1
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Teranikar T, Villarreal C, Salehin N, Ijaseun T, Lim J, Dominguez C, Nguyen V, Cao H, Chuong C, Lee J. SCALE SPACE DETECTOR FOR ANALYZING SPATIOTEMPORAL VENTRICULAR CONTRACTILITY AND NUCLEAR MORPHOGENESIS IN ZEBRAFISH. iScience 2022; 25:104876. [PMID: 36034231 PMCID: PMC9404658 DOI: 10.1016/j.isci.2022.104876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 04/01/2022] [Accepted: 07/29/2022] [Indexed: 11/15/2022] Open
Abstract
In vivo quantitative assessment of structural and functional biomarkers is essential for characterizing the pathophysiology of congenital disorders. In this regard, fixed tissue analysis has offered revolutionary insights into the underlying cellular architecture. However, histological analysis faces major drawbacks with respect to lack of spatiotemporal sampling and tissue artifacts during sample preparation. This study demonstrates the potential of light sheet fluorescence microscopy (LSFM) as a non-invasive, 4D (3days + time) optical sectioning tool for revealing cardiac mechano-transduction in zebrafish. Furthermore, we have described the utility of a scale and size-invariant feature detector, for analyzing individual morphology of fused cardiomyocyte nuclei and characterizing zebrafish ventricular contractility. Cardiac defect genes in humans have corresponding zebrafish orthologs Light sheet modality is very effective for non-invasive, 4D modeling of zebrafish Hessian detector is robust to varying nuclei scales and geometric transformations Watershed filter is effective for separating fused cellular volumes
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Affiliation(s)
- Tanveer Teranikar
- Joint Department of Bioengineering, UT Arlington/UT Southwestern, Arlington, TX, USA
| | - Cameron Villarreal
- Joint Department of Bioengineering, UT Arlington/UT Southwestern, Arlington, TX, USA
| | - Nabid Salehin
- Joint Department of Bioengineering, UT Arlington/UT Southwestern, Arlington, TX, USA
| | - Toluwani Ijaseun
- Joint Department of Bioengineering, UT Arlington/UT Southwestern, Arlington, TX, USA
| | - Jessica Lim
- Joint Department of Bioengineering, UT Arlington/UT Southwestern, Arlington, TX, USA
| | - Cynthia Dominguez
- Joint Department of Bioengineering, UT Arlington/UT Southwestern, Arlington, TX, USA
| | - Vivian Nguyen
- Martin High School/ UT Arlington, Arlington, TX, USA
| | - Hung Cao
- Department of Electrical Engineering, UC Irvine, Irvine, CA, USA
| | - Cheng–Jen Chuong
- Joint Department of Bioengineering, UT Arlington/UT Southwestern, Arlington, TX, USA
| | - Juhyun Lee
- Joint Department of Bioengineering, UT Arlington/UT Southwestern, Arlington, TX, USA
- Department of Medical Education, TCU and UNTHSC School of Medicine, Fort Worth, TX 76107, USA
- Corresponding author
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2
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Barry DJ, Gerri C, Bell DM, D'Antuono R, Niakan KK. GIANI: open-source software for automated analysis of 3D microscopy images. J Cell Sci 2022; 135:275227. [PMID: 35502739 PMCID: PMC9189431 DOI: 10.1242/jcs.259511] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/20/2022] [Indexed: 11/20/2022] Open
Abstract
The study of cellular and developmental processes in physiologically relevant three-dimensional (3D) systems facilitates an understanding of mechanisms underlying cell fate, disease and injury. While cutting-edge microscopy technologies permit the routine acquisition of 3D datasets, there is currently a limited number of open-source software packages to analyse such images. Here, we describe General Image Analysis of Nuclei-based Images (GIANI; https://djpbarry.github.io/Giani), new software for the analysis of 3D images. The design primarily facilitates segmentation of nuclei and cells, followed by quantification of morphology and protein expression. GIANI enables routine and reproducible batch-processing of large numbers of images, and comes with scripting and command line tools. We demonstrate the utility of GIANI by quantifying cell morphology and protein expression in confocal images of mouse early embryos and by segmenting nuclei from light-sheet microscopy images of the flour beetle embryo. We also validate the performance of the software using simulated data. More generally, we anticipate that GIANI will be a useful tool for researchers in a variety of biomedical fields. Summary: General Image Analysis of Nuclei-based Images (GIANI) is a new plugin for the popular FIJI platform, designed for the automated analysis of 3D microscopy images of a wide range of sample types.
