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Donato MT, Tolosa L. High-Content Screening for the Detection of Drug-Induced Oxidative Stress in Liver Cells. Antioxidants (Basel) 2021; 10:antiox10010106. [PMID: 33451093 PMCID: PMC7828515 DOI: 10.3390/antiox10010106] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/08/2021] [Accepted: 01/10/2021] [Indexed: 12/16/2022] Open
Abstract
Drug-induced liver injury (DILI) remains a major cause of drug development failure, post-marketing warnings and restriction of use. An improved understanding of the mechanisms underlying DILI is required for better drug design and development. Enhanced reactive oxygen species (ROS) levels may cause a wide spectrum of oxidative damage, which has been described as a major mechanism implicated in DILI. Several cell-based assays have been developed as in vitro tools for early safety risk assessments. Among them, high-content screening technology has been used for the identification of modes of action, the determination of the level of injury and the discovery of predictive biomarkers for the safety assessment of compounds. In this paper, we review the value of in vitro high-content screening studies and evaluate how to assess oxidative stress induced by drugs in hepatic cells, demonstrating the detection of pre-lethal mechanisms of DILI as a powerful tool in human toxicology.
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Affiliation(s)
- María Teresa Donato
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Valencia, 46010 Valencia, Spain
- Correspondence: (M.T.D.); (L.T.); Tel.: +34-961-246-649 (M.D.); +34-961-246-619 (L.T.)
| | - Laia Tolosa
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain
- Correspondence: (M.T.D.); (L.T.); Tel.: +34-961-246-649 (M.D.); +34-961-246-619 (L.T.)
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2
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Donato MT, Tolosa L. Application of high-content screening for the study of hepatotoxicity: Focus on food toxicology. Food Chem Toxicol 2020; 147:111872. [PMID: 33220391 DOI: 10.1016/j.fct.2020.111872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 10/12/2020] [Accepted: 11/15/2020] [Indexed: 01/17/2023]
Abstract
Safety evaluation of thousands of chemicals that are directly added to or come in contact with food is needed. Due to the central role of the liver in intermediary and energy metabolism and in the biotransformation of foreign compounds, the hepatotoxicity assessment is essential. New approach methodologies have been proposed for the safety evaluation of compounds with the idea of rapidly gaining insight into effects on biochemical mechanisms and cellular processes and screening large number of compounds. In this sense, high-content screening (HCS) is the application of automated microscopy and image analysis for better understanding of complex biological functions and mechanisms of toxicity. HCS multiparametric measurements have been shown to be a useful tool in early toxicity testing during drug development, but also in assessing the impact from food chemicals and environmental toxicants. Reviewing the use of cellular imaging technology in the safety evaluation of food-relevant chemicals offers evidence about the impact of this technology in safety assessment.
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Affiliation(s)
- M Teresa Donato
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe, Valencia, 46026, Spain; Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Valencia, Valencia, 46010, Spain.
| | - Laia Tolosa
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe, Valencia, 46026, Spain.
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3
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Waithe D, Brown JM, Reglinski K, Diez-Sevilla I, Roberts D, Eggeling C. Object detection networks and augmented reality for cellular detection in fluorescence microscopy. J Cell Biol 2020; 219:e201903166. [PMID: 32854116 PMCID: PMC7659718 DOI: 10.1083/jcb.201903166] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/05/2020] [Accepted: 07/21/2020] [Indexed: 01/10/2023] Open
Abstract
Object detection networks are high-performance algorithms famously applied to the task of identifying and localizing objects in photography images. We demonstrate their application for the classification and localization of cells in fluorescence microscopy by benchmarking four leading object detection algorithms across multiple challenging 2D microscopy datasets. Furthermore we develop and demonstrate an algorithm that can localize and image cells in 3D, in close to real time, at the microscope using widely available and inexpensive hardware. Furthermore, we exploit the fast processing of these networks and develop a simple and effective augmented reality (AR) system for fluorescence microscopy systems using a display screen and back-projection onto the eyepiece. We show that it is possible to achieve very high classification accuracy using datasets with as few as 26 images present. Using our approach, it is possible for relatively nonskilled users to automate detection of cell classes with a variety of appearances and enable new avenues for automation of fluorescence microscopy acquisition pipelines.
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Affiliation(s)
- Dominic Waithe
- Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Medical Research Council Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jill M. Brown
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Katharina Reglinski
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
- University Hospital Jena, Jena, Germany
| | - Isabel Diez-Sevilla
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - David Roberts
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Christian Eggeling
- Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Jena, Germany
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4
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Quantitative 3D analysis of complex single border cell behaviors in coordinated collective cell migration. Nat Commun 2017; 8:14905. [PMID: 28374738 PMCID: PMC5382290 DOI: 10.1038/ncomms14905] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 02/10/2017] [Indexed: 11/08/2022] Open
Abstract
Understanding the mechanisms of collective cell migration is crucial for cancer metastasis, wound healing and many developmental processes. Imaging a migrating cluster in vivo is feasible, but the quantification of individual cell behaviours remains challenging. We have developed an image analysis toolkit, CCMToolKit, to quantify the Drosophila border cell system. In addition to chaotic motion, previous studies reported that the migrating cells are able to migrate in a highly coordinated pattern. We quantify the rotating and running migration modes in 3D while also observing a range of intermediate behaviours. Running mode is driven by cluster external protrusions. Rotating mode is associated with cluster internal cell extensions that could not be easily characterized. Although the cluster moves slower while rotating, individual cells retain their mobility and are in fact slightly more active than in running mode. We also show that individual cells may exchange positions during migration.
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5
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Morphometry of organ cultured corneal endothelium using Voronoi segmentation. Cell Tissue Bank 2017; 18:167-183. [DOI: 10.1007/s10561-017-9622-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 03/29/2017] [Indexed: 10/19/2022]
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6
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Singh M, Kalaw EM, Giron DM, Chong KT, Tan CL, Lee HK. Gland segmentation in prostate histopathological images. J Med Imaging (Bellingham) 2017; 4:027501. [PMID: 28653016 PMCID: PMC5479152 DOI: 10.1117/1.jmi.4.2.027501] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/01/2017] [Indexed: 01/02/2023] Open
Abstract
Glandular structural features are important for the tumor pathologist in the assessment of cancer malignancy of prostate tissue slides. The varying shapes and sizes of glands combined with the tedious manual observation task can result in inaccurate assessment. There are also discrepancies and low-level agreement among pathologists, especially in cases of Gleason pattern 3 and pattern 4 prostate adenocarcinoma. An automated gland segmentation system can highlight various glandular shapes and structures for further analysis by the pathologist. These objective highlighted patterns can help reduce the assessment variability. We propose an automated gland segmentation system. Forty-three hematoxylin and eosin-stained images were acquired from prostate cancer tissue slides and were manually annotated for gland, lumen, periacinar retraction clefting, and stroma regions. Our automated gland segmentation system was trained using these manual annotations. It identifies these regions using a combination of pixel and object-level classifiers by incorporating local and spatial information for consolidating pixel-level classification results into object-level segmentation. Experimental results show that our method outperforms various texture and gland structure-based gland segmentation algorithms in the literature. Our method has good performance and can be a promising tool to help decrease interobserver variability among pathologists.
