
5
|
James E, Caetano A, Sharpe P. Computational Methods for Image Analysis in Craniofacial Development and Disease. J Dent Res 2024; 103:1340-1348. [PMID: 39272216 PMCID: PMC11633063 DOI: 10.1177/00220345241265048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2024] Open
Abstract
Observation is at the center of all biological sciences. Advances in imaging technologies are therefore essential to derive novel biological insights to better understand the complex workings of living systems. Recent high-throughput sequencing and imaging techniques are allowing researchers to simultaneously address complex molecular variations spatially and temporarily in tissues and organs. The availability of increasingly large dataset sizes has allowed for the evolution of robust deep learning models, designed to interrogate biomedical imaging data. These models are emerging as transformative tools in diagnostic medicine. Combined, these advances allow for dynamic, quantitative, and predictive observations of entire organisms and tissues. Here, we address 3 main tasks of bioimage analysis, image restoration, segmentation, and tracking and discuss new computational tools allowing for 3-dimensional spatial genomics maps. Finally, we demonstrate how these advances have been applied in studies of craniofacial development and oral disease pathogenesis.
Collapse
Affiliation(s)
- E. James
- Centre for Oral Immunobiology and Regenerative Medicine, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - A.J. Caetano
- Centre for Oral Immunobiology and Regenerative Medicine, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - P.T. Sharpe
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London, UK
| |
Collapse
|
6
|
Waliman M, Johnson RL, Natesan G, Peinado NA, Tan S, Santella A, Hong RL, Shah PK. Automated cell lineage reconstruction using label-free 4D microscopy. Genetics 2024; 228:iyae135. [PMID: 39139100 PMCID: PMC11457935 DOI: 10.1093/genetics/iyae135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/08/2024] [Accepted: 07/17/2024] [Indexed: 08/15/2024] Open
Abstract
Patterns of lineal descent play a critical role in the development of metazoan embryos. In eutelic organisms that generate a fixed number of somatic cells, invariance in the topology of their cell lineage provides a powerful opportunity to interrogate developmental events with empirical repeatability across individuals. Studies of embryonic development using the nematode Caenorhabditis elegans have been drivers of discovery. These studies have depended heavily on high-throughput lineage tracing enabled by 4D fluorescence microscopy and robust computer vision pipelines. For a range of applications, computer-aided yet manual lineage tracing using 4D label-free microscopy remains an essential tool. Deep learning approaches to cell detection and tracking in fluorescence microscopy have advanced significantly in recent years, yet solutions for automating cell detection and tracking in 3D label-free imaging of dense tissues and embryos remain inaccessible. Here, we describe embGAN, a deep learning pipeline that addresses the challenge of automated cell detection and tracking in label-free 3D time-lapse imaging. embGAN requires no manual data annotation for training, learns robust detections that exhibits a high degree of scale invariance, and generalizes well to images acquired in multiple labs on multiple instruments. We characterize embGAN's performance using lineage tracing in the C. elegans embryo as a benchmark. embGAN achieves near-state-of-the-art performance in cell detection and tracking, enabling high-throughput studies of cell lineage without the need for fluorescent reporters or transgenics.
Collapse
Affiliation(s)
- Matthew Waliman
- Department of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ryan L Johnson
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gunalan Natesan
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Neil A Peinado
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shiqin Tan
- Department of Computational and Systems Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anthony Santella
- Molecular Cytology Core, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ray L Hong
- Department of Biology, California State University, Northridge, Northridge, CA 91325, USA
| | - Pavak K Shah
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
7
|
Beckett LJ, Williams PM, Toh LS, Hessel V, Gerstweiler L, Fisk I, Toronjo-Urquiza L, Chauhan VM. Advancing insights into microgravity induced muscle changes using Caenorhabditis elegans as a model organism. NPJ Microgravity 2024; 10:79. [PMID: 39060303 PMCID: PMC11282318 DOI: 10.1038/s41526-024-00418-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Spaceflight presents significant challenges to the physiological state of living organisms. This can be due to the microgravity environment experienced during long-term space missions, resulting in alterations in muscle structure and function, such as atrophy. However, a comprehensive understanding of the adaptive mechanisms of biological systems is required to devise potential solutions and therapeutic approaches for adapting to spaceflight conditions. This review examines the current understanding of the challenges posed by spaceflight on physiological changes, alterations in metabolism, dysregulation of pathways and the suitability and advantages of using the model organism Caenorhabditis elegans nematodes to study the effects of spaceflight. Research has shown that changes in the gene and protein composition of nematodes significantly occur across various larval stages and rearing environments, including both microgravity and Earth gravity settings, often mirroring changes observed in astronauts. Additionally, the review explores significant insights into the fundamental metabolic changes associated with muscle atrophy and growth, which could lead to the development of diagnostic biomarkers and innovative techniques to prevent and counteract muscle atrophy. These insights not only advance our understanding of microgravity-induced muscle atrophy but also lay the groundwork for the development of targeted interventions to mitigate its effects in the future.
Collapse
Affiliation(s)
- Laura J Beckett
- School of Pharmacy, University of Nottingham, Nottingham, UK
- School of Chemical Engineering, North Terrace Campus, The University of Adelaide, Adelaide, SA, Australia
| | | | - Li Shean Toh
- School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Volker Hessel
- School of Chemical Engineering, North Terrace Campus, The University of Adelaide, Adelaide, SA, Australia
| | - Lukas Gerstweiler
- School of Chemical Engineering, North Terrace Campus, The University of Adelaide, Adelaide, SA, Australia
| | - Ian Fisk
- International Flavour Research Centre, Division of Food, Nutrition and Dietetics, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
- International Flavour Research Centre (Adelaide), School of Agriculture, Food and Wine and Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Luis Toronjo-Urquiza
- School of Chemical Engineering, North Terrace Campus, The University of Adelaide, Adelaide, SA, Australia
| | | |
Collapse
|
8
|
Guo M, Wu Y, Hobson CM, Su Y, Qian S, Krueger E, Christensen R, Kroeschell G, Bui J, Chaw M, Zhang L, Liu J, Hou X, Han X, Lu Z, Ma X, Zhovmer A, Combs C, Moyle M, Yemini E, Liu H, Liu Z, Benedetto A, La Riviere P, Colón-Ramos D, Shroff H. Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.15.562439. [PMID: 37986950 PMCID: PMC10659418 DOI: 10.1101/2023.10.15.562439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Optical aberrations hinder fluorescence microscopy of thick samples, reducing image signal, contrast, and resolution. Here we introduce a deep learning-based strategy for aberration compensation, improving image quality without slowing image acquisition, applying additional dose, or introducing more optics into the imaging path. Our method (i) introduces synthetic aberrations to images acquired on the shallow side of image stacks, making them resemble those acquired deeper into the volume and (ii) trains neural networks to reverse the effect of these aberrations. We use simulations and experiments to show that applying the trained 'de-aberration' networks outperforms alternative methods, providing restoration on par with adaptive optics techniques; and subsequently apply the networks to diverse datasets captured with confocal, light-sheet, multi-photon, and super-resolution microscopy. In all cases, the improved quality of the restored data facilitates qualitative image inspection and improves downstream image quantitation, including orientational analysis of blood vessels in mouse tissue and improved membrane and nuclear segmentation in C. elegans embryos.