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Affiliation(s)
- David J Barry
- Crick Advanced Light Microscopy, Francis Crick Institute, London, NW1 1ST, UK
| | - Claudia Gerri
- Human Embryo and Stem Cell Laboratory, Francis Crick Institute, London, NW1 1ST, UK.,Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Donald M Bell
- Crick Advanced Light Microscopy, Francis Crick Institute, London, NW1 1ST, UK
| | - Rocco D'Antuono
- Crick Advanced Light Microscopy, Francis Crick Institute, London, NW1 1ST, UK
| | - Kathy K Niakan
- Human Embryo and Stem Cell Laboratory, Francis Crick Institute, London, NW1 1ST, UK.,The Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, UK
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3
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Wu TC, Wang X, Li L, Bu Y, Umulis DM. Automatic wavelet-based 3D nuclei segmentation and analysis for multicellular embryo quantification. Sci Rep 2021; 11:9847. [PMID: 33972575 PMCID: PMC8110989 DOI: 10.1038/s41598-021-88966-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/09/2021] [Indexed: 02/03/2023] Open
Abstract
Identification of individual cells in tissues, organs, and in various developing systems is a well-studied problem because it is an essential part of objectively analyzing quantitative images in numerous biological contexts. We developed a size-dependent wavelet-based segmentation method that provides robust segmentation without any preprocessing, filtering or fine-tuning steps, and is robust to the signal-to-noise ratio. The wavelet-based method achieves robust segmentation results with respect to True Positive rate, Precision, and segmentation accuracy compared with other commonly used methods. We applied the segmentation program to zebrafish embryonic development IN TOTO for nuclei segmentation, image registration, and nuclei shape analysis. These new approaches to segmentation provide a means to carry out quantitative patterning analysis with single-cell precision throughout three dimensional tissues and embryos and they have a high tolerance for non-uniform and noisy image data sets.
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Affiliation(s)
- Tzu-Ching Wu
- grid.169077.e0000 0004 1937 2197Department of Agriculture and Biological Engineering, Purdue University, West Lafayette, IN 47907 USA
| | - Xu Wang
- grid.169077.e0000 0004 1937 2197Department of Agriculture and Biological Engineering, Purdue University, West Lafayette, IN 47907 USA ,grid.169077.e0000 0004 1937 2197Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907 USA ,grid.508040.9Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005 China
| | - Linlin Li
- grid.169077.e0000 0004 1937 2197Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907 USA
| | - Ye Bu
- grid.169077.e0000 0004 1937 2197Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907 USA
| | - David M. Umulis
- grid.169077.e0000 0004 1937 2197Department of Agriculture and Biological Engineering, Purdue University, West Lafayette, IN 47907 USA ,grid.169077.e0000 0004 1937 2197Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907 USA
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4
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Mitchell C, Caroff L, Solis-Lemus JA, Reyes-Aldasoro CC, Vigilante A, Warburton F, de Chaumont F, Dufour A, Dallongeville S, Olivo-Marin JC, Knight R. Cell Tracking Profiler - a user-driven analysis framework for evaluating 4D live-cell imaging data. J Cell Sci 2020; 133:jcs241422. [PMID: 33093241 PMCID: PMC7710012 DOI: 10.1242/jcs.241422] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 10/14/2020] [Indexed: 12/20/2022] Open
Abstract
Accurate measurements of cell morphology and behaviour are fundamentally important for understanding how disease, molecules and drugs affect cell function in vivo Here, by using muscle stem cell (muSC) responses to injury in zebrafish as our biological paradigm, we established a 'ground truth' for muSC behaviour. This revealed that segmentation and tracking algorithms from commonly used programs are error-prone, leading us to develop a fast semi-automated image analysis pipeline that allows user-defined parameters for segmentation and correction of cell tracking. Cell Tracking Profiler (CTP) is a package that runs two existing programs, HK Means and Phagosight within the Icy image analysis suite, to enable user-managed cell tracking from 3D time-lapse datasets to provide measures of cell shape and movement. We demonstrate how CTP can be used to reveal changes to cell behaviour of muSCs in response to manipulation of the cell cytoskeleton by small-molecule inhibitors. CTP and the associated tools we have developed for analysis of outputs thus provide a powerful framework for analysing complex cell behaviour in vivo from 4D datasets that are not amenable to straightforward analysis.