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Affiliation(s)
- Malay Singh
- National University of Singapore, School of Computing, Department of Computer Science, Singapore
- Bioinformatics Institute, Imaging Informatics Division, Matrix, Singapore
| | | | | | - Kian-Tai Chong
- Tan Tock Seng Hospital, Department of Urology, Novena, Singapore
| | - Chew Lim Tan
- National University of Singapore, School of Computing, Department of Computer Science, Singapore
| | - Hwee Kuan Lee
- National University of Singapore, School of Computing, Department of Computer Science, Singapore
- Bioinformatics Institute, Imaging Informatics Division, Matrix, Singapore
- Institute for Infocomm Research, Image and Pervasive Access Lab, Connexis, Singapore
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7
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Bougen-Zhukov N, Loh SY, Lee HK, Loo LH. Large-scale image-based screening and profiling of cellular phenotypes. Cytometry A 2016; 91:115-125. [PMID: 27434125 DOI: 10.1002/cyto.a.22909] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cellular phenotypes are observable characteristics of cells resulting from the interactions of intrinsic and extrinsic chemical or biochemical factors. Image-based phenotypic screens under large numbers of basal or perturbed conditions can be used to study the influences of these factors on cellular phenotypes. Hundreds to thousands of phenotypic descriptors can also be quantified from the images of cells under each of these experimental conditions. Therefore, huge amounts of data can be generated, and the analysis of these data has become a major bottleneck in large-scale phenotypic screens. Here, we review current experimental and computational methods for large-scale image-based phenotypic screens. Our focus is on phenotypic profiling, a computational procedure for constructing quantitative and compact representations of cellular phenotypes based on the images collected in these screens. © 2016 International Society for Advancement of Cytometry.
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Affiliation(s)
- Nicola Bougen-Zhukov
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, 138671, Singapore
| | - Sheng Yang Loh
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, 138671, Singapore
| | - Hwee Kuan Lee
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, 138671, Singapore
| | - Lit-Hsin Loo
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, 138671, Singapore.,Department of Pharmacology, School of Medicine, National University of Singapore, Singapore, 117600, Singapore
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8
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Ong KH, De J, Cheng L, Ahmed S, Yu W. NeuronCyto II: An automatic and quantitative solution for crossover neural cells in high throughput screening. Cytometry A 2016; 89:747-54. [PMID: 27233092 PMCID: PMC5089663 DOI: 10.1002/cyto.a.22872] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 04/04/2016] [Accepted: 04/21/2016] [Indexed: 11/21/2022]
Abstract
Microscopy is a fundamental technology driving new biological discoveries. Today microscopy allows a large number of images to be acquired using, for example, High Throughput Screening (HTS) and 4D imaging. It is essential to be able to interrogate these images and extract quantitative information in an automated fashion. In the context of neurobiology, it is important to automatically quantify the morphology of neurons in terms of neurite number, length, branching and complexity, etc. One major issue in quantification of neuronal morphology is the “crossover” problem where neurites cross and it is difficult to assign which neurite belongs to which cell body. In the present study, we provide a solution to the “crossover” problem, the software package NeuronCyto II. NeuronCyto II is an interactive and user‐friendly software package for automatic neurite quantification. It has a well‐designed graphical user interface (GUI) with only a few free parameters allowing users to optimize the software by themselves and extract relevant quantitative information routinely. Users are able to interact with the images and the numerical features through the Result Inspector. The processing of neurites without crossover was presented in our previous work. Our solution for the “crossover” problem is developed based on our recently published work with directed graph theory. Both methods are implemented in NeuronCyto II. The results show that our solution is able to significantly improve the reliability and accuracy of the neurons displaying “crossover.” NeuronCyto II is freely available at the website: https://sites.google.com/site/neuroncyto/, which includes user support and where software upgrades will also be placed in the future. © 2016 The Authors. Cytometry Part A Published by Wiley Periodicals, Inc. on behalf of ISAC.
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Affiliation(s)
- Kok Haur Ong
- Central Imaging Facility, Institute of Molecule and Cell Biology (IMCB), a*STAR, Singapore
| | - Jaydeep De
- Imaging Informatics Division, Bioinformatics Institute (BII), a*STAR, Singapore
| | - Li Cheng
- Imaging Informatics Division, Bioinformatics Institute (BII), a*STAR, Singapore
| | - Sohail Ahmed
- Neural Stem Cell Lab, Institute of Medical Biology (IMB), a*STAR, Singapore
| | - Weimiao Yu
- Central Imaging Facility, Institute of Molecule and Cell Biology (IMCB), a*STAR, Singapore
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9
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Xing F, Yang L. Robust Nucleus/Cell Detection and Segmentation in Digital Pathology and Microscopy Images: A Comprehensive Review. IEEE Rev Biomed Eng 2016; 9:234-63. [PMID: 26742143 PMCID: PMC5233461 DOI: 10.1109/rbme.2016.2515127] [Citation(s) in RCA: 212] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Digital pathology and microscopy image analysis is widely used for comprehensive studies of cell morphology or tissue structure. Manual assessment is labor intensive and prone to interobserver variations. Computer-aided methods, which can significantly improve the objectivity and reproducibility, have attracted a great deal of interest in recent literature. Among the pipeline of building a computer-aided diagnosis system, nucleus or cell detection and segmentation play a very important role to describe the molecular morphological information. In the past few decades, many efforts have been devoted to automated nucleus/cell detection and segmentation. In this review, we provide a comprehensive summary of the recent state-of-the-art nucleus/cell segmentation approaches on different types of microscopy images including bright-field, phase-contrast, differential interference contrast, fluorescence, and electron microscopies. In addition, we discuss the challenges for the current methods and the potential future work of nucleus/cell detection and segmentation.
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10
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Zhang X, Xing F, Su H, Yang L, Zhang S. High-throughput histopathological image analysis via robust cell segmentation and hashing. Med Image Anal 2015; 26:306-15. [PMID: 26599156 PMCID: PMC4679540 DOI: 10.1016/j.media.2015.10.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 05/13/2015] [Accepted: 10/16/2015] [Indexed: 11/27/2022]
Abstract
Computer-aided diagnosis of histopathological images usually requires to examine all cells for accurate diagnosis. Traditional computational methods may have efficiency issues when performing cell-level analysis. In this paper, we propose a robust and scalable solution to enable such analysis in a real-time fashion. Specifically, a robust segmentation method is developed to delineate cells accurately using Gaussian-based hierarchical voting and repulsive balloon model. A large-scale image retrieval approach is also designed to examine and classify each cell of a testing image by comparing it with a massive database, e.g., half-million cells extracted from the training dataset. We evaluate this proposed framework on a challenging and important clinical use case, i.e., differentiation of two types of lung cancers (the adenocarcinoma and squamous carcinoma), using thousands of lung microscopic tissue images extracted from hundreds of patients. Our method has achieved promising accuracy and running time by searching among half-million cells .