Collapse
|
9
|
Guan G, Chen Y, Wang H, Ouyang Q, Tang C. Characterizing Cellular Physiological States with Three-Dimensional Shape Descriptors for Cell Membranes. MEMBRANES 2024; 14:137. [PMID: 38921504 PMCID: PMC11205511 DOI: 10.3390/membranes14060137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024]
Abstract
The shape of a cell as defined by its membrane can be closely associated with its physiological state. For example, the irregular shapes of cancerous cells and elongated shapes of neuron cells often reflect specific functions, such as cell motility and cell communication. However, it remains unclear whether and which cell shape descriptors can characterize different cellular physiological states. In this study, 12 geometric shape descriptors for a three-dimensional (3D) object were collected from the previous literature and tested with a public dataset of ~400,000 independent 3D cell regions segmented based on fluorescent labeling of the cell membranes in Caenorhabditis elegans embryos. It is revealed that those shape descriptors can faithfully characterize cellular physiological states, including (1) cell division (cytokinesis), along with an abrupt increase in the elongation ratio; (2) a negative correlation of cell migration speed with cell sphericity; (3) cell lineage specification with symmetrically patterned cell shape changes; and (4) cell fate specification with differential gene expression and differential cell shapes. The descriptors established may be used to identify and predict the diverse physiological states in numerous cells, which could be used for not only studying developmental morphogenesis but also diagnosing human disease (e.g., the rapid detection of abnormal cells).
Collapse
Affiliation(s)
- Guoye Guan
- Center for Quantitative Biology, Peking University, Beijing 100871, China; (G.G.); (Q.O.)
| | - Yixuan Chen
- School of Physics, Peking University, Beijing 100871, China;
| | - Hongli Wang
- Center for Quantitative Biology, Peking University, Beijing 100871, China; (G.G.); (Q.O.)
- School of Physics, Peking University, Beijing 100871, China;
| | - Qi Ouyang
- Center for Quantitative Biology, Peking University, Beijing 100871, China; (G.G.); (Q.O.)
- School of Physics, Peking University, Beijing 100871, China;
- School of Physics, Zhejiang University, Hangzhou 310027, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing 100871, China; (G.G.); (Q.O.)
- School of Physics, Peking University, Beijing 100871, China;
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
10
|
Zhang L, Xue G, Zhou X, Huang J, Li Z. A mathematical framework for understanding the spontaneous emergence of complexity applicable to growing multicellular systems. PLoS Comput Biol 2024; 20:e1011882. [PMID: 38838038 PMCID: PMC11182560 DOI: 10.1371/journal.pcbi.1011882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/17/2024] [Accepted: 05/20/2024] [Indexed: 06/07/2024] Open
Abstract
In embryonic development and organogenesis, cells sharing identical genetic codes acquire diverse gene expression states in a highly reproducible spatial distribution, crucial for multicellular formation and quantifiable through positional information. To understand the spontaneous growth of complexity, we constructed a one-dimensional division-decision model, simulating the growth of cells with identical genetic networks from a single cell. Our findings highlight the pivotal role of cell division in providing positional cues, escorting the system toward states rich in information. Moreover, we pinpointed lateral inhibition as a critical mechanism translating spatial contacts into gene expression. Our model demonstrates that the spatial arrangement resulting from cell division, combined with cell lineages, imparts positional information, specifying multiple cell states with increased complexity-illustrated through examples in C.elegans. This study constitutes a foundational step in comprehending developmental intricacies, paving the way for future quantitative formulations to construct synthetic multicellular patterns.
Collapse
Affiliation(s)
- Lu Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gang Xue
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiaolin Zhou
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Jiandong Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhiyuan Li
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| |
Collapse
|
11
|
Waliman M, Johnson RL, Natesan G, Tan S, Santella A, Hong RL, Shah PK. Automated Cell Lineage Reconstruction using Label-Free 4D Microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576449. [PMID: 38328064 PMCID: PMC10849476 DOI: 10.1101/2024.01.20.576449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Here we describe embGAN, a deep learning pipeline that addresses the challenge of automated cell detection and tracking in label-free 3D time lapse imaging. embGAN requires no manual data annotation for training, learns robust detections that exhibits a high degree of scale invariance and generalizes well to images acquired in multiple labs on multiple instruments.
Collapse
Affiliation(s)
- Matthew Waliman
- Department of Electrical and Computer Engineering, University of California, Los Angeles, California, United States of America
| | - Ryan L Johnson
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United State of America
| | - Gunalan Natesan
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United State of America
| | - Shiqin Tan
- Department of Computational and Systems Biology, University of California, Los Angeles, California, United States of America
| | - Anthony Santella
- Molecular Cytology Core, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Ray L Hong
- Department of Biology, California State University, Northridge, California, United States of America
| | - Pavak K Shah
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United State of America
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
| |
Collapse
|
12
|
Natesan G, Hamilton T, Deeds EJ, Shah PK. Novel metrics reveal new structure and unappreciated heterogeneity in Caenorhabditis elegans development. PLoS Comput Biol 2023; 19:e1011733. [PMID: 38113280 PMCID: PMC10763962 DOI: 10.1371/journal.pcbi.1011733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 01/03/2024] [Accepted: 12/04/2023] [Indexed: 12/21/2023] Open
Abstract
High throughput experimental approaches are increasingly allowing for the quantitative description of cellular and organismal phenotypes. Distilling these large volumes of complex data into meaningful measures that can drive biological insight remains a central challenge. In the quantitative study of development, for instance, one can resolve phenotypic measures for single cells onto their lineage history, enabling joint consideration of heritable signals and cell fate decisions. Most attempts to analyze this type of data, however, discard much of the information content contained within lineage trees. In this work we introduce a generalized metric, which we term the branch edit distance, that allows us to compare any two embryos based on phenotypic measurements in individual cells. This approach aligns those phenotypic measurements to the underlying lineage tree, providing a flexible and intuitive framework for quantitative comparisons between, for instance, Wild-Type (WT) and mutant developmental programs. We apply this novel metric to data on cell-cycle timing from over 1300 WT and RNAi-treated Caenorhabditis elegans embryos. Our new metric revealed surprising heterogeneity within this data set, including subtle batch effects in WT embryos and dramatic variability in RNAi-induced developmental phenotypes, all of which had been missed in previous analyses. Further investigation of these results suggests a novel, quantitative link between pathways that govern cell fate decisions and pathways that pattern cell cycle timing in the early embryo. Our work demonstrates that the branch edit distance we propose, and similar metrics like it, have the potential to revolutionize our quantitative understanding of organismal phenotype.