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Affiliation(s)
- Claire Mitchell
- Centre for Craniofacial and Regenerative Biology, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Lauryanne Caroff
- Centre for Craniofacial and Regenerative Biology, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Jose Alonso Solis-Lemus
- School of Mathematics, Computer Science and Engineering, City, University of London, Tait Building, Northampton Square, London EC1V 0HB, UK
| | - Constantino Carlos Reyes-Aldasoro
- School of Mathematics, Computer Science and Engineering, City, University of London, Tait Building, Northampton Square, London EC1V 0HB, UK
| | - Alessandra Vigilante
- Centre for Stem Cells and Regenerative Medicine, King's College London, Tower Wing, Guy's Hospital, London SE1 9RT, UK
| | - Fiona Warburton
- Centre for Oral, Clinical and Translational Sciences, King's College London, Guy's Hospital, London SE1 9RT, UK
| | | | - Alexandre Dufour
- Bioimage Analysis Unit, Institut Pasteur, Paris CEDEX 15, France
| | | | | | - Robert Knight
- Centre for Craniofacial and Regenerative Biology, King's College London, Guy's Hospital, London SE1 9RT, UK
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5
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Tokuoka Y, Yamada TG, Mashiko D, Ikeda Z, Hiroi NF, Kobayashi TJ, Yamagata K, Funahashi A. 3D convolutional neural networks-based segmentation to acquire quantitative criteria of the nucleus during mouse embryogenesis. NPJ Syst Biol Appl 2020; 6:32. [PMID: 33082352 PMCID: PMC7575569 DOI: 10.1038/s41540-020-00152-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 09/11/2020] [Indexed: 12/13/2022] Open
Abstract
During embryogenesis, cells repeatedly divide and dynamically change their positions in three-dimensional (3D) space. A robust and accurate algorithm to acquire the 3D positions of the cells would help to reveal the mechanisms of embryogenesis. To acquire quantitative criteria of embryogenesis from time-series 3D microscopic images, image processing algorithms such as segmentation have been applied. Because the cells in embryos are considerably crowded, an algorithm to segment individual cells in detail and accurately is needed. To quantify the nuclear region of every cell from a time-series 3D fluorescence microscopic image of living cells, we developed QCANet, a convolutional neural network-based segmentation algorithm for 3D fluorescence bioimages. We demonstrated that QCANet outperformed 3D Mask R-CNN, which is currently considered as the best algorithm of instance segmentation. We showed that QCANet can be applied not only to developing mouse embryos but also to developing embryos of two other model species. Using QCANet, we were able to extract several quantitative criteria of embryogenesis from 11 early mouse embryos. We showed that the extracted criteria could be used to evaluate the differences between individual embryos. This study contributes to the development of fundamental approaches for assessing embryogenesis on the basis of extracted quantitative criteria.
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Affiliation(s)
- Yuta Tokuoka
- Department of Biosciences and Informatics, Keio University, Kanagawa, 223-8522, Japan
| | - Takahiro G Yamada
- Department of Biosciences and Informatics, Keio University, Kanagawa, 223-8522, Japan
| | - Daisuke Mashiko
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, 649-6493, Japan
| | - Zenki Ikeda
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, 649-6493, Japan
| | - Noriko F Hiroi
- Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Yamaguchi, 756-0884, Japan
| | - Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan
| | - Kazuo Yamagata
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, 649-6493, Japan
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio University, Kanagawa, 223-8522, Japan.
