Article (Scientific journals)
Automated Processing of Zebrafish Imaging Data: A Survey
Mikut, Ralf; Dickmeis, Thomas; Driever, Wolfgang et al.
2013In Zebrafish, 10 (3), p. 401-421
Peer reviewed
 

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Abstract :
[en] 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.
Research center :
Giga-Systems Biology and Chemical Biology - ULiège
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Mikut, Ralf
Dickmeis, Thomas
Driever, Wolfgang
Geurts, Pierre ;  Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Systèmes et modélisation
Hamprecht, Fred A.
Kausler, Bernhard X.
Ledesma-Carbayo, Maria J.
Maree, Raphael  ;  Université de Liège - ULiège
Mikula, Karol
Pantazis, Periklis
Ronneberger, Olaf
Santos, Andres
Stotzka, Rainer
Strahle, Uwe
Peyrieras, Nadine
More authors (5 more) Less
Language :
English
Title :
Automated Processing of Zebrafish Imaging Data: A Survey
Publication date :
August 2013
Journal title :
Zebrafish
ISSN :
1545-8547
eISSN :
1557-8542
Publisher :
Mary Ann Liebert Inc.
Volume :
10
Issue :
3
Pages :
401-421
Peer reviewed :
Peer reviewed
Name of the research project :
WIST3 Cytomine 1017072
Funders :
FEDER - Fonds Européen de Développement Régional [BE]
Région wallonne: Direction générale opérationnelle de l'Economie, de l'Emploi & de la Recherche (DGO6)
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since 22 June 2013

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