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 highthroughput/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.

Automatic Zebrafish Heartbeat Detection and Analysis for Zebrafish Embryos

“…Up to date, an assessment of the heart rate is often practiced manually by counting heartbeats from slow motion replay of videotape recordings, what is neither practical for large numbers of hearts to be analyzed nor is it accurate when determining beat-to-beat intervals as needed for detection of arrhythmias. 7 Existing software for semiautomated analysis of heartbeats [7][8][9][10][11][12][13] has several limitations. One is that the embryos have to be anesthetized by adding Tricaine 11,14 or MS-222 12 to avoid movement of zebrafish embryos during videoing.…”

Nonlinear PDE based numerical methods for cell tracking in zebrafish embryogenesis

“…For the discretization of Eq. (11) we use spatially the 4D Rouy-Tourin scheme [20]. The constrained distance function, which we look for, is obtained as an equilibrium of the numerical solution, i.e.…”

“…by a combination of various image processing techniques and manual inspection, for the zebrafish developmental stages up to about one thousand cells [19], there is a great challenge to study embryogenesis at very complex stages of development with thousands of cells present. In [12,22,18,3] new efficient and robust 3D filtering and segmentation algorithms together with a workflow for performing various analyses of such complex developmental stages were suggested and studied.…”

A framework for feedback-based segmentation of 3D image stacks

“…to analyze model organisms like mouse [1], zebrafish [2] or fruit fly [3]. An important aim is to reconstruct 3D surfaces or volumes from a set of 2D images called stack.…”