Phenotype Classification of Zebrafish Embryos by Supervised Learning

Jeanray, Nathalie; Marée, Raphaël; Pruvot, Benoist; Stern, Olivier; Geurts, Pierre; Wehenkel, Louis; Müller, Marc

doi:10.1371/journal.pone.0116989

Cited by 53 publications

(69 citation statements)

References 32 publications

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“…Jeanray et al. () showed that the scoring of morphology is the main rate‐ and quality‐limiting step in ZEBDET, and may be prone to subjectivity. The large number of substances to be tested and the need for accurate results call for methods allowing automation of data acquisition, as well as identification of defects and classification of the acquired images.…”

Section: Machine Learning For Objective Morphological Assessmentmentioning

confidence: 99%

“…Other morphological changes, such as a curved trunk and hemostasis, can also be detected by machine learning, albeit less accurately (Jeanray et al. ). Because novel algorithms of machine learning are actively developed, it is likely that various morphological abnormalities in ZEBDET could be assessed automatically and objectively using machine learning (Mikut et al.…”

Section: Machine Learning For Objective Morphological Assessmentmentioning

confidence: 99%

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Using zebrafish in systems toxicology for developmental toxicity testing

Nishimura

Inoue

Sasagawa

et al. 2016

Congenital Anomalies

170

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With the high cost and the long-term assessment of developmental toxicity testing in mammals, the vertebrate zebrafish has become a useful alternative model organism for high-throughput developmental toxicity testing. Zebrafish is also very favorable for the 3R perspective in toxicology; however, the methodologies used by research groups vary greatly, posing considerable challenges to integrative analysis. In this review, we discuss zebrafish developmental toxicity testing, focusing on the methods of chemical exposure, the assessment of morphological abnormalities, housing conditions and their effects on the production of healthy embryos, and future directions. Zebrafish as a systems toxicology model has the potential to elucidate developmental toxicity pathways, and to provide a sound basis for human health risk assessments.

show abstract

Section: Machine Learning For Objective Morphological Assessmentmentioning

confidence: 99%

Section: Machine Learning For Objective Morphological Assessmentmentioning

confidence: 99%

Using zebrafish in systems toxicology for developmental toxicity testing

Nishimura

Inoue

Sasagawa

et al. 2016

Congenital Anomalies

170

View full text Add to dashboard Cite

show abstract

“…Automation of image capture and phenotype analysis will improve the ability of researchers to screen larger libraries of compounds over wider concentration ranges, while limiting bias in the assays (Deal et al, 2016; Jeanray et al, 2015; Mikut et al, 2013). Optimized techniques for embryo immobilization will enable imaging the developing zebrafish larvae using state of the art techniques including light sheet fluorescence microscopy (Höckendorf, Thumberger, Wittbrodt, 2012; Kaufmann, Mickoleit, Weber, & Huisken, 2012).…”

Section: Assessing Health Impacts Of Environmental Exposures Usingmentioning

confidence: 99%

Zebrafish in Toxicology and Environmental Health

Bambino

Chu

2017

Current Topics in Developmental Biology

325

152

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As manufacturing processes and development of new synthetic compounds increase to keep pace with the expanding global demand, environmental health, and the effects of toxicant exposure are emerging as critical public health concerns. Additionally, chemicals that naturally occur in the environment, such as metals, have profound effects on human and animal health. Many of these compounds are in the news: lead, arsenic, and endocrine disruptors such as bisphenol A have all been widely publicized as causing disease or damage to humans and wildlife in recent years. Despite the widespread appreciation that environmental toxins can be harmful, there is limited understanding of how many toxins cause disease. Zebrafish are at the forefront of toxicology research; this system has been widely used as a tool to detect toxins in water samples and to investigate the mechanisms of action of environmental toxins and their related diseases. The benefits of zebrafish for studying vertebrate development are equally useful for studying teratogens. Here, we review how zebrafish are being used both to detect the presence of some toxins as well as to identify how environmental exposures affect human health and disease. We focus on areas where zebrafish have been most effectively used in ecotoxicology and in environmental health, including investigation of exposures to endocrine disruptors, industrial waste byproducts, and arsenic.

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“…This aspect of HTS can be time-consuming and subject to variability depending on the reviewer and lab. There have been promising efforts recently with advanced optical imaging platforms, such as optical projection tomography (OPT), to automate in vivo phenotyping of developing zebrafish embryos 120–122 . Ongoing advances in imaging and analysis of different developmental phenotypes should augment the speed and reproducibility of zebrafish HTS platforms.…”

Section: Hts Platforms Targeting Early Developmentmentioning

confidence: 99%

Zebrafish as an in vivo model for sustainable chemical design

2016

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Heightened public awareness about the many thousands of chemicals in use and present as persistent contaminants in the environment has increased the demand for safer chemicals and more rigorous toxicity testing. There is a growing recognition that the use of traditional test models and empirical approaches is impractical for screening for toxicity the many thousands of chemicals in the environment and the hundreds of new chemistries introduced each year. These realities coupled with the green chemistry movement have prompted efforts to implement more predictive-based approaches to evaluate chemical toxicity early in product development. While used for many years in environmental toxicology and biomedicine, zebrafish use has accelerated more recently in genetic toxicology, high throughput screening (HTS), and behavioral testing. This review describes major advances in these testing methods that have positioned the zebrafish as a highly applicable model in chemical safety evaluations and sustainable chemistry efforts. Many toxic responses have been shown to be shared among fish and mammals owing to their generally well-conserved development, cellular networks, and organ systems. These shared responses have been observed for chemicals that impair endocrine functioning, development, and reproduction, as well as those that elicit cardiotoxicity and carcinogenicity, among other diseases. HTS technologies with zebrafish enable screening large chemical libraries for bioactivity that provide opportunities for testing early in product development. A compelling attribute of the zebrafish centers on being able to characterize toxicity mechanisms across multiple levels of biological organization from the genome to receptor interactions and cellular processes leading to phenotypic changes such as developmental malformations. Finally, there is a growing recognition of the links between human and wildlife health and the need for approaches that allow for assessment of real world multi-chemical exposures. The zebrafish is poised to be an important model in bridging these two conventionally separate areas of toxicology and characterizing the biological effects of chemical mixtures that could augment its role in sustainable chemistry.

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Phenotype Classification of Zebrafish Embryos by Supervised Learning

Cited by 53 publications

References 32 publications

Using zebrafish in systems toxicology for developmental toxicity testing

Using zebrafish in systems toxicology for developmental toxicity testing

Zebrafish in Toxicology and Environmental Health

Zebrafish as an in vivo model for sustainable chemical design

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