What’s next for Zebrafish microscopy in 2023?

Dr. Jason Otterstrom talks about the benefits and challenges of using Zebrafish as an emerging model for life science research. He discusses how new automated approaches for analyzing microscopy images of Zebrafish samples are enabling new insights. In particular, he focuses on IDEA Bio-Medical’s new automated, AI-powered analysis software, Athena.  This innovation removes the bottleneck of manual quantification and is poised to enhance the rate of discovery to previously unachievable levels.  Athena is now available for download in a novel pay-per-use basis. 

Why did Zebrafish become popular models for research purposes?

Zebrafish are a promising and exciting emergent model system for performing biomedical research in the life sciences. They have a number of advantages over existing mouse models, such as very fast reproductive times and a more economical husbandry. Additionally, higher experimental throughput is possible due to their short reproductive time.

Moreover, their genetic sequence has around 70% similarity to humans, which makes them genetically relevant, while also being amenable to genetic manipulation for introduction of fluorescent proteins as a reporter mechanism.

The size of the zebrafish is also an important advantage. Zebrafish form very small embryos and larvae, so in their young stages, they are transparent, making them very amenable to microscopy.

Even with bright-field imaging, the fish is clearly observable. Detailed internal anatomy can be seen along with biological functions happening in a living, multi-organ system, which is advantageous for pharmacokinetics, toxicity studies, and genetic knockouts.

There is also the benefit of the fluorescence giving a high contrast readout that is very binary. I believe there are many advantages that are going to push zebrafish into new fields in the coming decade.

Screen shot from IDEA Bio-Medical's new Zebrafish analysis software. Analysis parameters calibration screen and attributes table are shown. The anatomy identified is coupled to fluorescence channels to permit anatomy-specific study of fluorescence changes.

What challenges do researchers face using zebrafish models?

With all the exciting potential that zebrafish hold for the future of life science research, there are several challenges when applying them as a model system for microscopy. While their transparency is an advantage and they can be imaged on many types of microscopes, placing them in the right orientation is a substantial challenge. This is because, depending on how they are oriented, you can see some of their internal anatomies better, or they can become obfuscated and unobservable, both in bright-field and in fluorescence.

Many researchers struggle with the challenge of getting the fish oriented to see the anatomy that is of interest with the highest fidelity.

There are different approaches to address this; some involve specialized alignment plates, others involve agarose gels – but none are fully meeting the throughput needs. Such approaches require a lot of manual intervention, contributing to the difficulty of overcoming this challenge.

Another challenge is, once the images have been acquired, to extract meaningful data from them. The images themselves to a human are easily interpretable; the fish and its organs can be seen, but a computer does not always register this.

Until now, many have relied on ImageJ and other types of programable software to manually identify areas of interest or simply look at the fluorescence channel and disregard anatomical context to obtain simplistic fluorescence readouts. As a result, meaningful information from disregarded anatomy is not considered. 

How is IDEA Bio-Medical able to offer potential solutions to these challenges?

IDEA Bio-Medical specializes in automating solutions for image acquisition and image analysis. Our Hermes platform, which includes the Hermes microscope and the accompanying Athena software, has been cited in over a hundred scientific journals supporting high impact research globally. As a small company, we work very closely with our clients and, through them, have recognized the need for image analysis in zebrafish.

At IDEA Bio-Medical, we come from a background of high-content screening where everything is automated. We have over a decade of experience now empowering life science researchers to automate their microscopy research in image acquisition and image analysis.

Tell us about the relationship you have with your clients and how IDEA Bio-Medical helps support users in their research?

As I mentioned previously, we, as a small company, take pride in working closely with our clients and their unique needs as scientific innovators. Through them, we came to understand the image analysis challenge zebrafish researchers face and the bottleneck it causes to their workflows. Together with our clients, we have developed a novel, deep learning-based algorithm to identify the fish and its internal anatomy in bright-field images, a completely label-free image acquisition requirement.

From that image analysis, we are able to extract the fish contour and all of the internal anatomy. We then extract quantitative information about the morphology of the fish and its internal anatomy, using that information also to study the fluorescent signal that may be present. Studying the specific localization of the fluorescence within the zebrafish anatomy is possible as a result. Ultimately, we enable true high-content imaging in zebrafish for the first time.

How accessible is the Athena software to researchers as a whole, do they require exclusive access to the Hermes microscope?

Up until now, the Athena software package was integrated exclusively into the Hermes platform. We are excited to now make Athena open to a broader audience by offering it as a stand-alone product to support all zebrafish researchers. To do so, we have adapted Athena to accept and analyze images from all types of microscopes in virtually any image format, be it open-source TIFF or proprietary.

Thus, images can be acquired on upright microscopes, inverted microscopes, or stereo microscopes. In this way, we hope to support a broad range of researchers who need to analyze anywhere from a few dozen to hundreds of Zebrafish images per week. There is no throughput limit and we offer a range of packages to adapt to each lab’s throughput requirements. Overall, we at IDEA empower zebrafish researchers to extract more from their data and aim higher with their research goals.

About The Speaker

Dr. Jason Otterstrom  has a diverse background in biophysics including microscopy, optical design, image analysis and sample labeling. His expertise is adapting biological assays to benefit from utilization of automated microscopy methods. He obtained a Bachelor of Arts in Applied Physics at the University of Utah. After he obtained his PhD in Biophysics & Microscopy at Harvard University,  He went on to obtain a Marie Curie fellowship to utilize super-resolution imaging at the Institute of Photonic Sciences (ICFO) near Barcelona, Spain.

As a business development manager for IDEA Bio-Medical , Jason supports clients with adapting their diverse experiments and assays to be performed in the context of automated microscopy on the company’s flagship product, the WiScan Hermes.