Collapse
Affiliation(s)
- Gunalan Natesan
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States of America
| | - Timothy Hamilton
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California, United States of America
| | - Eric J. Deeds
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California, United States of America
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
| | - Pavak K. Shah
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States of America
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
| |
Collapse
|
13
|
Ichbiah S, Delbary F, McDougall A, Dumollard R, Turlier H. Embryo mechanics cartography: inference of 3D force atlases from fluorescence microscopy. Nat Methods 2023; 20:1989-1999. [PMID: 38057527 PMCID: PMC10703677 DOI: 10.1038/s41592-023-02084-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/12/2023] [Indexed: 12/08/2023]
Abstract
Tissue morphogenesis results from a tight interplay between gene expression, biochemical signaling and mechanics. Although sequencing methods allow the generation of cell-resolved spatiotemporal maps of gene expression, creating similar maps of cell mechanics in three-dimensional (3D) developing tissues has remained a real challenge. Exploiting the foam-like arrangement of cells, we propose a robust end-to-end computational method called 'foambryo' to infer spatiotemporal atlases of cellular forces from fluorescence microscopy images of cell membranes. Our method generates precise 3D meshes of cells' geometry and successively predicts relative cell surface tensions and pressures. We validate it with 3D foam simulations, study its noise sensitivity and prove its biological relevance in mouse, ascidian and worm embryos. 3D force inference allows us to recover mechanical features identified previously, but also predicts new ones, unveiling potential new insights on the spatiotemporal regulation of cell mechanics in developing embryos. Our code is freely available and paves the way for unraveling the unknown mechanochemical feedbacks that control embryo and tissue morphogenesis.
Collapse
Affiliation(s)
- Sacha Ichbiah
- Center for Interdisciplinary Research in Biology, College of France, CNRS, INSERM, University of PSL, Paris, France
| | - Fabrice Delbary
- Center for Interdisciplinary Research in Biology, College of France, CNRS, INSERM, University of PSL, Paris, France
| | - Alex McDougall
- Laboratory of Developmental Biology of the Villefranche-sur-Mer, Institute of Villefranche-sur-Mer, Sorbonne University, CNRS, Villefranche-sur-Mer, France
| | - Rémi Dumollard
- Laboratory of Developmental Biology of the Villefranche-sur-Mer, Institute of Villefranche-sur-Mer, Sorbonne University, CNRS, Villefranche-sur-Mer, France
| | - Hervé Turlier
- Center for Interdisciplinary Research in Biology, College of France, CNRS, INSERM, University of PSL, Paris, France.
| |
Collapse
|
14
|
Naturale VF, Pickett MA, Feldman JL. Persistent cell contacts enable E-cadherin/HMR-1- and PAR-3-based symmetry breaking within a developing C. elegans epithelium. Dev Cell 2023; 58:1830-1846.e12. [PMID: 37552986 PMCID: PMC10592304 DOI: 10.1016/j.devcel.2023.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 05/10/2023] [Accepted: 07/17/2023] [Indexed: 08/10/2023]
Abstract
Tissue-wide patterning is essential to multicellular development, requiring cells to individually generate polarity axes and coordinate them in space and time with neighbors. Using the C. elegans intestinal epithelium, we identified a patterning mechanism that is informed by cell contact lifetime asymmetry and executed via the scaffolding protein PAR-3 and the transmembrane protein E-cadherin/HMR-1. Intestinal cells break symmetry as PAR-3 and HMR-1 recruit apical determinants into punctate "local polarity complexes" (LPCs) at homotypic contacts. LPCs undergo an HMR-1-based migration to a common midline, thereby establishing tissue-wide polarity. Thus, symmetry breaking results from PAR-3-dependent intracellular polarization coupled to HMR-1-based tissue-level communication, which occurs through a non-adhesive signaling role for HMR-1. Differential lifetimes between homotypic and heterotypic cell contacts are created by neighbor exchanges and oriented divisions, patterning where LPCs perdure and thereby breaking symmetry. These cues offer a logical and likely conserved framework for how epithelia without obvious molecular asymmetries can polarize.
Collapse
Affiliation(s)
| | - Melissa A Pickett
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Biological Sciences, San José State University, San José, CA 95192, USA
| | - Jessica L Feldman
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
15
|
Skinner DJ, Jeckel H, Martin AC, Drescher K, Dunkel J. Topological packing statistics of living and nonliving matter. SCIENCE ADVANCES 2023; 9:eadg1261. [PMID: 37672580 PMCID: PMC10482333 DOI: 10.1126/sciadv.adg1261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 07/27/2023] [Indexed: 09/08/2023]
Abstract
Complex disordered matter is of central importance to a wide range of disciplines, from bacterial colonies and embryonic tissues in biology to foams and granular media in materials science to stellar configurations in astrophysics. Because of the vast differences in composition and scale, comparing structural features across such disparate systems remains challenging. Here, by using the statistical properties of Delaunay tessellations, we introduce a mathematical framework for measuring topological distances between general three-dimensional point clouds. The resulting system-agnostic metric reveals subtle structural differences between bacterial biofilms as well as between zebrafish brain regions, and it recovers temporal ordering of embryonic development. We apply the metric to construct a universal topological atlas encompassing bacterial biofilms, snowflake yeast, plant shoots, zebrafish brain matter, organoids, and embryonic tissues as well as foams, colloidal packings, glassy materials, and stellar configurations. Living systems localize within a bounded island-like region of the atlas, reflecting that biological growth mechanisms result in characteristic topological properties.
Collapse
Affiliation(s)
- Dominic J Skinner
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Hannah Jeckel
- Department of Physics, Philipps-Universität Marburg, Renthof 6, 35032 Marburg, Germany
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Adam C Martin
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Knut Drescher
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| |
Collapse
|
16
|
Natesan G, Hamilton T, Deeds EJ, Shah PK. Novel metrics reveal new structure and unappreciated heterogeneity in C. elegans development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.12.540617. [PMID: 37292606 PMCID: PMC10245744 DOI: 10.1101/2023.05.12.540617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
High throughput experimental approaches are increasingly allowing for the quantitative description of cellular and organismal phenotypes. Distilling these large volumes of complex data into meaningful measures that can drive biological insight remains a central challenge. In the quantitative study of development, for instance, one can resolve phenotypic measures for single cells onto their lineage history, enabling joint consideration of heritable signals and cell fate decisions. Most attempts to analyze this type of data, however, discard much of the information content contained within lineage trees. In this work we introduce a generalized metric, which we term the branch distance, that allows us to compare any two embryos based on phenotypic measurements in individual cells. This approach aligns those phenotypic measurements to the underlying lineage tree, providing a flexible and intuitive framework for quantitative comparisons between, for instance, Wild-Type (WT) and mutant developmental programs. We apply this novel metric to data on cell-cycle timing from over 1300 WT and RNAi-treated Caenorhabditis elegans embryos. Our new metric revealed surprising heterogeneity within this data set, including subtle batch effects in WT embryos and dramatic variability in RNAi-induced developmental phenotypes, all of which had been missed in previous analyses. Further investigation of these results suggests a novel, quantitative link between pathways that govern cell fate decisions and pathways that pattern cell cycle timing in the early embryo. Our work demonstrates that the branch distance we propose, and similar metrics like it, have the potential to revolutionize our quantitative understanding of organismal phenotype.