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Affiliation(s)
- Xiaofan Zhang
- Department of Computer Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Fuyong Xing
- Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Hai Su
- Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Lin Yang
- Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL 32611, USA; Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Shaoting Zhang
- Department of Computer Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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Detection of Dendritic Spines Using Wavelet-Based Conditional Symmetric Analysis and Regularized Morphological Shared-Weight Neural Networks. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2015; 2015:454076. [PMID: 26692046 PMCID: PMC4672122 DOI: 10.1155/2015/454076] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/02/2015] [Accepted: 09/27/2015] [Indexed: 01/17/2023]
Abstract
Identification and detection of dendritic spines in neuron images are of high interest in diagnosis and treatment of neurological and psychiatric disorders (e.g., Alzheimer's disease, Parkinson's diseases, and autism). In this paper, we have proposed a novel automatic approach using wavelet-based conditional symmetric analysis and regularized morphological shared-weight neural networks (RMSNN) for dendritic spine identification involving the following steps: backbone extraction, localization of dendritic spines, and classification. First, a new algorithm based on wavelet transform and conditional symmetric analysis has been developed to extract backbone and locate the dendrite boundary. Then, the RMSNN has been proposed to classify the spines into three predefined categories (mushroom, thin, and stubby). We have compared our proposed approach against the existing methods. The experimental result demonstrates that the proposed approach can accurately locate the dendrite and accurately classify the spines into three categories with the accuracy of 99.1% for “mushroom” spines, 97.6% for “stubby” spines, and 98.6% for “thin” spines.
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12
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Lim J, Lee HK, Yu W, Ahmed S. Light sheet fluorescence microscopy (LSFM): past, present and future. Analyst 2015; 139:4758-68. [PMID: 25118817 DOI: 10.1039/c4an00624k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Light sheet fluorescence microscopy (LSFM) has emerged as an important imaging modality to follow biology in live 3D samples over time with reduced phototoxicity and photobleaching. In particular, LSFM has been instrumental in revealing the detail of early embryonic development of Zebrafish, Drosophila, and C. elegans. Open access projects, DIY-SPIM, OpenSPIM, and OpenSPIN, now allow LSFM to be set-up easily and at low cost. The aim of this paper is to facilitate the set-up and use of LSFM by reviewing and comparing open access projects, image processing tools and future challenges.
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Affiliation(s)
- John Lim
- Institute of Medical Biology, 8A Biomedical Grove, Immunos 5.37, Singapore 138648, Singapore.
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13
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Bajcsy P, Cardone A, Chalfoun J, Halter M, Juba D, Kociolek M, Majurski M, Peskin A, Simon C, Simon M, Vandecreme A, Brady M. Survey statistics of automated segmentations applied to optical imaging of mammalian cells. BMC Bioinformatics 2015; 16:330. [PMID: 26472075 PMCID: PMC4608288 DOI: 10.1186/s12859-015-0762-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 10/07/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The goal of this survey paper is to overview cellular measurements using optical microscopy imaging followed by automated image segmentation. The cellular measurements of primary interest are taken from mammalian cells and their components. They are denoted as two- or three-dimensional (2D or 3D) image objects of biological interest. In our applications, such cellular measurements are important for understanding cell phenomena, such as cell counts, cell-scaffold interactions, cell colony growth rates, or cell pluripotency stability, as well as for establishing quality metrics for stem cell therapies. In this context, this survey paper is focused on automated segmentation as a software-based measurement leading to quantitative cellular measurements. METHODS We define the scope of this survey and a classification schema first. Next, all found and manually filteredpublications are classified according to the main categories: (1) objects of interests (or objects to be segmented), (2) imaging modalities, (3) digital data axes, (4) segmentation algorithms, (5) segmentation evaluations, (6) computational hardware platforms used for segmentation acceleration, and (7) object (cellular) measurements. Finally, all classified papers are converted programmatically into a set of hyperlinked web pages with occurrence and co-occurrence statistics of assigned categories. RESULTS The survey paper presents to a reader: (a) the state-of-the-art overview of published papers about automated segmentation applied to optical microscopy imaging of mammalian cells, (b) a classification of segmentation aspects in the context of cell optical imaging, (c) histogram and co-occurrence summary statistics about cellular measurements, segmentations, segmented objects, segmentation evaluations, and the use of computational platforms for accelerating segmentation execution, and (d) open research problems to pursue. CONCLUSIONS The novel contributions of this survey paper are: (1) a new type of classification of cellular measurements and automated segmentation, (2) statistics about the published literature, and (3) a web hyperlinked interface to classification statistics of the surveyed papers at https://isg.nist.gov/deepzoomweb/resources/survey/index.html.
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Affiliation(s)
- Peter Bajcsy
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Antonio Cardone
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Joe Chalfoun
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Michael Halter
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Derek Juba
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | | | - Michael Majurski
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Adele Peskin
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Carl Simon
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Mylene Simon
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Antoine Vandecreme
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Mary Brady
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
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14
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Liempi A, Castillo C, Cerda M, Droguett D, Duaso J, Barahona K, Hernández A, Díaz-Luján C, Fretes R, Härtel S, Kemmerling U. Trypanosoma cruzi infectivity assessment in "in vitro" culture systems by automated cell counting. Acta Trop 2015; 143:47-50. [PMID: 25553972 DOI: 10.1016/j.actatropica.2014.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 11/04/2014] [Accepted: 12/09/2014] [Indexed: 10/24/2022]
Abstract
Chagas disease is an endemic, neglected tropical disease in Latin America that is caused by the protozoan parasite Trypanosoma cruzi. In vitro models constitute the first experimental approach to study the physiopathology of the disease and to assay potential new trypanocidal agents. Here, we report and describe clearly the use of commercial software (MATLAB(®)) to quantify T. cruzi amastigotes and infected mammalian cells (BeWo) and compared this analysis with the manual one. There was no statistically significant difference between the manual and the automatic quantification of the parasite; the two methods showed a correlation analysis r(2) value of 0.9159. The most significant advantage of the automatic quantification was the efficiency of the analysis. The drawback of this automated cell counting method was that some parasites were assigned to the wrong BeWo cell, however this data did not exceed 5% when adequate experimental conditions were chosen. We conclude that this quantification method constitutes an excellent tool for evaluating the parasite load in cells and therefore constitutes an easy and reliable ways to study parasite infectivity.
