Automated processing of zebrafish imaging data: a survey
| Autor: | Nadine Peyriéras, Maria J. Ledesma-Carbayo, Wolfgang Driever, Bernhard X. Kausler, Karol Mikula, Periklis Pantazis, Pierre Geurts, Raphaël Marée, Rainer Stotzka, Thomas Dickmeis, Fred A. Hamprecht, Andres Santos, Olaf Ronneberger, Uwe Strähle, Ralf Mikut |
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| Přispěvatelé: | Karlsruhe Institute of Technology (KIT), BIOSS Centre for Biological Signalling Studies, University of Freiburg [Freiburg], Department of Electrical Engineering and Computer Science (Institut Montefiore), Université de Liège, Heidelberg Collaboratory for Image Processing (HCI), Universität Heidelberg [Heidelberg], Biomedical Image Technologies, Biomedical Research Center (CIBER-BBN), Universidad Politécnica de Madrid (UPM), Department of Mathematics (STUBA), Slovak University of Technology in Bratislava, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Neurobiologie et Développement (N&eD), Centre National de la Recherche Scientifique (CNRS), Institut des Systèmes Complexes - Paris Ile-de-France (ISC-PIF), École normale supérieure - Cachan (ENS Cachan)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris-Sud - Paris 11 (UP11)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-École polytechnique (X), Institut de Neurobiologie Alfred Fessard (INAF), Universität Heidelberg [Heidelberg] = Heidelberg University, École normale supérieure - Cachan (ENS Cachan)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris-Sud - Paris 11 (UP11)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École polytechnique (X)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS), Fonds Européen de Développement Régional - FEDER [sponsor], Région wallonne: Direction générale opérationnelle de l'Economie, de l'Emploi & de la Recherche (DGO6) [sponsor], Giga-Systems Biology and Chemical Biology [research center] |
| Jazyk: | angličtina |
| Rok vydání: | 2013 |
| Předmět: |
animal structures
Image processing Review Terabyte computer.software_genre Bioinformatics 03 medical and health sciences 0302 clinical medicine Software Image Processing Computer-Assisted Animals Preprocessor Zebrafish 030304 developmental biology 0303 health sciences Telecomunicaciones biology business.industry Biochemistry biophysics & molecular biology [Life sciences] Biochimie biophysique & biologie moléculaire [Sciences du vivant] Brain atlas Modular design biology.organism_classification 13. Climate action Data quality Animal Science and Zoology [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC] Electrónica Data mining business computer 030217 neurology & neurosurgery Developmental Biology |
| Zdroj: | Zebrafish, ISSN 1545-8547, 2013-08, Vol. 10, No. 3 Zebrafish Zebrafish, Mary Ann Liebert, 2013, 10 (3), pp.401-421. ⟨10.1089/zeb.2013.0886⟩ Zebrafish, 2013, 10 (3), pp.401-421. ⟨10.1089/zeb.2013.0886⟩ Zebrafish, 10(3), 401-421. Mary Ann Liebert Inc (2013). OpenAIRE Open Repository and Bibliography-University of Liège Archivo Digital UPM Europe PubMed Central instname |
| ISSN: | 1545-8547 |
| DOI: | 10.1089/zeb.2013.0886⟩ |
| Popis: | International audience; Abstract Due to the relative transparency of its embryos and larvae, the zebrafish is an ideal model organism for bioimaging approaches in vertebrates. Novel microscope technologies allow the imaging of developmental processes in unprecedented detail, and they enable the use of complex image-based read-outs for high-throughput/high-content screening. Such applications can easily generate Terabytes of image data, the handling and analysis of which becomes a major bottleneck in extracting the targeted information. Here, we describe the current state of the art in computational image analysis in the zebrafish system. We discuss the challenges encountered when handling high-content image data, especially with regard to data quality, annotation, and storage. We survey methods for preprocessing image data for further analysis, and describe selected examples of automated image analysis, including the tracking of cells during embryogenesis, heartbeat detection, identification of dead embryos, recognition of tissues and anatomical landmarks, and quantification of behavioral patterns of adult fish. We review recent examples for applications using such methods, such as the comprehensive analysis of cell lineages during early development, the generation of a three-dimensional brain atlas of zebrafish larvae, and high-throughput drug screens based on movement patterns. Finally, we identify future challenges for the zebrafish image analysis community, notably those concerning the compatibility of algorithms and data formats for the assembly of modular analysis pipelines. |
| Databáze: | OpenAIRE |
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