Collapse
Affiliation(s)
- Gunalan Natesan
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA
| | - Timothy Hamilton
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA
| | - Eric J. Deeds
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA
| | - Pavak K. Shah
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA
| |
Collapse
|
17
|
Smith MB, Sparks H, Almagro J, Chaigne A, Behrens A, Dunsby C, Salbreux G. Active mesh and neural network pipeline for cell aggregate segmentation. Biophys J 2023; 122:1586-1599. [PMID: 37002604 PMCID: PMC10183373 DOI: 10.1016/j.bpj.2023.03.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/16/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
Segmenting cells within cellular aggregates in 3D is a growing challenge in cell biology due to improvements in capacity and accuracy of microscopy techniques. Here, we describe a pipeline to segment images of cell aggregates in 3D. The pipeline combines neural network segmentations with active meshes. We apply our segmentation method to cultured mouse mammary gland organoids imaged over 24 h with oblique plane microscopy, a high-throughput light-sheet fluorescence microscopy technique. We show that our method can also be applied to images of mouse embryonic stem cells imaged with a spinning disc microscope. We segment individual cells based on nuclei and cell membrane fluorescent markers, and track cells over time. We describe metrics to quantify the quality of the automated segmentation. Our segmentation pipeline involves a Fiji plugin that implements active mesh deformation and allows a user to create training data, automatically obtain segmentation meshes from original image data or neural network prediction, and manually curate segmentation data to identify and correct mistakes. Our active meshes-based approach facilitates segmentation postprocessing, correction, and integration with neural network prediction.
Collapse
Affiliation(s)
| | - Hugh Sparks
- Photonics Group, Department of Physics, Imperial College London, London, United Kingdom
| | | | - Agathe Chaigne
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Axel Behrens
- Cancer Stem Cell Team, The Institute of Cancer Research, London, United Kingdom
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, London, United Kingdom
| | - Guillaume Salbreux
- The Francis Crick Institute, London, United Kingdom; Department of Genetics and Evolution, Geneva, Switzerland.
| |
Collapse
|
18
|
Mitrakas AG, Tsolou A, Didaskalou S, Karkaletsou L, Efstathiou C, Eftalitsidis E, Marmanis K, Koffa M. Applications and Advances of Multicellular Tumor Spheroids: Challenges in Their Development and Analysis. Int J Mol Sci 2023; 24:ijms24086949. [PMID: 37108113 PMCID: PMC10138394 DOI: 10.3390/ijms24086949] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Biomedical research requires both in vitro and in vivo studies in order to explore disease processes or drug interactions. Foundational investigations have been performed at the cellular level using two-dimensional cultures as the gold-standard method since the early 20th century. However, three-dimensional (3D) cultures have emerged as a new tool for tissue modeling over the last few years, bridging the gap between in vitro and animal model studies. Cancer has been a worldwide challenge for the biomedical community due to its high morbidity and mortality rates. Various methods have been developed to produce multicellular tumor spheroids (MCTSs), including scaffold-free and scaffold-based structures, which usually depend on the demands of the cells used and the related biological question. MCTSs are increasingly utilized in studies involving cancer cell metabolism and cell cycle defects. These studies produce massive amounts of data, which demand elaborate and complex tools for thorough analysis. In this review, we discuss the advantages and disadvantages of several up-to-date methods used to construct MCTSs. In addition, we also present advanced methods for analyzing MCTS features. As MCTSs more closely mimic the in vivo tumor environment, compared to 2D monolayers, they can evolve to be an appealing model for in vitro tumor biology studies.
Collapse
Affiliation(s)
- Achilleas G Mitrakas
- Cell Biology Lab, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Avgi Tsolou
- Cell Biology Lab, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Stylianos Didaskalou
- Cell Biology Lab, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Lito Karkaletsou
- Cell Biology Lab, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Christos Efstathiou
- Cell Biology Lab, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Evgenios Eftalitsidis
- Cell Biology Lab, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Konstantinos Marmanis
- Cell Biology Lab, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Maria Koffa
- Cell Biology Lab, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| |
Collapse
|
19
|
Kuang X, Guan G, Tang C, Zhang L. MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies. NPJ Syst Biol Appl 2023; 9:6. [PMID: 36806172 PMCID: PMC9938209 DOI: 10.1038/s41540-023-00265-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 01/04/2023] [Indexed: 02/19/2023] Open
Abstract
The phase field model can accurately simulate the evolution of microstructures with complex morphologies, and it has been widely used for cell modeling in the last two decades. However, compared to other cellular models such as the coarse-grained model and the vertex model, its high computational cost caused by three-dimensional spatial discretization hampered its application and scalability, especially for multicellular organisms. Recently, we built a phase field model coupled with in vivo imaging data to accurately reconstruct the embryonic morphogenesis of Caenorhabditis elegans from 1- to 8-cell stages. In this work, we propose an improved phase field model by using the stabilized numerical scheme and modified volume constriction. Then we present a scalable phase-field framework, MorphoSim, which is 100 times more efficient than the previous one and can simulate over 100 mechanically interacting cells. Finally, we demonstrate how MorphoSim can be successfully applied to reproduce the assembly, self-repairing, and dissociation of a synthetic artificial multicellular system - the synNotch system.
Collapse
Affiliation(s)
- Xiangyu Kuang
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Guoye Guan
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- School of Physics, Peking University, Beijing, 100871, China.
| | - Lei Zhang
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.
- Beijing International Center for Mathematical Research, Peking University, Beijing, 100871, China.
- Center for Machine Learning Research, Peking University, Beijing, 100871, China.
| |
Collapse
|
20
|
Azuma Y, Okada H, Onami S. Systematic analysis of cell morphodynamics in C. elegans early embryogenesis. FRONTIERS IN BIOINFORMATICS 2023; 3:1082531. [PMID: 37026092 PMCID: PMC10070942 DOI: 10.3389/fbinf.2023.1082531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023] Open
Abstract
The invariant cell lineage of Caenorhabditis elegans allows unambiguous assignment of the identity for each cell, which offers a unique opportunity to study developmental dynamics such as the timing of cell division, dynamics of gene expression, and cell fate decisions at single-cell resolution. However, little is known about cell morphodynamics, including the extent to which they are variable between individuals, mainly due to the lack of sufficient amount and quality of quantified data. In this study, we systematically quantified the cell morphodynamics in 52 C. elegans embryos from the two-cell stage to mid-gastrulation at the high spatiotemporal resolution, 0.5 μm thickness of optical sections, and 30-second intervals of recordings. Our data allowed systematic analyses of the morphological features. We analyzed sphericity dynamics and found a significant increase at the end of metaphase in every cell, indicating the universality of the mitotic cell rounding. Concomitant with the rounding, the volume also increased in most but not all cells, suggesting less universality of the mitotic swelling. Combining all features showed that cell morphodynamics was unique for each cell type. The cells before the onset of gastrulation could be distinguished from all the other cell types. Quantification of reproducibility in cell-cell contact revealed that variability in division timings and cell arrangements produced variability in contacts between the embryos. However, the area of such contacts occupied less than 5% of the total area, suggesting the high reproducibility of spatial occupancies and adjacency relationships of the cells. By comparing the morphodynamics of identical cells between the embryos, we observed diversity in the variability between cells and found it was determined by multiple factors, including cell lineage, cell generation, and cell-cell contact. We compared the variabilities of cell morphodynamics and cell-cell contacts with those in ascidian Phallusia mammillata embryos. The variabilities were larger in C. elegans, despite smaller differences in embryo size and number of cells at each developmental stage.
Collapse
|
21
|
Malin-Mayor C, Hirsch P, Guignard L, McDole K, Wan Y, Lemon WC, Kainmueller D, Keller PJ, Preibisch S, Funke J. Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations. Nat Biotechnol 2023; 41:44-49. [PMID: 36065022 PMCID: PMC7614077 DOI: 10.1038/s41587-022-01427-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/12/2022] [Indexed: 01/19/2023]
Abstract
We present a method to automatically identify and track nuclei in time-lapse microscopy recordings of entire developing embryos. The method combines deep learning and global optimization. On a mouse dataset, it reconstructs 75.8% of cell lineages spanning 1 h, as compared to 31.8% for the competing method. Our approach improves understanding of where and when cell fate decisions are made in developing embryos, tissues, and organs.