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15
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Herr KJ, Tsang YHN, Ong JWE, Li Q, Yap LL, Yu W, Yin H, Bogorad RL, Dahlman JE, Chan YG, Bay BH, Singaraja R, Anderson DG, Koteliansky V, Viasnoff V, Thiery JP. Loss of α-catenin elicits a cholestatic response and impairs liver regeneration. Sci Rep 2014; 4:6835. [PMID: 25355493 PMCID: PMC4213774 DOI: 10.1038/srep06835] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/10/2014] [Indexed: 12/25/2022] Open
Abstract
The liver is unique in its capacity to regenerate after injury, during which hepatocytes actively divide and establish cell-cell contacts through cell adhesion complexes. Here, we demonstrate that the loss of α-catenin, a well-established adhesion component, dramatically disrupts liver regeneration. Using a partial hepatectomy model, we show that regenerated livers from α-catenin knockdown mice are grossly larger than control regenerated livers, with an increase in cell size and proliferation. This increased proliferation correlated with increased YAP activation, implicating α-catenin in the Hippo/YAP pathway. Additionally, α-catenin knockdown mice exhibited a phenotype reminiscent of clinical cholestasis, with drastically altered bile canaliculi, elevated levels of bile components and signs of jaundice and inflammation. The disrupted regenerative capacity is a result of actin cytoskeletal disorganisation, leading to a loss of apical microvilli, dilated lumens in the bile canaliculi, and leaky tight junctions. This study illuminates a novel, essential role for α-catenin in liver regeneration.
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Affiliation(s)
- Keira Joann Herr
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Ying-hung Nicole Tsang
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Joanne Wei En Ong
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Qiushi Li
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Lai Lai Yap
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Weimiao Yu
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Hao Yin
- Koch Institute for Integrative Cancer Research, MIT, Massachusetts, U.S.A
| | - Roman L Bogorad
- Koch Institute for Integrative Cancer Research, MIT, Massachusetts, U.S.A
| | - James E Dahlman
- 1] Koch Institute for Integrative Cancer Research, MIT, Massachusetts, U.S.A [2] Department of Biology, MIT, Massachusetts, U.S.A [3] Institute for Medical Engineering and Science, MIT, Massachusetts, U.S.A
| | - Yee Gek Chan
- Department of Anatomy, National University of Singapore, Singapore
| | - Boon Huat Bay
- Department of Anatomy, National University of Singapore, Singapore
| | - Roshni Singaraja
- Translational Laboratory in Genetic Medicine, A*STAR, Singapore, Singapore
| | - Daniel G Anderson
- 1] Koch Institute for Integrative Cancer Research, MIT, Massachusetts, U.S.A [2] Institute for Medical Engineering and Science, MIT, Massachusetts, U.S.A [3] Department of Chemical Engineering, MIT, Massachusetts, U.S.A [4] Department of Anaesthesiology, Children's Hospital Boston, Harvard Medical School, Massachusetts, U.S.A
| | - Victor Koteliansky
- Skolkovo Institute of Science and Technology ul, Skolkovo, Russian Federation
| | - Virgile Viasnoff
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Jean Paul Thiery
- 1] Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore [2] Department of Biochemistry School of Medicine National University of Singapore, Singapore [3] Cancer Science Institute National University of Singapore, Singapore
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Su H, Xing F, Lee JD, Peterson CA, Yang L. Automatic Myonuclear Detection in Isolated Single Muscle Fibers Using Robust Ellipse Fitting and Sparse Representation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2014; 11:714-726. [PMID: 26356342 PMCID: PMC4669954 DOI: 10.1109/tcbb.2013.151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Accurate and robust detection of myonuclei in isolated single muscle fibers is required to calculate myonuclear domain size. However, this task is challenging because: 1) shape and size variations of the nuclei, 2) overlapping nuclear clumps, and 3) multiple z-stack images with out-of-focus regions. In this paper, we have proposed a novel automatic detection algorithm to robustly quantify myonuclei in isolated single skeletal muscle fibers. The original z-stack images are first converted into one all-in-focus image using multi-focus image fusion. A sufficient number of ellipse fitting hypotheses are then generated from the myonuclei contour segments using heteroscedastic errors-in-variables (HEIV) regression. A set of representative training samples and a set of discriminative features are selected by a two-stage sparse model. The selected samples with representative features are utilized to train a classifier to select the best candidates. A modified inner geodesic distance based mean-shift clustering algorithm is used to produce the final nuclei detection results. The proposed method was extensively tested using 42 sets of z-stack images containing over 1,500 myonuclei. The method demonstrates excellent results that are better than current state-of-the-art approaches.
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17
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Quan T, Li J, Zhou H, Li S, Zheng T, Yang Z, Luo Q, Gong H, Zeng S. Digital reconstruction of the cell body in dense neural circuits using a spherical-coordinated variational model. Sci Rep 2014; 4:4970. [PMID: 24829141 PMCID: PMC4021323 DOI: 10.1038/srep04970] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 04/09/2014] [Indexed: 02/03/2023] Open
Abstract
Mapping the neuronal circuits is essential to understand brain function. Recent technological advancements have made it possible to acquire the brain atlas at single cell resolution. Digital reconstruction of the neural circuits down to this level across the whole brain would significantly facilitate brain studies. However, automatic reconstruction of the dense neural connections from microscopic image still remains a challenge. Here we developed a spherical-coordinate based variational model to reconstruct the shape of the cell body i.e. soma, as one of the procedures for this purpose. When intuitively processing the volumetric images in the spherical coordinate system, the reconstruction of somas with variational model is no longer sensitive to the interference of the complicated neuronal morphology, and could automatically and robustly achieve accurate soma shape regardless of the dense spatial distribution, and diversity in cell size, and morphology. We believe this method would speed drawing the neural circuits and boost brain studies.
