title: Automated processing of zebrafish imaging data: a survey.
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.
authors.affiliation: Karlsruhe Institute of Technology, Karlsruhe, Germany. ralf.mikut@kit.edu
authors.forename: Ralf
authors.initials: R
authors.lastname: Mikut
authors.forename: Thomas
authors.initials: T
authors.lastname: Dickmeis
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Driever
authors.forename: Pierre
authors.initials: P
authors.lastname: Geurts
authors.forename: Fred A
authors.initials: FA
authors.lastname: Hamprecht
authors.forename: Bernhard X
authors.initials: BX
authors.lastname: Kausler
authors.forename: María J
authors.initials: MJ
authors.lastname: Ledesma-Carbayo
authors.forename: Raphaël
authors.initials: R
authors.lastname: Marée
authors.forename: Karol
authors.initials: K
authors.lastname: Mikula
authors.forename: Periklis
authors.initials: P
authors.lastname: Pantazis
authors.forename: Olaf
authors.initials: O
authors.lastname: Ronneberger
authors.forename: Andres
authors.initials: A
authors.lastname: Santos
authors.forename: Rainer
authors.initials: R
authors.lastname: Stotzka
authors.forename: Uwe
authors.initials: U
authors.lastname: Strähle
authors.forename: Nadine
authors.initials: N
authors.lastname: Peyriéras
mesh_terms: D000818:Animals; D007091:Image Processing, Computer-Assisted; D012984:Software; D015027:Zebrafish