Collapse
Affiliation(s)
| | - Peter Hirsch
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Faculty of Mathematics and Natural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Leo Guignard
- HHMI Janelia, Ashburn, VA, USA
- CNRS, UTLN, LIS 7020, Turing Centre for Living Systems, Aix Marseille University, Marseille, France
| | - Katie McDole
- HHMI Janelia, Ashburn, VA, USA
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Yinan Wan
- HHMI Janelia, Ashburn, VA, USA
- Biozentrum, University of Basel, Basel, Switzerland
| | | | - Dagmar Kainmueller
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Faculty of Mathematics and Natural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | | | | |
Collapse
|
22
|
Lauziere A, Christensen R, Shroff H, Balan R. An Exact Hypergraph Matching algorithm for posture identification in embryonic C. elegans. PLoS One 2022; 17:e0277343. [PMID: 36445888 PMCID: PMC9707761 DOI: 10.1371/journal.pone.0277343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 10/25/2022] [Indexed: 12/03/2022] Open
Abstract
The nematode Caenorhabditis elegans (C. elegans) is a model organism used frequently in developmental biology and neurobiology [White, (1986), Sulston, (1983), Chisholm, (2016) and Rapti, (2020)]. The C. elegans embryo can be used for cell tracking studies to understand how cell movement drives the development of specific embryonic tissues. Analyses in late-stage development are complicated by bouts of rapid twitching motions which invalidate traditional cell tracking approaches. However, the embryo possesses a small set of cells which may be identified, thereby defining the coiled embryo's posture [Christensen, 2015]. The posture serves as a frame of reference, facilitating cell tracking even in the presence of twitching. Posture identification is nevertheless challenging due to the complete repositioning of the embryo between sampled images. Current approaches to posture identification rely on time-consuming manual efforts by trained users which limits the efficiency of subsequent cell tracking. Here, we cast posture identification as a point-set matching task in which coordinates of seam cell nuclei are identified to jointly recover the posture. Most point-set matching methods comprise coherent point transformations that use low order objective functions [Zhou, (2016) and Zhang, (2019)]. Hypergraphs, an extension of traditional graphs, allow more intricate modeling of relationships between objects, yet existing hypergraphical point-set matching methods are limited to heuristic algorithms which do not easily scale to handle higher degree hypergraphs [Duchenne, (2010), Chertok, (2010) and Lee, (2011)]. Our algorithm, Exact Hypergraph Matching (EHGM), adapts the classical branch-and-bound paradigm to dynamically identify a globally optimal correspondence between point-sets under an arbitrarily intricate hypergraphical model. EHGM with hypergraphical models inspired by C. elegans embryo shape identified posture more accurately (56%) than established point-set matching methods (27%), correctly identifying twice as many sampled postures as a leading graphical approach. Posterior region seeding empowered EHGM to correctly identify 78% of postures while reducing runtime, demonstrating the efficacy of the method on a cutting-edge problem in developmental biology.
Collapse
Affiliation(s)
- Andrew Lauziere
- Department of Mathematics, University of Maryland, College Park, MD, United States of America
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, United States of America
- * E-mail:
| | - Ryan Christensen
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, United States of America
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, United States of America
| | - Radu Balan
- Department of Mathematics, University of Maryland, College Park, MD, United States of America
- Center for Scientific Computation and Mathematical Modeling (CSCAMM), University of Maryland, College Park, MD, United States of America
| |
Collapse
|
23
|
Wong MK, Ho VWS, Huang X, Chan LY, Xie D, Li R, Ren X, Guan G, Ma Y, Hu B, Yan H, Zhao Z. Initial characterization of gap phase introduction in every cell cycle of C. elegans embryogenesis. Front Cell Dev Biol 2022; 10:978962. [PMID: 36393848 PMCID: PMC9641140 DOI: 10.3389/fcell.2022.978962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/20/2022] [Indexed: 11/28/2022] Open
Abstract
Early embryonic cell cycles usually alternate between S and M phases without any gap phase. When the gap phases are developmentally introduced in various cell types remains poorly defined especially during embryogenesis. To establish the cell-specific introduction of gap phases in embryo, we generate multiple fluorescence ubiquitin cell cycle indicators (FUCCI) in C. elegans. Time-lapse 3D imaging followed by lineal expression profiling reveals sharp and differential accumulation of the FUCCI reporters, allowing the systematic demarcation of cell cycle phases throughout embryogenesis. Accumulation of the reporters reliably identifies both G1 and G2 phases only in two embryonic cells with an extended cell cycle length, suggesting that the remaining cells divide either without a G1 phase, or with a brief G1 phase that is too short to be picked up by our reporters. In summary, we provide an initial picture of gap phase introduction in a metazoan embryo. The newly developed FUCCI reporters pave the way for further characterization of developmental control of cell cycle progression.
Collapse
Affiliation(s)
- Ming-Kin Wong
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Vincy Wing Sze Ho
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Xiaotai Huang
- School of Computer Science and Technology, Xidian University, Xi’an, China
- Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Lu-Yan Chan
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Xiaoliang Ren
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Guoye Guan
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Yiming Ma
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Boyi Hu
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Hong Yan
- Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
- *Correspondence: Zhongying Zhao,
| |
Collapse
|
24
|
Wu Y, Wu S, Wang X, Lang C, Zhang Q, Wen Q, Xu T. Rapid detection and recognition of whole brain activity in a freely behaving Caenorhabditis elegans. PLoS Comput Biol 2022; 18:e1010594. [PMID: 36215325 PMCID: PMC9584436 DOI: 10.1371/journal.pcbi.1010594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 10/20/2022] [Accepted: 09/22/2022] [Indexed: 11/07/2022] Open
Abstract
Advanced volumetric imaging methods and genetically encoded activity indicators have permitted a comprehensive characterization of whole brain activity at single neuron resolution in Caenorhabditis elegans. The constant motion and deformation of the nematode nervous system, however, impose a great challenge for consistent identification of densely packed neurons in a behaving animal. Here, we propose a cascade solution for long-term and rapid recognition of head ganglion neurons in a freely moving C. elegans. First, potential neuronal regions from a stack of fluorescence images are detected by a deep learning algorithm. Second, 2-dimensional neuronal regions are fused into 3-dimensional neuron entities. Third, by exploiting the neuronal density distribution surrounding a neuron and relative positional information between neurons, a multi-class artificial neural network transforms engineered neuronal feature vectors into digital neuronal identities. With a small number of training samples, our bottom-up approach is able to process each volume—1024 × 1024 × 18 in voxels—in less than 1 second and achieves an accuracy of 91% in neuronal detection and above 80% in neuronal tracking over a long video recording. Our work represents a step towards rapid and fully automated algorithms for decoding whole brain activity underlying naturalistic behaviors. An important question in neuroscience is to understand the relationship between brain dynamics and naturalistic behaviors when an animal is freely exploring its environment. In the last decade, it has become possible to genetically engineer animals whose neurons produce fluorescence reporters that change their brightness in response to brain activity. In small animals such as the nematode C. elegans, we can now record the fluorescence changes in and thereby infer neural activity from most neurons in the head of a worm, when the animal is freely moving. These neurons are densely packed in a small volume. Since the brain and body are moving and its shape undergoes significant deformation, a human expert, even after long hours of inspection, may still have difficulty to tell where the neurons are and who they are. We sought to develop an automatic method for rapidly detecting and tracking most of these neurons in a moving animal. To do this, we asked a human expert to annotate all head neurons—their locations and digital identities—across a small number of volumes. Then, we trained a computer to learn the locations and digital identities of these neurons across different imaging volumes. Our machine inference method is fast and accurate. While it takes a human expert several hours to complete a sequence of volumes, a machine can finish the task in a few minutes. We hope our method provides a better and more efficient engine for extracting knowledge from whole brain imaging datasets and animal behaviors.