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Affiliation(s)
- Tingwei Quan
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology- Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
- School of Mathematics and Statistics, Hubei University of Education, Wuhan 430205, China
- These authors contributed equally to this work
| | - Jing Li
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology- Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
- These authors contributed equally to this work
| | - Hang Zhou
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology- Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shiwei Li
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology- Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Ting Zheng
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology- Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zhongqing Yang
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology- Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Qingming Luo
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology- Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology- Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shaoqun Zeng
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology- Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
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18
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Schmitz C, Eastwood BS, Tappan SJ, Glaser JR, Peterson DA, Hof PR. Current automated 3D cell detection methods are not a suitable replacement for manual stereologic cell counting. Front Neuroanat 2014; 8:27. [PMID: 24847213 PMCID: PMC4019880 DOI: 10.3389/fnana.2014.00027] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 04/16/2014] [Indexed: 12/27/2022] Open
Abstract
Stereologic cell counting has had a major impact on the field of neuroscience. A major bottleneck in stereologic cell counting is that the user must manually decide whether or not each cell is counted according to three-dimensional (3D) stereologic counting rules by visual inspection within hundreds of microscopic fields-of-view per investigated brain or brain region. Reliance on visual inspection forces stereologic cell counting to be very labor-intensive and time-consuming, and is the main reason why biased, non-stereologic two-dimensional (2D) “cell counting” approaches have remained in widespread use. We present an evaluation of the performance of modern automated cell detection and segmentation algorithms as a potential alternative to the manual approach in stereologic cell counting. The image data used in this study were 3D microscopic images of thick brain tissue sections prepared with a variety of commonly used nuclear and cytoplasmic stains. The evaluation compared the numbers and locations of cells identified unambiguously and counted exhaustively by an expert observer with those found by three automated 3D cell detection algorithms: nuclei segmentation from the FARSIGHT toolkit, nuclei segmentation by 3D multiple level set methods, and the 3D object counter plug-in for ImageJ. Of these methods, FARSIGHT performed best, with true-positive detection rates between 38 and 99% and false-positive rates from 3.6 to 82%. The results demonstrate that the current automated methods suffer from lower detection rates and higher false-positive rates than are acceptable for obtaining valid estimates of cell numbers. Thus, at present, stereologic cell counting with manual decision for object inclusion according to unbiased stereologic counting rules remains the only adequate method for unbiased cell quantification in histologic tissue sections.
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Affiliation(s)
- Christoph Schmitz
- Department of Neuroanatomy, Ludwig-Maximilians-University of Munich Munich, Germany
| | | | - Susan J Tappan
- MBF Bioscience Williston, VT, USA ; MBF Laboratories Williston, VT, USA
| | - Jack R Glaser
- MBF Bioscience Williston, VT, USA ; MBF Laboratories Williston, VT, USA
| | - Daniel A Peterson
- Center for Stem Cell and Regenerative Medicine, Rosalind Franklin University of Medicine and Science North Chicago, IL, USA
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
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19
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Maurya AK, Ben J, Zhao Z, Lee RTH, Niah W, Ng ASM, Iyu A, Yu W, Elworthy S, van Eeden FJM, Ingham PW. Positive and negative regulation of Gli activity by Kif7 in the zebrafish embryo. PLoS Genet 2013; 9:e1003955. [PMID: 24339784 PMCID: PMC3854788 DOI: 10.1371/journal.pgen.1003955] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 09/30/2013] [Indexed: 12/21/2022] Open
Abstract
Loss of function mutations of Kif7, the vertebrate orthologue of the Drosophila Hh pathway component Costal2, cause defects in the limbs and neural tubes of mice, attributable to ectopic expression of Hh target genes. While this implies a functional conservation of Cos2 and Kif7 between flies and vertebrates, the association of Kif7 with the primary cilium, an organelle absent from most Drosophila cells, suggests their mechanisms of action may have diverged. Here, using mutant alleles induced by Zinc Finger Nuclease-mediated targeted mutagenesis, we show that in zebrafish, Kif7 acts principally to suppress the activity of the Gli1 transcription factor. Notably, we find that endogenous Kif7 protein accumulates not only in the primary cilium, as previously observed in mammalian cells, but also in cytoplasmic puncta that disperse in response to Hh pathway activation. Moreover, we show that Drosophila Costal2 can substitute for Kif7, suggesting a conserved mode of action of the two proteins. We show that Kif7 interacts with both Gli1 and Gli2a and suggest that it functions to sequester Gli proteins in the cytoplasm, in a manner analogous to the regulation of Ci by Cos2 in Drosophila. We also show that zebrafish Kif7 potentiates Gli2a activity by promoting its dissociation from the Suppressor of Fused (Sufu) protein and present evidence that it mediates a Smo dependent modification of the full length form of Gli2a. Surprisingly, the function of Kif7 in the zebrafish embryo appears restricted principally to mesodermal derivatives, its inactivation having little effect on neural tube patterning, even when Sufu protein levels are depleted. Remarkably, zebrafish lacking all Kif7 function are viable, in contrast to the peri-natal lethality of mouse kif7 mutants but similar to some Acrocallosal or Joubert syndrome patients who are homozygous for loss of function KIF7 alleles.
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Affiliation(s)
- Ashish Kumar Maurya
- A*STAR Institute of Molecular & Cell Biology, Proteos, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Jin Ben
- A*STAR Institute of Molecular & Cell Biology, Proteos, Singapore
| | - Zhonghua Zhao
- A*STAR Institute of Molecular & Cell Biology, Proteos, Singapore
| | | | - Weixin Niah
- A*STAR Institute of Molecular & Cell Biology, Proteos, Singapore
| | | | - Audrey Iyu
- A*STAR Institute of Molecular & Cell Biology, Proteos, Singapore
| | - Weimiao Yu
- A*STAR Institute of Molecular & Cell Biology, Proteos, Singapore
| | - Stone Elworthy
- MRC Centre for Developmental and Biomedical Genetics, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Fredericus J. M. van Eeden
- MRC Centre for Developmental and Biomedical Genetics, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Philip William Ingham
- A*STAR Institute of Molecular & Cell Biology, Proteos, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
- MRC Centre for Developmental and Biomedical Genetics, University of Sheffield, Western Bank, Sheffield, United Kingdom
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20
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Jaccard N, Griffin LD, Keser A, Macown RJ, Super A, Veraitch FS, Szita N. Automated method for the rapid and precise estimation of adherent cell culture characteristics from phase contrast microscopy images. Biotechnol Bioeng 2013; 111:504-17. [PMID: 24037521 PMCID: PMC4260842 DOI: 10.1002/bit.25115] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 07/23/2013] [Accepted: 09/09/2013] [Indexed: 12/12/2022]
Abstract
The quantitative determination of key adherent cell culture characteristics such as confluency, morphology, and cell density is necessary for the evaluation of experimental outcomes and to provide a suitable basis for the establishment of robust cell culture protocols. Automated processing of images acquired using phase contrast microscopy (PCM), an imaging modality widely used for the visual inspection of adherent cell cultures, could enable the non-invasive determination of these characteristics. We present an image-processing approach that accurately detects cellular objects in PCM images through a combination of local contrast thresholding and post hoc correction of halo artifacts. The method was thoroughly validated using a variety of cell lines, microscope models and imaging conditions, demonstrating consistently high segmentation performance in all cases and very short processing times (<1 s per 1,208 × 960 pixels image). Based on the high segmentation performance, it was possible to precisely determine culture confluency, cell density, and the morphology of cellular objects, demonstrating the wide applicability of our algorithm for typical microscopy image processing pipelines. Furthermore, PCM image segmentation was used to facilitate the interpretation and analysis of fluorescence microscopy data, enabling the determination of temporal and spatial expression patterns of a fluorescent reporter. We created a software toolbox (PHANTAST) that bundles all the algorithms and provides an easy to use graphical user interface. Source-code for MATLAB and ImageJ is freely available under a permissive open-source license. Biotechnol. Bioeng. 2014;111: 504–517. © 2013 Wiley Periodicals, Inc.