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6
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Trivedi MM, Mills JK. Centroid calculation of the blastomere from 3D Z-Stack image data of a 2-cell mouse embryo. Biomed Signal Process Control 2020. [DOI: 10.1016/j.bspc.2019.101726] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Ii K, Mashimo K, Ozeki M, Yamada TG, Hiroi N, Funahashi A. XitoSBML: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images. Front Genet 2019; 10:1027. [PMID: 31749833 PMCID: PMC6842926 DOI: 10.3389/fgene.2019.01027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 09/24/2019] [Indexed: 11/26/2022] Open
Abstract
XitoSBML is a software tool designed to create an SBML (Systems Biology Markup Language) Level 3 Version 1 document from microscopic cellular images. It is implemented as an ImageJ plug-in and is designed to create spatial models that reflect the three-dimensional cellular geometry. With XitoSBML, users can perform spatial model simulations based on realistic cellular geometry by using SBML-supported software tools, including simulators such as Virtual Cell and Spatial Simulator. XitoSBML is open-source and is available at https://github.com/spatialsimulator/XitoSBML/. XitoSBML is confirmed to run on most 32/64-bit operating systems: Windows, MacOS, and Linux.
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Affiliation(s)
- Kaito Ii
- Systems Biology Laboratory, Department of Biosciences and Informatics, Keio University, Yokohama, Japan
| | - Kota Mashimo
- Systems Biology Laboratory, Department of Biosciences and Informatics, Keio University, Yokohama, Japan
| | - Mitsunori Ozeki
- Systems Biology Laboratory, Department of Biosciences and Informatics, Keio University, Yokohama, Japan
| | - Takahiro G Yamada
- Systems Biology Laboratory, Department of Biosciences and Informatics, Keio University, Yokohama, Japan
| | - Noriko Hiroi
- Systems Biology Laboratory, Department of Biosciences and Informatics, Keio University, Yokohama, Japan.,Laboratory of Physical Chemistry for Life Science, Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Sanyo-Onoda City, Japan
| | - Akira Funahashi
- Systems Biology Laboratory, Department of Biosciences and Informatics, Keio University, Yokohama, Japan
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8
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3D Engineering of Ocular Tissues for Disease Modeling and Drug Testing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1186:171-193. [DOI: 10.1007/978-3-030-28471-8_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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9
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Information flow in the presence of cell mixing and signaling delays during embryonic development. Semin Cell Dev Biol 2018; 93:26-35. [PMID: 30261318 DOI: 10.1016/j.semcdb.2018.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 09/10/2018] [Accepted: 09/20/2018] [Indexed: 11/23/2022]
Abstract
Embryonic morphogenesis is organized by an interplay between intercellular signaling and cell movements. Both intercellular signaling and cell movement involve multiple timescales. A key timescale for signaling is the time delay caused by preparation of signaling molecules and integration of received signals into cells' internal state. Movement of cells relative to their neighbors may introduce exchange of positions between cells during signaling. When cells change their relative positions in a tissue, the impact of signaling delays on intercellular signaling increases because the delayed information that cells receive may significantly differ from the present state of the tissue. The time it takes to perform a neighbor exchange sets a timescale of cell mixing that may be important for the outcome of signaling. Here we review recent theoretical work on the interplay of timescales between cell mixing and signaling delays adopting the zebrafish segmentation clock as a model system. We discuss how this interplay can lead to spatial patterns of gene expression that could disrupt the normal formation of segment boundaries in the embryo. The effect of cell mixing and signaling delays highlights the importance of theoretical and experimental frameworks to understand collective cellular behaviors arising from the interplay of multiple timescales in embryonic developmental processes.