Collapse
Affiliation(s)
- Yuxiang Wu
- Chinese Academy of Sciences Key Laboratory of Brain Function and Diseases, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Shang Wu
- Chinese Academy of Sciences Key Laboratory of Brain Function and Diseases, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Xin Wang
- John Hopcroft Center for Computer Science, School of electronic information and electrical engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chengtian Lang
- Department of Electronic Engineering and Information Science, University of Science and Technology of China, Hefei, China
| | - Quanshi Zhang
- John Hopcroft Center for Computer Science, School of electronic information and electrical engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Quan Wen
- Chinese Academy of Sciences Key Laboratory of Brain Function and Diseases, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
- * E-mail: (QW); (TX)
| | - Tianqi Xu
- Chinese Academy of Sciences Key Laboratory of Brain Function and Diseases, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
- * E-mail: (QW); (TX)
| |
Collapse
|
25
|
Guan G, Zhao Z, Tang C. Delineating the mechanisms and design principles of Caenorhabditis elegans embryogenesis using in toto high-resolution imaging data and computational modeling. Comput Struct Biotechnol J 2022; 20:5500-5515. [PMID: 36284714 PMCID: PMC9562942 DOI: 10.1016/j.csbj.2022.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/19/2022] Open
Abstract
The nematode (roundworm) Caenorhabditis elegans is one of the most popular animal models for the study of developmental biology, as its invariant development and transparent body enable in toto cellular-resolution fluorescence microscopy imaging of developmental processes at 1-min intervals. This has led to the development of various computational tools for the systematic and automated analysis of imaging data to delineate the molecular and cellular processes throughout the embryogenesis of C. elegans, such as those associated with cell lineage, cell migration, cell morphology, and gene activity. In this review, we first introduce C. elegans embryogenesis and the development of techniques for tracking cell lineage and reconstructing cell morphology during this process. We then contrast the developmental modes of C. elegans and the customized technologies used for studying them with the ones of other animal models, highlighting its advantage for studying embryogenesis with exceptional spatial and temporal resolution. This is followed by an examination of the physical models that have been devised-based on accurate determinations of developmental processes afforded by analyses of imaging data-to interpret the early embryonic development of C. elegans from subcellular to intercellular levels of multiple cells, which focus on two key processes: cell polarization and morphogenesis. We subsequently discuss how quantitative data-based theoretical modeling has improved our understanding of the mechanisms of C. elegans embryogenesis. We conclude by summarizing the challenges associated with the acquisition of C. elegans embryogenesis data, the construction of algorithms to analyze them, and the theoretical interpretation.
Collapse
Affiliation(s)
- Guoye Guan
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong 999077, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing 100871, China
- Peking–Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- School of Physics, Peking University, Beijing 100871, China
| |
Collapse
|
26
|
Gómez-Gálvez P, Vicente-Munuera P, Anbari S, Tagua A, Gordillo-Vázquez C, Andrés-San Román JA, Franco-Barranco D, Palacios AM, Velasco A, Capitán-Agudo C, Grima C, Annese V, Arganda-Carreras I, Robles R, Márquez A, Buceta J, Escudero LM. A quantitative biophysical principle to explain the 3D cellular connectivity in curved epithelia. Cell Syst 2022; 13:631-643.e8. [PMID: 35835108 DOI: 10.1016/j.cels.2022.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 02/15/2022] [Accepted: 06/15/2022] [Indexed: 01/26/2023]
Abstract
Epithelial cell organization and the mechanical stability of tissues are closely related. In this context, it has been recently shown that packing optimization in bended or folded epithelia is achieved by an energy minimization mechanism that leads to a complex cellular shape: the "scutoid". Here, we focus on the relationship between this shape and the connectivity between cells. We use a combination of computational, experimental, and biophysical approaches to examine how energy drivers affect the three-dimensional (3D) packing of tubular epithelia. We propose an energy-based stochastic model that explains the 3D cellular connectivity. Then, we challenge it by experimentally reducing the cell adhesion. As a result, we observed an increment in the appearance of scutoids that correlated with a decrease in the energy barrier necessary to connect with new cells. We conclude that tubular epithelia satisfy a quantitative biophysical principle that links tissue geometry and energetics with the average cellular connectivity.
Collapse
Affiliation(s)
- Pedro Gómez-Gálvez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain.
| | - Pablo Vicente-Munuera
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Samira Anbari
- Chemical and Biomolecular Engineering Department, Lehigh University, Bethlehem, PA 18018, USA
| | - Antonio Tagua
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Carmen Gordillo-Vázquez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Jesús A Andrés-San Román
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Daniel Franco-Barranco
- Department of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), San Sebastian, Spain; Donostia International Physics Center (DIPC), San Sebastian, Spain
| | - Ana M Palacios
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Antonio Velasco
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain
| | - Carlos Capitán-Agudo
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain
| | - Clara Grima
- Departamento de Matemática Aplicada I, Universidad de Sevilla, Seville 41012, Spain
| | - Valentina Annese
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Ignacio Arganda-Carreras
- Department of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), San Sebastian, Spain; Donostia International Physics Center (DIPC), San Sebastian, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Rafael Robles
- Departamento de Matemática Aplicada I, Universidad de Sevilla, Seville 41012, Spain
| | - Alberto Márquez
- Departamento de Matemática Aplicada I, Universidad de Sevilla, Seville 41012, Spain
| | - Javier Buceta
- Institute for Integrative Systems Biology (I2SysBio), CSIC-UV, Paterna 46980, Spain.
| | - Luis M Escudero
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain.
| |
Collapse
|
27
|
EmbedSeg: Embedding-based Instance Segmentation for Biomedical Microscopy Data. Med Image Anal 2022; 81:102523. [DOI: 10.1016/j.media.2022.102523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 05/02/2022] [Accepted: 06/24/2022] [Indexed: 11/20/2022]
|
28
|
Shah P, Bao Z, Zaidel-Bar R. Visualizing and quantifying molecular and cellular processes in C. elegans using light microscopy. Genetics 2022; 221:6619563. [PMID: 35766819 DOI: 10.1093/genetics/iyac068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 04/14/2022] [Indexed: 11/14/2022] Open
Abstract
Light microscopes are the cell and developmental biologists' "best friend", providing a means to see structures and follow dynamics from the protein to the organism level. A huge advantage of C. elegans as a model organism is its transparency, which coupled with its small size means that nearly every biological process can be observed and measured with the appropriate probe and light microscope. Continuous improvement in microscope technologies along with novel genome editing techniques to create transgenic probes have facilitated the development and implementation of a dizzying array of methods for imaging worm embryos, larvae and adults. In this review we provide an overview of the molecular and cellular processes that can be visualized in living worms using light microscopy. A partial inventory of fluorescent probes and techniques successfully used in worms to image the dynamics of cells, organelles, DNA, and protein localization and activity is followed by a practical guide to choosing between various imaging modalities, including widefield, confocal, lightsheet, and structured illumination microscopy. Finally, we discuss the available tools and approaches, including machine learning, for quantitative image analysis tasks, such as colocalization, segmentation, object tracking, and lineage tracing. Hopefully, this review will inspire worm researchers who have not yet imaged their worms to begin, and push those who are imaging to go faster, finer, and longer.