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Affiliation(s)
- Nicolas Jaccard
- Department of Biochemical Engineering, University College London, Torrington Place, London, WC1E 7JE, United Kingdom; Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London, United Kingdom
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21
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Aref AR, Huang RYJ, Yu W, Chua KN, Sun W, Tu TY, Bai J, Sim WJ, Zervantonakis IK, Thiery JP, Kamm RD. Screening therapeutic EMT blocking agents in a three-dimensional microenvironment. Integr Biol (Camb) 2013; 5:381-9. [PMID: 23172153 DOI: 10.1039/c2ib20209c] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Epithelial-mesenchymal transition (EMT) plays a critical role in the early stages of dissemination of carcinoma leading to metastatic tumors, which are responsible for over 90% of all cancer-related deaths. Current therapeutic regimens, however, have been ineffective in the cure of metastatic cancer, thus an urgent need exists to revisit existing protocols and to improve the efficacy of newly developed therapeutics. Strategies based on preventing EMT could potentially contribute to improving the outcome of advanced stage cancers. To achieve this goal new assays are needed to identify targeted drugs capable of interfering with EMT or to revert the mesenchymal-like phenotype of carcinoma to an epithelial-like state. Current assays are limited to examining the dispersion of carcinoma cells in isolation in conventional 2-dimensional (2D) microwell systems, an approach that fails to account for the 3-dimensional (3D) environment of the tumor or the essential interactions that occur with other nearby cell types in the tumor microenvironment. Here we present a microfluidic system that integrates tumor cell spheroids in a 3D hydrogel scaffold, in close co-culture with an endothelial monolayer. Drug candidates inhibiting receptor activation or signal transduction pathways implicated in EMT have been tested using dispersion of A549 lung adenocarcinoma cell spheroids as a metric of effectiveness. We demonstrate significant differences in response to drugs between 2D and 3D, and between monoculture and co-culture.
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Affiliation(s)
- Amir R Aref
- BioSystems and Micromechanics IRG, S16-07, SMART, Singapore 117543, Singapore
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22
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Automated and accurate detection of soma location and surface morphology in large-scale 3D neuron images. PLoS One 2013; 8:e62579. [PMID: 23638117 PMCID: PMC3634810 DOI: 10.1371/journal.pone.0062579] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 03/21/2013] [Indexed: 11/19/2022] Open
Abstract
Automated and accurate localization and morphometry of somas in 3D neuron images is essential for quantitative studies of neural networks in the brain. However, previous methods are limited in obtaining the location and surface morphology of somas with variable size and uneven staining in large-scale 3D neuron images. In this work, we proposed a method for automated soma locating in large-scale 3D neuron images that contain relatively sparse soma distributions. This method involves three steps: (i) deblocking the image with overlap between adjacent sub-stacks; (ii) locating the somas in each small sub-stack using multi-scale morphological close and adaptive thresholds; and (iii) fusion of the repeatedly located somas in all sub-stacks. We also describe a new method for the accurate detection of the surface morphology of somas containing hollowness; this was achieved by improving the classical Rayburst Sampling with a new gradient-based criteria. Three 3D neuron image stacks of different sizes were used to quantitatively validate our methods. For the soma localization algorithm, the average recall and precision were greater than 93% and 96%, respectively. For the soma surface detection algorithm, the overlap of the volumes created by automatic detection of soma surfaces and manually segmenting soma volumes was more than 84% for 89% of all correctly detected somas. Our method for locating somas can reveal the soma distributions in large-scale neural networks more efficiently. The method for soma surface detection will serve as a valuable tool for systematic studies of neuron types based on neuron structure.
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Held C, Wenzel J, Wiesmann V, Palmisano R, Lang R, Wittenberg T. Enhancing automated micrograph-based evaluation of LPS-stimulated macrophage spreading. Cytometry A 2013; 83:409-18. [PMID: 23307590 DOI: 10.1002/cyto.a.22248] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 11/10/2012] [Accepted: 11/29/2012] [Indexed: 11/06/2022]
Abstract
To evaluate macrophage spreading in immunofluorescence images of macrophages for surface protein CD11b and nuclear counterstaining with DAPI, it is necessary to measure the size of the macrophages at different time points after stimulation. Manual evaluation of fluorescent micrographs is usually a time-consuming and error-prone task, with poor reproducibility. Automatic image analysis methods can be used to improve the results. The quality of the analysis with these methods mainly depends on the quality of the image segmentation. A segmentation and quantification scheme based on shading correction, k-means clustering, and fast marching level sets has been developed for the purpose. An initial application of this approach showed that separating touching and overlapping cells in particular suffers severely in the inevitably blurred conditions, leading to partly erroneous measurements of macrophage spreading. An alternative method of segmentation in fluorescent micrographs was therefore investigated and evaluated in this study. The proposed approach uses a methodology that separates foreground objects from background objects on the basis of Boykov's graph cuts. In this process, a rough estimation of background pixels is used for background seeds. To identify foreground seeds, a difference of Gaussian band pass filter based workflow is developed. Information on foreground and background seeds is then used for a gradient magnitude based graph cut resulting in a robust figure-ground separation method. In addition, a fast marching level set approach is used in the post-processing step, which makes it possible to split touching cells by incorporating information about the cell nuclei. An evaluation based on a total of 553 manually labeled macrophages depicted in 21 micrographs showed that the proposed method significantly improves segmentation and splitting performance for fluorescent micrographs of LPS-stimulated macrophages and reduces the rate of error in automated analysis of macrophage spreading in comparison with alternative methods.
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Affiliation(s)
- Christian Held
- Department of Image Processing and Biomedical Engineering, Fraunhofer Institute for Integrated Circuits (IIS), Erlangen, Germany.
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24
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Milde F, Franco D, Ferrari A, Kurtcuoglu V, Poulikakos D, Koumoutsakos P. Cell Image Velocimetry (CIV): boosting the automated quantification of cell migration in wound healing assays. Integr Biol (Camb) 2012; 4:1437-47. [DOI: 10.1039/c2ib20113e] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Florian Milde
- Computational Science and Engineering Laboratory, ETH Zürich, CH-8092, Switzerland
| | - Davide Franco
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zürich, CH-8092, Switzerland
| | - Aldo Ferrari
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zürich, CH-8092, Switzerland
| | | | - Dimos Poulikakos
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zürich, CH-8092, Switzerland
| | - Petros Koumoutsakos
- Computational Science and Engineering Laboratory, ETH Zürich, CH-8092, Switzerland
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25
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Bergeest JP, Rohr K. Efficient globally optimal segmentation of cells in fluorescence microscopy images using level sets and convex energy functionals. Med Image Anal 2012; 16:1436-44. [PMID: 22795525 DOI: 10.1016/j.media.2012.05.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 04/20/2012] [Accepted: 05/28/2012] [Indexed: 11/19/2022]
Abstract
In high-throughput applications, accurate and efficient segmentation of cells in fluorescence microscopy images is of central importance for the quantification of protein expression and the understanding of cell function. We propose an approach for segmenting cell nuclei which is based on active contours using level sets and convex energy functionals. Compared to previous work, our approach determines the global solution. Thus, the approach does not suffer from local minima and the segmentation result does not depend on the initialization. We consider three different well-known energy functionals for active contour-based segmentation and introduce convex formulations of these functionals. We also suggest a numeric approach for efficiently computing the solution. The performance of our approach has been evaluated using fluorescence microscopy images from different experiments comprising different cell types. We have also performed a quantitative comparison with previous segmentation approaches.