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10
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Xie L, Koukos G, Barck K, Foreman O, Lee WP, Brendza R, Eastham-Anderson J, McKenzie BS, Peterson A, Carano RAD. Micro-CT imaging and structural analysis of glomeruli in a model of Adriamycin-induced nephropathy. Am J Physiol Renal Physiol 2018; 316:F76-F89. [PMID: 30256127 DOI: 10.1152/ajprenal.00331.2018] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Glomeruli number and size are important for determining the pathogenesis of glomerular disease, chronic kidney disease, and hypertension. Moreover, renal injury can occur in specific cortical layers and alter glomerular spatial distribution. In this study, we present a comprehensive structural analysis of glomeruli in a model of Adriamycin (doxorubicin) nephropathy. Glomeruli are imaged (micro-CT at 10 × 10 × 10 μm3) in kidney specimens from C57Bl/6 mouse cohorts: control treated with saline ( n = 9) and Adriamycin treated with 20 mg/kg Adriamycin ( n = 7). Several indices were examined, including glomerular number, glomerular volume, glomerular volume heterogeneity, and spatial density at each glomerulus and in each cortical layer (superficial, midcortical, and juxtamedullary). In the Adriamycin-treated animals, glomerular number decreased significantly in the left kidney [control: 8,298 ± 221, Adriamycin: 6,781 ± 630 (mean ± SE)] and right kidney (control: 7,317 ± 367, Adriamycin: 5,522 ± 508), and glomerular volume heterogeneity increased significantly in the left kidney (control: 0.642 ± 0.015, Adriamycin: 0.786 ± 0.018) and right kidney (control: 0.739 ± 0.016, Adriamycin: 0.937 ± 0.023). Glomerular spatial density was not affected. Glomerular volume heterogeneity increased significantly in the superficial and midcortical layers of the Adriamycin cohort. Adriamycin did not affect glomerular volume or density metrics in the juxtamedullary region, suggesting a compensatory mechanism of juxtamedullary glomeruli to injury in the outer cortical layers. Left/right asymmetry was observed in kidney size and various glomeruli metrics. The methods presented here can be used to evaluate renal disease models with subtle changes in glomerular endowment locally or across the entire kidney, and they provide an imaging tool to investigate diverse interventions and therapeutic drugs.
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Affiliation(s)
- Luke Xie
- Biomedical Imaging, Genentech, South San Francisco, California
| | - Georgios Koukos
- Molecular Biology, Genentech, South San Francisco, California
| | - Kai Barck
- Biomedical Imaging, Genentech, South San Francisco, California
| | - Oded Foreman
- Pathology, Genentech, South San Francisco, California
| | - Wyne P Lee
- Translation Immunology, Genentech, South San Francisco, California
| | - Robert Brendza
- Neuroscience, Genentech, South San Francisco, California
| | | | - Brent S McKenzie
- Translation Immunology, Genentech, South San Francisco, California
| | - Andrew Peterson
- Molecular Biology, Genentech, South San Francisco, California
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11
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Boutin ME, Voss TC, Titus SA, Cruz-Gutierrez K, Michael S, Ferrer M. A high-throughput imaging and nuclear segmentation analysis protocol for cleared 3D culture models. Sci Rep 2018; 8:11135. [PMID: 30042482 PMCID: PMC6057966 DOI: 10.1038/s41598-018-29169-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 07/06/2018] [Indexed: 01/12/2023] Open
Abstract
Imaging and subsequent segmentation analysis in three-dimensional (3D) culture models are complicated by the light scattering that occurs when collecting fluorescent signal through multiple cell and extracellular matrix layers. For 3D cell culture models to be usable for drug discovery, effective and efficient imaging and analysis protocols need to be developed that enable high-throughput data acquisition and quantitative analysis of fluorescent signal. Here we report the first high-throughput protocol for optical clearing of spheroids, fluorescent high-content confocal imaging, 3D nuclear segmentation, and post-segmentation analysis. We demonstrate nuclear segmentation in multiple cell types, with accurate identification of fluorescently-labeled subpopulations, and develop a metric to assess the ability of clearing to improve nuclear segmentation deep within the tissue. Ultimately this analysis pipeline allows for previously unattainable segmentation throughput of 3D culture models due to increased sample clarity and optimized batch-processing analysis.
