Toxicology Workshop

“Advanced tools for the analysis of zebrafish embryo toxicology data – imaging, behaviour and databases” 

Please register here

Stefan Scholz, Riccardo Massei, Paul Michaelis, Julia Nöth, Nils Klüver, …. 
Start: 10.00 am., Sunday 9th July 2023.
Duration: 5-10 min each section and subsequent application and QnA session (total duration 2 h)

Zebrafish embryos are increasingly used in toxicology given their complexity but small scale. They are attractive screening models since e.g. in Europe they are considered as alternative models similar as in vitro cellular test systems. Over the past decades tools for automatic assessment of zebrafish embryo tests have been developed and appropriate devices have been commercialised. The automated assessment generates huge datasets of images, videos and dataset, calling also for advancements in data analysis. The Helmholtz Centre of Environmental Research has developed a variety of tools that intend to support the assessment of toxicological data obtained with zebrafish embryos. The tools are already publicly (open source) available or will be made available soon.

Training workshop overview

We would like to demonstrate the tools to the zebrafish community and help other scientist to automate their assessment and remove bias from their analyses. In our training workshop we would like to present the following approaches/tools:
- FishInspector, FishTrainer, FishClassificator: This suite of software products support the automated annotation of structural features. A first version was published in 2019 (Teixido et al.) but has recently (unpublished) been advanced to use artificial intelligence for the recognition of structures or classification.
- EmbryoMotion: A software to assess PMR (photomotor response) and STC (spontaneous tail contractions) from videos of 96well plates (available from Gitlab soon).
- FishCardiologist is a new software that allows to automatically extract heart rate from videos and generate difference images to visualise the cardiovascular systems. It aims at high user friendliness and uses special image stabilisation and subtraction approaches.
- Using KNIME for automated analysis of data obtained from imaging software
- A toxicogenomic fingerprint-browser ( was developed to support visualisation and analysis of zebrafish transcriptome data.
- INTOB-DB: At present data from zebrafish embryo toxicity tests are stored in multiple repositories, journal articles or internal institutional repositories. We developed a software with included database for zebrafish embryo toxicity experiments from standard toxicity observation with light microscopy to advanced automated screening assays. Using the software enables FAIR data management from experimental design to raw result data including all relevant meta data.
We will demonstrate the above listed tools. For some of the products (FishInspector, FishCardiologist) we can provide evaluation copies (principally unrestricted use) when a specific license is signed. This would allow users to check these tools in advance, use the tools during the training workshop and ask specific questions. 

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