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Affiliation(s)
- Jan-Philip Bergeest
- University of Heidelberg, BIOQUANT, IPMB, and DKFZ Heidelberg, Dept. of Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.
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26
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Erdmann G, Volz C, Boutros M. Systematic approaches to dissect biological processes in stem cells by image-based screening. Biotechnol J 2012; 7:768-78. [DOI: 10.1002/biot.201200117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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27
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A Bag-of-Words Model for Cellular Image Segmentation. ADVANCES IN INTELLIGENT AND SOFT COMPUTING 2012. [DOI: 10.1007/978-3-642-25547-2_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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28
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Qi X, Xing F, Foran DJ, Yang L. Robust segmentation of overlapping cells in histopathology specimens using parallel seed detection and repulsive level set. IEEE Trans Biomed Eng 2011; 59:754-65. [PMID: 22167559 DOI: 10.1109/tbme.2011.2179298] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Automated image analysis of histopathology specimens could potentially provide support for early detection and improved characterization of breast cancer. Automated segmentation of the cells comprising imaged tissue microarrays (TMAs) is a prerequisite for any subsequent quantitative analysis. Unfortunately, crowding and overlapping of cells present significant challenges for most traditional segmentation algorithms. In this paper, we propose a novel algorithm that can reliably separate touching cells in hematoxylin-stained breast TMA specimens that have been acquired using a standard RGB camera. The algorithm is composed of two steps. It begins with a fast, reliable object center localization approach that utilizes single-path voting followed by mean-shift clustering. Next, the contour of each cell is obtained using a level set algorithm based on an interactive model. We compared the experimental results with those reported in the most current literature. Finally, performance was evaluated by comparing the pixel-wise accuracy provided by human experts with that produced by the new automated segmentation algorithm. The method was systematically tested on 234 image patches exhibiting dense overlap and containing more than 2200 cells. It was also tested on whole slide images including blood smears and TMAs containing thousands of cells. Since the voting step of the seed detection algorithm is well suited for parallelization, a parallel version of the algorithm was implemented using graphic processing units (GPU) that resulted in significant speedup over the C/C++ implementation.
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Affiliation(s)
- Xin Qi
- Department of Pathology and Laboratory Medicine, University of Medicine and Dentistry New Jersey (UMDNJ)-Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA.
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29
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Zheng B, Tan L, Mo X, Yu W, Wang Y, Tucker-Kellogg L, Welsch RE, So PTC, Yu H. Predicting in vivo anti-hepatofibrotic drug efficacy based on in vitro high-content analysis. PLoS One 2011; 6:e26230. [PMID: 22073152 PMCID: PMC3206809 DOI: 10.1371/journal.pone.0026230] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 09/22/2011] [Indexed: 01/11/2023] Open
Abstract
Background/Aims Many anti-fibrotic drugs with high in vitro efficacies fail to produce significant effects in vivo. The aim of this work is to use a statistical approach to design a numerical predictor that correlates better with in vivo outcomes. Methods High-content analysis (HCA) was performed with 49 drugs on hepatic stellate cells (HSCs) LX-2 stained with 10 fibrotic markers. ∼0.3 billion feature values from all cells in >150,000 images were quantified to reflect the drug effects. A systematic literature search on the in vivo effects of all 49 drugs on hepatofibrotic rats yields 28 papers with histological scores. The in vivo and in vitro datasets were used to compute a single efficacy predictor (Epredict). Results We used in vivo data from one context (CCl4 rats with drug treatments) to optimize the computation of Epredict. This optimized relationship was independently validated using in vivo data from two different contexts (treatment of DMN rats and prevention of CCl4 induction). A linear in vitro-in vivo correlation was consistently observed in all the three contexts. We used Epredict values to cluster drugs according to efficacy; and found that high-efficacy drugs tended to target proliferation, apoptosis and contractility of HSCs. Conclusions The Epredict statistic, based on a prioritized combination of in vitro features, provides a better correlation between in vitro and in vivo drug response than any of the traditional in vitro markers considered.
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Affiliation(s)
- Baixue Zheng
- Computation and Systems Biology Program, Singapore-MIT Alliance, National University of Singapore, Singapore, Singapore
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Looling Tan
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
| | - Xuejun Mo
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Weimiao Yu
- Imaging Informatics Division, Bioinformatics Institute, A*STAR, Singapore, Singapore
- Central Imaging Facility, Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Yan Wang
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
- Department of Hepatobiliary Surgery, Southern Medical University Affiliated Zhujiang Hospital, Guangzhou, China
| | - Lisa Tucker-Kellogg
- Computation and Systems Biology Program, Singapore-MIT Alliance, National University of Singapore, Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Roy E. Welsch
- Computation and Systems Biology Program, Singapore-MIT Alliance, National University of Singapore, Singapore, Singapore
- Engineering Systems Division, Sloan School of Management, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Peter T. C. So
- Computation and Systems Biology Program, Singapore-MIT Alliance, National University of Singapore, Singapore, Singapore
- Singapore-MIT Alliance for Research and Technology, BioSyM, Singapore, Singapore
- Department of Mechanical Engineering and Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Hanry Yu
- Computation and Systems Biology Program, Singapore-MIT Alliance, National University of Singapore, Singapore, Singapore
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Singapore-MIT Alliance for Research and Technology, BioSyM, Singapore, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Sciences, National University of Singapore, Singapore, Singapore
- NUS Tissue-Engineering Programme, National University of Singapore, Singapore, Singapore
- Department of Mechanical Engineering and Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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30
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Lee MY, Racine V, Jagadpramana P, Sun L, Yu W, Du T, Spencer-Dene B, Rubin N, Le L, Ndiaye D, Bellusci S, Kratochwil K, Veltmaat JM. Ectodermal influx and cell hypertrophy provide early growth for all murine mammary rudiments, and are differentially regulated among them by Gli3. PLoS One 2011; 6:e26242. [PMID: 22046263 PMCID: PMC3203106 DOI: 10.1371/journal.pone.0026242] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 09/22/2011] [Indexed: 11/29/2022] Open
Abstract
Mammary gland development starts in utero with one or several pairs of mammary rudiments (MRs) budding from the surface ectodermal component of the mammalian embryonic skin. Mice develop five pairs, numbered MR1 to MR5 from pectoral to inguinal position. We have previously shown that Gli3Xt-J/Xt-J mutant embryos, which lack the transcription factor Gli3, do not form MR3 and MR5. We show here that two days after the MRs emerge, Gli3Xt-J/Xt-J MR1 is 20% smaller, and Gli3Xt-J/Xt-J MR2 and MR4 are 50% smaller than their wild type (wt) counterparts. Moreover, while wt MRs sink into the underlying dermis, Gli3Xt-J/Xt-J MR4 and MR2 protrude outwardly, to different extents. To understand why each of these five pairs of functionally identical organs has its own, distinct response to the absence of Gli3, we determined which cellular mechanisms regulate growth of the individual MRs, and whether and how Gli3 regulates these mechanisms. We found a 5.5 to 10.7-fold lower cell proliferation rate in wt MRs compared to their adjacent surface ectoderm, indicating that MRs do not emerge or grow via locally enhanced cell proliferation. Cell-tracing experiments showed that surface ectodermal cells are recruited toward the positions where MRs emerge, and contribute to MR growth during at least two days. During the second day of MR development, peripheral cells within the MRs undergo hypertrophy, which also contributes to MR growth. Limited apoptotic cell death counterbalances MR growth. The relative contribution of each of these processes varies among the five MRs. Furthermore, each of these processes is impaired in the absence of Gli3, but to different extents in each MR. This differential involvement of Gli3 explains the variation in phenotype among Gli3Xt-J/Xt-J MRs, and may help to understand the variation in numbers and positions of mammary glands among mammals.