Collapse
Affiliation(s)
- Pavak Shah
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles 90095, USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - Ronen Zaidel-Bar
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| |
Collapse
|
29
|
Niu B, Nguyen Bach T, Chen X, Raghunath Chandratre K, Isaac Murray J, Zhao Z, Zhang M. Computational modeling and analysis of the morphogenetic domain signaling networks regulating C. elegans embryogenesis. Comput Struct Biotechnol J 2022; 20:3653-3666. [PMID: 35891777 PMCID: PMC9289785 DOI: 10.1016/j.csbj.2022.05.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 11/03/2022] Open
Abstract
Caenorhabditis elegans, often referred to as the ‘roundworm’, provides a powerful model for studying cell autonomous and cell–cell interactions through the direct observation of embryonic development in vivo. By leveraging the precisely mapped cell lineage at single cell resolution, we are able to study at a systems level how early embryonic cells communicate across morphogenetic domains for the coordinated processes of gene expressions and collective cellular behaviors that regulate tissue morphogenesis. In this study, we developed a computational framework for the exploration of the morphogenetic domain cell signaling networks that may regulate C. elegans gastrulation and embryonic organogenesis. We demonstrated its utility by producing the following results, i) established a virtual reference model of developing C. elegans embryos through the spatiotemporal alignment of individual embryo cell nuclear imaging samples; ii) integrated the single cell spatiotemporal gene expression profile with the established virtual embryo model by data pooling; iii) trained a Machine Learning model (Random Forest Regression), which predicts accurately the spatial positions of the cells given their gene expression profiles for a given developmental time (e.g. total cell number of the embryo); iv) enabled virtual 4-dimensional tomographic graphical modeling of single cell data; v) inferred the biology signaling pathways that act in each of morphogenetic domains by meta-data analysis. It is intriguing that the morphogenetic domain cell signaling network seems to involve some crosstalk of multiple biology signaling pathways during the formation of tissue boundary pattern. Lastly, we developed the Software tool ‘Embryo aligner version 1.0’ and provided it as an Open Source program to the research community for virtual embryo modeling, and phenotype perturbation analyses (https://github.com/csniuben/embryo_aligner/wiki and https://bioinfo89.github.io/C.elegansEmbryonicOrganogenesisweb/).
Collapse
|
30
|
Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning. Nat Biotechnol 2022; 40:555-565. [PMID: 34795433 PMCID: PMC9010346 DOI: 10.1038/s41587-021-01094-0] [Citation(s) in RCA: 378] [Impact Index Per Article: 126.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 09/14/2021] [Indexed: 02/07/2023]
Abstract
A principal challenge in the analysis of tissue imaging data is cell segmentation-the task of identifying the precise boundary of every cell in an image. To address this problem we constructed TissueNet, a dataset for training segmentation models that contains more than 1 million manually labeled cells, an order of magnitude more than all previously published segmentation training datasets. We used TissueNet to train Mesmer, a deep-learning-enabled segmentation algorithm. We demonstrated that Mesmer is more accurate than previous methods, generalizes to the full diversity of tissue types and imaging platforms in TissueNet, and achieves human-level performance. Mesmer enabled the automated extraction of key cellular features, such as subcellular localization of protein signal, which was challenging with previous approaches. We then adapted Mesmer to harness cell lineage information in highly multiplexed datasets and used this enhanced version to quantify cell morphology changes during human gestation. All code, data and models are released as a community resource.
Collapse
|
31
|
Kuang X, Guan G, Wong MK, Chan LY, Zhao Z, Tang C, Zhang L. Computable early Caenorhabditis elegans embryo with a phase field model. PLoS Comput Biol 2022; 18:e1009755. [PMID: 35030161 PMCID: PMC8794267 DOI: 10.1371/journal.pcbi.1009755] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 01/27/2022] [Accepted: 12/14/2021] [Indexed: 01/11/2023] Open
Abstract
Morphogenesis is a precise and robust dynamic process during metazoan embryogenesis, consisting of both cell proliferation and cell migration. Despite the fact that much is known about specific regulations at molecular level, how cell proliferation and migration together drive the morphogenesis at cellular and organismic levels is not well understood. Using Caenorhabditis elegans as the model animal, we present a phase field model to compute early embryonic morphogenesis within a confined eggshell. With physical information about cell division obtained from three-dimensional time-lapse cellular imaging experiments, the model can precisely reproduce the early morphogenesis process as seen in vivo, including time evolution of location and morphology of each cell. Furthermore, the model can be used to reveal key cell-cell attractions critical to the development of C. elegans embryo. Our work demonstrates how genetic programming and physical forces collaborate to drive morphogenesis and provides a predictive model to decipher the underlying mechanism. Embryonic development is a precise process involving cell division, cell-cell interaction, and cell migration. During the process, how each cell reaches its supposed location and be in contact with the right neighbors, and what roles genetic factors and physical forces play are important and fascinating questions. Using the worm Caenorhabditis elegans as a model system, we build a phase field model to simulate early morphogenesis. With a few physical inputs, the model can precisely reproduce the early morphological development of the worm. Such an accurate simulator can not only teach us how physical forces work together with genetic factors to shape up the complex process of development, but also make predictions, such as key cell-cell attractions critical in the process.
Collapse
Affiliation(s)
- Xiangyu Kuang
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Guoye Guan
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Ming-Kin Wong
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Lu-Yan Chan
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- School of Physics, Peking University, Beijing, China
- * E-mail: (CT); (LZ)
| | - Lei Zhang
- Center for Quantitative Biology, Peking University, Beijing, China
- Beijing International Center for Mathematical Research, Peking University, Beijing, China
- * E-mail: (CT); (LZ)
| |
Collapse
|
32
|
Guan G, Wong MK, Zhao Z, Tang LH, Tang C. Volume segregation programming in a nematode's early embryogenesis. Phys Rev E 2021; 104:054409. [PMID: 34942757 DOI: 10.1103/physreve.104.054409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 10/15/2021] [Indexed: 11/07/2022]
Abstract
Nematode species are well-known for their invariant cell lineage pattern during development. Combining knowledge about the fate specification induced by asymmetric division and the anti-correlation between cell cycle length and cell volume in Caenorhabditis elegans, we propose a minimal model to simulate lineage initiation by altering cell volume segregation ratio in each division, and quantify the derived pattern's performance in proliferation speed, fate diversity, and space robustness. The stereotypic pattern in C. elegans embryo is found to be one of the most optimal solutions taking minimum time to achieve the cell number before gastrulation, by programming asymmetric divisions as a strategy.
