Ever wondered what life looks like inside a zebrafish research facility? From rows of clear tanks to the daily routines of dedicated scientists, these labs are where small fish make a big impact on biomedical discovery. In this exclusive interview, we go behind the tanks with one of our partner facilities to explore how automation is reshaping zebrafish research to make it faster, more reliable, and ready for the challenges of tomorrow.
Introduction
Zebrafish have become one of the most important model organisms in life sciences, widely used in fields ranging from developmental biology to toxicology and drug discovery. Behind each of these breakthroughs lies the dedicated work of specialized facilities, where teams manage thousands of fish, maintain complex aquatic systems, and ensure reliable experimental outcomes. From daily care to delicate embryo handling, it is the expertise of facility staff that makes zebrafish research possible.
In this article, we spotlight the Zebrafish Facility of the Biomedical Research Center of Qatar University in Doha, Qatar, and speak with Enas Al Absi, the lead laboratory technologist. She shares what it takes to keep a zebrafish facility running, the challenges they face, and how automation with Bionomous technology is helping them push research forward.
Interview
Could you describe your facility in a few sentences?
The Zebrafish Facility (ZF) at the Biomedical Research Center (BRC) is a cutting-edge facility, established in 2014 and recognized as the first of its kind in Qatar and the region. As part of the BRC, a leading hub for biomedical research at Qatar University, the facility not only provides essential infrastructure but also contributes to capacity building by training students and researchers. The BRC however, hosts a wide spectrum of research programs, including infectious diseases, complementary and alternative medicine, bioengineering, ecosystems, making it a multidisciplinary environment where zebrafish research can directly support and complement other scientific domains. Over the years, we have delivered specialized workshops, conferences, and hands-on training sessions — most recently the Basic Training on Utilization of Zebrafish as an Animal Model in Research held in August 2025 — to equip the local and regional scientific community with the skills needed to advance zebrafish-based research.
The ZF serves as a hub for innovative biomedical research, featuring two adult experimental rooms and two embryo experimental rooms, all equipped with high-end instrumentation. Our laboratories include advanced equipment for high-resolution imaging, video recording, heart and blood flow analysis, locomotor activity studies, and histology. The system supports around 5,000 adult fish across five zebrafish lines and currently handles 30 projects per semester, 40% involving graduate and undergraduate students. Operated by two dedicated technologists and guided by a scientific committee of five principal investigators, the facility is committed to collaboration and actively partners with local and international institutions to advance scientific discovery, counting more than 372 publications over the past 10 years.
What are zebrafish used for within your institution?
- Toxicology: Studying the toxic effects of chemicals and pollutants to enhance safety and understand environmental risks.
- Cardiovascular Diseases: Investigating heart disease mechanisms and potential treatments, leveraging zebrafish’s heart regeneration capabilities.
- Alternative Medicine: Evaluating natural treatments for safety and efficacy.
- Neurobiology: Exploring brain function and developing treatments for diseases like Alzheimer’s and Parkinson’s.
- Regenerative Medicine: Understanding tissue regeneration to aid human organ repair.
- Metabolic Diseases: Researching diabetes and obesity through genetic similarities to humans.
- Cancer Research: Analyzing tumor development and testing treatments applicable to human cancers.
- Genetic Manipulation Studies: Using CRISPR and morpholino techniques to study gene downregulation or upregulation in various disease models, helping to elucidate gene functions and disease mechanisms.
What do you personally like the most about the zebrafish model?
The zebrafish model is particularly fascinating due to its rapid development, genetic tractability, and the clarity it provides for observing developmental processes in real-time. These features speed up the process of testing when compared to other animal models. Having worked with zebrafish for over 10 years, I especially appreciate its remarkable transparency during early stages, which enables direct visualization of tissue and organ formation. Its short life cycle and genetic similarity to humans make it a versatile and powerful tool for studying complex biological processes and diseases. Additionally, compared to other laboratory animals, zebrafish are easier to house and maintain, requiring less space, effort, and time. I also enjoy working with this model because of its wide use across various research fields, offering exposure to many disciplines and cutting-edge research applications, making it an ideal system for scientific growth and discovery.
What does a regular day in your role look like?
A typical day involves overseeing the daily husbandry and management of the zebrafish facility, including routine water quality testing, maintaining optimal environmental conditions, and ensuring the health and well-being of the fish through regular monitoring and health checks. A key part of my role is to monitor all zebrafish users in the facility, providing technical support, guidance on husbandry and experimental procedures, and ensuring compliance with safety and ethical standards. Additionally, I troubleshoot equipment issues and document all activities to maintain a high standard of operation, supporting both ongoing research and the training of new staff and students. Another key aspect of my role is to conduct experiments and research projects, serving as part of the facility’s service to partner institutions and supporting their scientific objectives.
What challenges does your facility face?
The facility is in high demand, with many new projects, students, and collaborators interested in working with us. However, our space and staff capacity are limited, which poses a challenge in efficiently accommodating all requests. To address this, we are constantly seeking innovative ways to improve accuracy and efficiency. Recently, we collaborated with Bionomous to add the EggSorter as to leverage technology for better workflow and precise embryo management. Continually exploring such solutions remains an ongoing priority to ensure high-quality, timely support for all users.
How many zebrafish embryos and lines do you handle per day?
The facility includes five main lines of zebrafish, in addition to the wild-type AB line. All are being used for experimental work. Before introducing the new technology , we used to serve around 18 projects/ semester and produce an estimate of 1500 embryos per day; however, after it  was introduced, we have been able to increase the capacity to 30 projects with around 3000 -3500 embryos per day.
In which ways does the EggSorter influence your workflow?
Embryo counting was done manually, consuming time and effort from the facility technologists. However, after this technology , embryo counting and sorting have become more efficient, so that the time used for counting is now being utilized in more complex tasks, allowing technologists to reallocate resources and concentrate on other essential research activities.
How would you qualify the quality of your outputs using the EggSorter?
We have conducted an initial evaluation of the machine and found that it provides consistent counting and sorting performance, in addition to improved time efficiency, so the technologists load the embryos into the machine to be counted or sorted while conducting other tasks at the same time.
Which characteristics do you look for the most in embryos for your research?
We look for all characteristics like fertility status, developmental stage, and fluorescence, since we handle a high volume of embryos daily for research and colony management, including fluorescent lines.
Conclusions & outlooks
The insights shared by Enas El Absi highlight how automation is becoming a cornerstone of zebrafish research. By reducing manual bottlenecks, improving reproducibility, and scaling up workflows, technologies like the EggSorter are not just easing day-to-day operations, they are enabling new levels of scientific reliability and throughput.
As facilities look to the future, automation will be key to meeting the growing demand for zebrafish in biomedical research and to ensuring data that is both robust and reproducible. With innovative tools at their side, researchers can focus less on repetitive tasks and more on what truly matters: accelerating discoveries that impact human health.
References
- Qatar University, Biomedical Research Center, Zebrafish facility, https://www.qu.edu.qa/en-us/research/brc/facilities/zebrafish-facility
- Link to publications: https://scholar.google.com/scholar?start=20&q=%22zebrafish%22+AND+%22Qatar+University%22&hl=en&as_sdt=0,5&as_ylo=2005&as_yhi=2025