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Affiliation(s)
- May Yin Lee
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
- Graduate School for Integrative Sciences and Engineering, National University of Singapore, Centre for Life Sciences (CeLS), Singapore, Singapore
| | - Victor Racine
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Peter Jagadpramana
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Li Sun
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Weimiao Yu
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Tiehua Du
- Bio-Informatics Institute, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Bradley Spencer-Dene
- Experimental Histopathology Laboratory, Cancer Research UK London Research Institute, London, United Kingdom
| | - Nicole Rubin
- Developmental Biology Program, The Saban Research Institute of Children's Hospital Los Angeles, Los Angeles, California, United States of America
| | - Lendy Le
- Developmental Biology Program, The Saban Research Institute of Children's Hospital Los Angeles, Los Angeles, California, United States of America
| | - Delphine Ndiaye
- Institut Curie/CNRS-UMR144, Equipe de Morphogenèse Cellulaire et Progression Tumorale, Paris, France
| | - Saverio Bellusci
- Developmental Biology Program, The Saban Research Institute of Children's Hospital Los Angeles, Los Angeles, California, United States of America
| | | | - Jacqueline M. Veltmaat
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University Health System, Singapore, Singapore
- * E-mail:
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31
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Held C, Palmisano R, Häberle L, Hensel M, Wittenberg T. Comparison of parameter-adapted segmentation methods for fluorescence micrographs. Cytometry A 2011; 79:933-45. [PMID: 22002887 DOI: 10.1002/cyto.a.21122] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 06/06/2011] [Accepted: 07/18/2011] [Indexed: 11/06/2022]
Abstract
Interpreting images from fluorescence microscopy is often a time-consuming task with poor reproducibility. Various image processing routines that can help investigators evaluate the images are therefore useful. The critical aspect for a reliable automatic image analysis system is a robust segmentation algorithm that can perform accurate segmentation for different cell types. In this study, several image segmentation methods were therefore compared and evaluated in order to identify the most appropriate segmentation schemes that are usable with little new parameterization and robustly with different types of fluorescence-stained cells for various biological and biomedical tasks. The study investigated, compared, and enhanced four different methods for segmentation of cultured epithelial cells. The maximum-intensity linking (MIL) method, an improved MIL, a watershed method, and an improved watershed method based on morphological reconstruction were used. Three manually annotated datasets consisting of 261, 817, and 1,333 HeLa or L929 cells were used to compare the different algorithms. The comparisons and evaluations showed that the segmentation performance of methods based on the watershed transform was significantly superior to the performance of the MIL method. The results also indicate that using morphological opening by reconstruction can improve the segmentation of cells stained with a marker that exhibits the dotted surface of cells.
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Affiliation(s)
- Christian Held
- Department of Image Processisng and Biomedical Engineering, Fraunhofer Institute for Integrated Circuits IIS, Erlangen, Germany
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32
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Du CJ, Marcello M, Spiller DG, White MRH, Bretschneider T. Interactive segmentation of clustered cells via geodesic commute distance and constrained density weighted Nyström method. Cytometry A 2011; 77:1137-47. [PMID: 21069796 DOI: 10.1002/cyto.a.20993] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
An interactive method is proposed for complex cell segmentation, in particular of clustered cells. This article has two main contributions: First, we explore a hybrid combination of the random walk and the geodesic graph based methods for image segmentation and propose the novel concept of geodesic commute distance to classify pixels. The computation of geodesic commute distance requires an eigenvector decomposition of the weighted Laplacian matrix of a graph constructed from the image to be segmented. Second, by incorporating pairwise constraints from seeds into the algorithm, we present a novel method for eigenvector decomposition, namely a constrained density weighted Nyström method. Both visual and quantitative comparison with other semiautomatic algorithms including Voronoi-based segmentation, grow cut, graph cuts, random walk, and geodesic method are given to evaluate the performance of the proposed method, which is a powerful tool for quantitative analysis of clustered cell images in live cell imaging.
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Affiliation(s)
- Cheng-Jin Du
- Warwick Systems Biology Centre, University of Warwick, Coventry, United Kingdom.
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33
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Khairy K, Keller PJ. Reconstructing embryonic development. Genesis 2011; 49:488-513. [DOI: 10.1002/dvg.20698] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 11/22/2010] [Accepted: 11/24/2010] [Indexed: 01/22/2023]
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34
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Discriminative segmentation of microscopic cellular images. MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION : MICCAI ... INTERNATIONAL CONFERENCE ON MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION 2011; 14:637-44. [PMID: 22003672 DOI: 10.1007/978-3-642-23623-5_80] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Microscopic cellular images segmentation has become an important routine procedure in modern biological research, due to the rapid advancement of fluorescence probes and robotic microscopes in recent years. In this paper we advocate a discriminative learning approach for cellular image segmentation. In particular, three new features are proposed to capture the appearance, shape and context information, respectively. Experiments are conducted on three different cellular image datasets. Despite the significant disparity among these datasets, the proposed approach is demonstrated to perform reasonably well. As expected, for a particular dataset, some features turn out to be more suitable than others. Interestingly, we observe that a further gain can often be obtained on top of using the "good" features, by also retaining those features that perform poorly. This might be due to the complementary nature of these features, as well as the capacity of our approach to better integrate and exploit different sources of information.
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