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Affiliation(s)
- Molly E Boutin
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, 9800 Medical Center Drive, Building B, Rockville, Maryland, 20850, USA.
| | - Ty C Voss
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, 9800 Medical Center Drive, Building B, Rockville, Maryland, 20850, USA
| | - Steven A Titus
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, 9800 Medical Center Drive, Building B, Rockville, Maryland, 20850, USA
| | - Kennie Cruz-Gutierrez
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, 9800 Medical Center Drive, Building B, Rockville, Maryland, 20850, USA
| | - Sam Michael
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, 9800 Medical Center Drive, Building B, Rockville, Maryland, 20850, USA
| | - Marc Ferrer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, 9800 Medical Center Drive, Building B, Rockville, Maryland, 20850, USA
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12
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Ju M, Choi Y, Seo J, Sa J, Lee S, Chung Y, Park D. A Kinect-Based Segmentation of Touching-Pigs for Real-Time Monitoring. SENSORS 2018; 18:s18061746. [PMID: 29843479 PMCID: PMC6021839 DOI: 10.3390/s18061746] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/23/2018] [Accepted: 05/27/2018] [Indexed: 02/06/2023]
Abstract
Segmenting touching-pigs in real-time is an important issue for surveillance cameras intended for the 24-h tracking of individual pigs. However, methods to do so have not yet been reported. We particularly focus on the segmentation of touching-pigs in a crowded pig room with low-contrast images obtained using a Kinect depth sensor. We reduce the execution time by combining object detection techniques based on a convolutional neural network (CNN) with image processing techniques instead of applying time-consuming operations, such as optimization-based segmentation. We first apply the fastest CNN-based object detection technique (i.e., You Only Look Once, YOLO) to solve the separation problem for touching-pigs. If the quality of the YOLO output is not satisfied, then we try to find the possible boundary line between the touching-pigs by analyzing the shape. Our experimental results show that this method is effective to separate touching-pigs in terms of both accuracy (i.e., 91.96%) and execution time (i.e., real-time execution), even with low-contrast images obtained using a Kinect depth sensor.
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Affiliation(s)
- Miso Ju
- Department of Computer Convergence Software, Korea University, Sejong City 30019, Korea.
| | - Younchang Choi
- Department of Computer Convergence Software, Korea University, Sejong City 30019, Korea.
| | - Jihyun Seo
- Department of Computer Convergence Software, Korea University, Sejong City 30019, Korea.
| | - Jaewon Sa
- Department of Computer Convergence Software, Korea University, Sejong City 30019, Korea.
| | - Sungju Lee
- Department of Computer Convergence Software, Korea University, Sejong City 30019, Korea.
| | - Yongwha Chung
- Department of Computer Convergence Software, Korea University, Sejong City 30019, Korea.
| | - Daihee Park
- Department of Computer Convergence Software, Korea University, Sejong City 30019, Korea.
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13
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Liao BK, Oates AC. Delta-Notch signalling in segmentation. ARTHROPOD STRUCTURE & DEVELOPMENT 2017; 46:429-447. [PMID: 27888167 PMCID: PMC5446262 DOI: 10.1016/j.asd.2016.11.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 11/20/2016] [Accepted: 11/21/2016] [Indexed: 06/06/2023]
Abstract
Modular body organization is found widely across multicellular organisms, and some of them form repetitive modular structures via the process of segmentation. It's vastly interesting to understand how these regularly repeated structures are robustly generated from the underlying noise in biomolecular interactions. Recent studies from arthropods reveal similarities in segmentation mechanisms with vertebrates, and raise the possibility that the three phylogenetic clades, annelids, arthropods and chordates, might share homology in this process from a bilaterian ancestor. Here, we discuss vertebrate segmentation with particular emphasis on the role of the Notch intercellular signalling pathway. We introduce vertebrate segmentation and Notch signalling, pointing out historical milestones, then describe existing models for the Notch pathway in the synchronization of noisy neighbouring oscillators, and a new role in the modulation of gene expression wave patterns. We ask what functions Notch signalling may have in arthropod segmentation and explore the relationship between Notch-mediated lateral inhibition and synchronization. Finally, we propose open questions and technical challenges to guide future investigations into Notch signalling in segmentation.
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Affiliation(s)
- Bo-Kai Liao
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK
| | - Andrew C Oates
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK; Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK.
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14
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Bhavna R, Uriu K, Valentin G, Tinevez JY, Oates AC. Correction: Object Segmentation and Ground Truth in 3D Embryonic Imaging. PLoS One 2016; 11:e0161550. [PMID: 27529424 PMCID: PMC4986982 DOI: 10.1371/journal.pone.0161550] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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