Automated processing of zebrafish imaging data: a survey.

@article{Mikut2013AutomatedPO,
  title={Automated processing of zebrafish imaging data: a survey.},
  author={Ralf Mikut and Thomas Dickmeis and Wolfgang Driever and Pierre Geurts and Fred A. Hamprecht and Bernhard X. Kausler and Mar{\'i}a J. Ledesma-Carbayo and Rapha{\"e}l Mar{\'e}e and Karol Mikula and Periklis Pantazis and Olaf Ronneberger and Andr{\'e}s Santos and Rainer Stotzka and Uwe Str{\"a}hle and Nadine Peyri{\'e}ras},
  journal={Zebrafish},
  year={2013},
  volume={10 3},
  pages={
          401-21
        }
}
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… 

Figures from this paper

Unsupervised image analysis for zebrafish embryogenesis using lab-on-a-chip embryo arrays

TLDR
A novel image analysis algorithm is developed to automatically recognise dead embryos and the first two stages of the zebrafish embryo development in order to detect anomalies caused by an applied chemical agent during embryogenesis.

Fast Segmentation of Stained Nuclei in Terabyte-Scale, Time Resolved 3D Microscopy Image Stacks

TLDR
This work presents a fast parallelized segmentation method that is especially suited for the extraction of stained nuclei from microscopy images, e.g., of developing zebrafish embryos, with an up to ten-fold decrease in processing times, allowing it to process large data sets while still providing reasonable segmentation results.

A Smart Imaging Workflow for Organ-Specific Screening in a Cystic Kidney Zebrafish Disease Model

TLDR
An automated imaging pipeline to identify chemical modifiers of glomerular cyst formation in a zebrafish model for human cystic kidney disease is presented and enables highly efficient profiling of entire compound libraries and scoring of kidney-specific morphological phenotypes in thousands of zebra fish embryos.

Automated phenotype pattern recognition of zebrafish for high-throughput screening

TLDR
A prototype platform for image acquisition together with a classification software that helps automatize the distribution of embryos and larvae into standard microtiter plates or other sample holders for screening, often according to phenotypical features.

Fully Automated Pipetting Sorting System for Different Morphological Phenotypes of Zebrafish Embryos

TLDR
It is shown that the variable phenotypes of the mutant embryos can be safely distinguished from phenotypic wild-type zebrafish embryos and sorted from onePetri dish into another petri dish or into a 96-well microtiter plate.

Image Analysis in Light Sheet Fluorescence Microscopy Images of Transgenic Zebrafish Vascular Development

TLDR
This paper focuses on data acquisition by lightsheet fluorescence microscopy, data properties, image pre-processing, and vasculature segmentation, and proposes future work to derive quantifications of zebrafish neurovasculature development.

A New Software Tool for Computer Assisted In Vivo High-Content Analysis of Transplanted Fluorescent Cells in intact Zebrafish Larvae

TLDR
A software-tool to segment cells from confocal images and track characteristics such as volume, location in the larva and fluorescent intensity on a single-cell basis is presented, able to characterize the responses of the cancer cell lines Molm-13 and MDS-L to established treatments.

Watching the embryo: Evolution of the microscope for the study of embryogenesis

TLDR
The evolution of microscopes and the optical technologies that have been instrumental in studying various developmental processes provide mechanistic insights into the dynamic cellular and molecular events which drive lineage commitment and morphogenetic changes in the developing embryo.
...

References

SHOWING 1-10 OF 111 REFERENCES

Automated feature detection and imaging for high-resolution screening of zebrafish embryos.

TLDR
A toolset for automated intelligent high-content screening of whole zebrafish embryos at cellular resolution on a standard wide-field screening microscope and the development of a mold design for accurate orientation of zebra fish embryos for dorsal imaging is reported, thereby facilitating standardized imaging of internal organs and cellular structures.

A High-Throughput Analysis Method to Detect Regions of Interest and Quantify Zebrafish Embryo Images

TLDR
This work develops an image processing focused on detecting and quantifying pigments in zebrafish embryos that is robust in terms that it can detect and quantify pigments even when the embryos have different orientations and curvatures.

Computational techniques in zebrafish image processing and analysis

High-Throughput Screening of Zebrafish Embryos Using Automated Heart Detection and Imaging

TLDR
An intelligent robotic microscope is presented, which automatically identifies the orientation of a zebrafish in a micro well, and a predefined region of interest, such as the heart, is detected automatically and a video with higher magnification is recorded.

Automated image‐based phenotypic analysis in zebrafish embryos

TLDR
An automated system for imaging and analyzing zebrafish embryos in multi‐well plates regardless of embryo orientation and without user intervention is developed, demonstrating it is feasible to adapt image‐based high‐content screening methodology to measure complex whole organism phenotypes.

An Automated Method for Cell Detection in Zebrafish

TLDR
This work presents a novel cell detection method for the automatic quantification of zebrafish neuronal cells, including primary motor neurons, Rohon–Beard neurons, and retinal cells, and shows that it consistently displays high sensitivity and specificity.

Methods for Automated High-Throughput Toxicity Testing Using Zebrafish Embryos

TLDR
The presented approach was designed for real high-throughput screening including data handling and the results are stored in a long-time data storage and prepared to be processed on a cluster computing system being build up in the KIT.
...