ReviewZebrafish2013
Automated processing of zebrafish imaging data: a survey.
Review in Zebrafish, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed, 82 citations in OpenAlex.
- Automated Embryo Sorting in Zebrafish Facilities: Performance Benchmarking Against Manual Processing.Biology · 2026Article
- Zebrafish as a tool for autism research: unraveling the roles of Shank3, Cntnap2, Neuroligin3, and Arid1b in synaptic and behavioral abnormalities.Neurogenetics · 2025Review
- Recent Advances in Bioimage Analysis Methods for Detecting Skeletal Deformities in Biomedical and Aquaculture Fish Species.Biomolecules · 2023Review
- Unlocking the Potential of Zebrafish Research with Artificial Intelligence: Advancements in Tracking, Processing, and Visualization.Medical & biological engineering & computing · 2023Review
- A new software tool for computer assisted in vivo high-content analysis of transplanted fluorescent cells in intact zebrafish larvae.Biology open · 2022Article
- Screening of Mineralogenic and Osteogenic Compounds in Zebrafish-Tools to Improve Assay Throughput and Data Accuracy.Pharmaceuticals (Basel, Switzerland) · 2022Review
- Light sheet fluorescence microscopy for the investigation of blood-sucking arthropods dyed via artificial membrane feeding.Parasites & vectors · 2022Article
- Performance of computational methods for the evaluation of pericentriolar material 1 missense variants in CAGI-5.Human mutation · 2019Article
- A Smart Imaging Workflow for Organ-Specific Screening in a Cystic Kidney Zebrafish Disease Model.International journal of molecular sciences · 2019Article
- Fishing forward and reverse: Advances in zebrafish phenomics.Mechanisms of development · 2018Review
- An automated quantitative image analysis pipeline ofJournal of biological methods · 2018Article
- Zebrafish as a Model for Drug Screening in Genetic Kidney Diseases.Frontiers in pediatrics · 2018Review
- Zebrafish: an emerging real-time model system to study Alzheimer's disease and neurospecific drug discovery.Cell death discovery · 2018Article
- Automatic multiple zebrafish larvae tracking in unconstrained microscopic video conditions.Scientific reports · 2017Article
- Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System.Frontiers in neuroinformatics · 2017Article
- The rise of photoresponsive protein technologies applicationsF1000Research · 2017Review
- Midbrain-Hindbrain Boundary Morphogenesis: At the Intersection of Wnt and Fgf Signaling.Frontiers in neuroanatomy · 2017Review
- Systems Biology to Support Nanomaterial Grouping.Advances in experimental medicine and biology · 2017Review
- Zebrafish in Toxicology and Environmental Health.Current topics in developmental biology · 2017Review
- Extensive Regulation of Diurnal Transcription and Metabolism by Glucocorticoids.PLoS genetics · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors at 8 institutions in 7 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.