Collapse
Affiliation(s)
- Guoye Guan
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Ming-Kin Wong
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.,State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
| | - Lei-Han Tang
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China.,Department of Physics and Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Hong Kong, China.,Complex Systems Division, Beijing Computational Science Research Center, Beijing 100094, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.,School of Physics, Peking University, Beijing 100871, China
| |
Collapse
|
33
|
Mendonca T, Jones AA, Pozo JM, Baxendale S, Whitfield TT, Frangi AF. Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data. PLoS Comput Biol 2021; 17:e1009063. [PMID: 34723957 PMCID: PMC8584784 DOI: 10.1371/journal.pcbi.1009063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 11/11/2021] [Accepted: 10/13/2021] [Indexed: 11/18/2022] Open
Abstract
A common feature of morphogenesis is the formation of three-dimensional structures from the folding of two-dimensional epithelial sheets, aided by cell shape changes at the cellular-level. Changes in cell shape must be studied in the context of cell-polarised biomechanical processes within the epithelial sheet. In epithelia with highly curved surfaces, finding single-cell alignment along a biological axis can be difficult to automate in silico. We present 'Origami', a MATLAB-based image analysis pipeline to compute direction-variant cell shape features along the epithelial apico-basal axis. Our automated method accurately computed direction vectors denoting the apico-basal axis in regions with opposing curvature in synthetic epithelia and fluorescence images of zebrafish embryos. As proof of concept, we identified different cell shape signatures in the developing zebrafish inner ear, where the epithelium deforms in opposite orientations to form different structures. Origami is designed to be user-friendly and is generally applicable to fluorescence images of curved epithelia.
Collapse
Affiliation(s)
- Tania Mendonca
- Centre for Computational Imaging and Simulation Technologies in Biomedicine (CISTIB), Department of Electronic and Electrical Engineering, University of Sheffield, Sheffield, United Kingdom
- Department of Biomedical Science, Bateson Centre and Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom
- * E-mail: (TM); (AFF)
| | - Ana A. Jones
- Department of Biomedical Science, Bateson Centre and Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom
| | - Jose M. Pozo
- Centre for Computational Imaging and Simulation Technologies in Biomedicine (CISTIB), Department of Electronic and Electrical Engineering, University of Sheffield, Sheffield, United Kingdom
- Centre for Computational Imaging and Simulation Technologies in Biomedicine (CISTIB), School of Computing and School of Medicine, University of Leeds, Leeds, United Kingdom
| | - Sarah Baxendale
- Department of Biomedical Science, Bateson Centre and Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom
| | - Tanya T. Whitfield
- Department of Biomedical Science, Bateson Centre and Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom
| | - Alejandro F. Frangi
- Centre for Computational Imaging and Simulation Technologies in Biomedicine (CISTIB), Department of Electronic and Electrical Engineering, University of Sheffield, Sheffield, United Kingdom
- Centre for Computational Imaging and Simulation Technologies in Biomedicine (CISTIB), School of Computing and School of Medicine, University of Leeds, Leeds, United Kingdom
- Medical Imaging Research Center (MIRC), University Hospital Gasthuisberg, Cardiovascular Sciences and Electrical Engineering Departments, KU Leuven, Belgium
- * E-mail: (TM); (AFF)
| |
Collapse
|
34
|
Hallou A, Yevick HG, Dumitrascu B, Uhlmann V. Deep learning for bioimage analysis in developmental biology. Development 2021; 148:dev199616. [PMID: 34490888 PMCID: PMC8451066 DOI: 10.1242/dev.199616] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Deep learning has transformed the way large and complex image datasets can be processed, reshaping what is possible in bioimage analysis. As the complexity and size of bioimage data continues to grow, this new analysis paradigm is becoming increasingly ubiquitous. In this Review, we begin by introducing the concepts needed for beginners to understand deep learning. We then review how deep learning has impacted bioimage analysis and explore the open-source resources available to integrate it into a research project. Finally, we discuss the future of deep learning applied to cell and developmental biology. We analyze how state-of-the-art methodologies have the potential to transform our understanding of biological systems through new image-based analysis and modelling that integrate multimodal inputs in space and time.
Collapse
Affiliation(s)
- Adrien Hallou
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
- Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Hannah G. Yevick
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Bianca Dumitrascu
- Computer Laboratory, Cambridge, University of Cambridge, Cambridge, CB3 0FD, UK
| | - Virginie Uhlmann
- European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK
| |
Collapse
|
35
|
Gómez-Gálvez P, Anbari S, Escudero LM, Buceta J. Mechanics and self-organization in tissue development. Semin Cell Dev Biol 2021; 120:147-159. [PMID: 34417092 DOI: 10.1016/j.semcdb.2021.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/25/2021] [Accepted: 07/01/2021] [Indexed: 01/01/2023]
Abstract
Self-organization is an all-important feature of living systems that provides the means to achieve specialization and functionality at distinct spatio-temporal scales. Herein, we review this concept by addressing the packing organization of cells, the sorting/compartmentalization phenomenon of cell populations, and the propagation of organizing cues at the tissue level through traveling waves. We elaborate on how different theoretical models and tools from Topology, Physics, and Dynamical Systems have improved the understanding of self-organization by shedding light on the role played by mechanics as a driver of morphogenesis. Altogether, by providing a historical perspective, we show how ideas and hypotheses in the field have been revisited, developed, and/or rejected and what are the open questions that need to be tackled by future research.
Collapse
Affiliation(s)
- Pedro Gómez-Gálvez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla and Departamento de Biologia Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain
| | - Samira Anbari
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Luis M Escudero
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla and Departamento de Biologia Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain
| | - Javier Buceta
- Institute for Integrative Systems Biology (I2SysBio), CSIC-UV, Paterna, 46980 Valencia, Spain.
| |
Collapse
|
36
|
Thiels W, Smeets B, Cuvelier M, Caroti F, Jelier R. spheresDT/Mpacts-PiCS: Cell Tracking and Shape Retrieval in Membrane-labeled Embryos. Bioinformatics 2021; 37:4851-4856. [PMID: 34329378 PMCID: PMC8665764 DOI: 10.1093/bioinformatics/btab557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/16/2021] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
Motivation Uncovering the cellular and mechanical processes that drive embryo formation requires an accurate read out of cell geometries over time. However, automated extraction of 3D cell shapes from time-lapse microscopy remains challenging, especially when only membranes are labeled. Results We present an image analysis framework for automated tracking and three-dimensional cell segmentation in confocal time lapses. A sphere clustering approach allows for local thresholding and application of logical rules to facilitate tracking and unseeded segmentation of variable cell shapes. Next, the segmentation is refined by a discrete element method simulation where cell shapes are constrained by a biomechanical cell shape model. We apply the framework on Caenorhabditis elegans embryos in various stages of early development and analyze the geometry of the 7- and 8-cell stage embryo, looking at volume, contact area and shape over time. Availability and implementation The Python code for the algorithm and for measuring performance, along with all data needed to recreate the results is freely available at 10.5281/zenodo.5108416 and 10.5281/zenodo.4540092. The most recent version of the software is maintained at https://bitbucket.org/pgmsembryogenesis/sdt-pics. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Wim Thiels
- CMPG, KU Leuven, Heverlee, 3001, Belgium
| | | | | | | | - Rob Jelier
- CMPG, KU Leuven, Heverlee, 3001, Belgium
| |
Collapse
|