On this interview, NewsMedical talks to Jason Otterstrom concerning the role of AI-based Athena Zebrafish software in exploring Zebrafish imaging results and its importance for bio-medical research using Zebrafish models.  Athena is now available for download with a versatile pay-per-use license. 

How can high-content imaging of Zebrafish revolutionize the bio-medical research field? 

Zebrafish (Danio rerio) are a promising emergent model system for biomedical research with the potential to enable fast, high throughput studies of human disease in living vertebrates. 

Humans and zebrafish have a lot of the same organs, share 70% of the identical genes, and 84% of the genes related to human disease have zebrafish counterparts.

Zebrafish embryos are transparent and may be manipulated on the single-cell stage, then quickly grow into larvae in a matter of days. This physiological development may be imaged with a microscope using hundreds of individual fish to directly visualize the effect of treatments on organ systems, development and physiology.

No other well-characterized biological model system is currently in a position to offer these benefits. 

Dr. Otterstrom: “We provide three reasonably priced license packages for various throughput needs. With an efficient price between $0.15 and $0.29 USD per image analyzed, any Zebrafish lab or researcher can use Athena software to boost their evaluation workflows.” Image Credit: IDEA Bio-Medical Ltd.

How are images of zebrafish used, and why are they essential for researchers? 

Microscopy images of zebrafish are analyzed to extract numerical or quantitative information concerning the embryos and larvae. The animal’s transparent body makes much of the fish’s internal anatomy observable, even with easy bright-field imaging.

Genetic manipulation permits the insertion of fluorescent proteins into the live zebrafish for tissue-specific imaging and evaluation.

Life science researchers then analyze images of zebrafish to check and measure biological and physiological changes happening in numerous anatomical regions inside a living fish. For instance, organ development and cellular proliferation or death in relation to pharmacokinetics, toxicity, cancer, and genetic changes may be directly observed and measured. 

How can AI assist in these investigations? 

Analyzing images of zebrafish is a time-consuming bottleneck in screening studies. While the pictures could also be easily interpretable by a human, conventional image evaluation algorithms don’t readily detect the fish or its anatomy. As an alternative, measurements are performed manually using single images. 

IDEA Bio-Medical learned of this challenge from our clients, so we created a novel deep-learning AI (artificial intelligence) algorithm to mechanically analyze their Zebrafish images for them.

The AI training process is complex and error-prone, requiring substantial effort and time that our biology-focused clients couldn’t do themselves. The AI we’ve developed can now robustly discover objects just like the zebrafish contour and its internal anatomy which can be clearly visible to us humans.

We now have the desire to make this tool available to all zebrafish researchers, irrespective of which microscope they use.

IDEA’s Zebrafish evaluation software was developed with our clients, for our clients.Play

Athena software permits parameter-free Zebrafish evaluation using easy bright-field images, extracting the fish contour and far of its internal anatomy (yolk sac, eye, notocord and more), together with body regions of the pinnacle, trunk, and tail. Image Credit: IDEA Bio-Medical Ltd.

Why do we’d like details about Zebrafish anatomy to interpret fluorescence signals? 

Many processes investigated using zebrafish happen or begin in specific organs or regions inside the body. They may be marked with fluorescence labeling to image the tissue or cells of interest. Nonetheless, these have to be distinguished from undesired signals and autofluorescence.

For instance, within the zebrafish larva, hematopoietic stem cells (HSC) originate in a selected area inside the tail – otherwise often called the caudal hematopoietic tissue (CHT). It’s analogous to the mammalian fetal liver and relevant to leukemia in humans. Studies taking a look at the proliferation of GFP-labeled HSC must focus specifically on the tail and ignore those fluorescent signals present elsewhere, resembling circulating cells and yolk sac autofluorescence. 

Athena is currently the one software available that allows high-content screening on this context. It permits automated cell counts exclusively inside specific parts of the fish to maximise each throughput and data extracted. 

It contrasts common approaches, resembling easy intensity thresholding, which ignores the visible anatomy. As an alternative, all fluorescence is gathered together, no matter its origin, producing noisy data. Manual collection of the tail would improve quality but severely limit achievable throughput. 

Athena is a first-of-its-kind automated image evaluation software dedicated to zebrafish microscopy. Image Credit: IDEA Bio-Medical Ltd.

What’s Athena image evaluation software, and the way can or not it’s used? 

Athena Zebrafish is a stand-alone software developed and offered by IDEA Bio-Medical to empower all zebrafish researchers. It enables true high-content imaging in zebrafish for the primary time.

Athena permits parameter-free zebrafish evaluation using easy bright-field images. It mechanically detects zebrafish embryos and larvae as much as 5 days old (dpf), extracting the fish contour and far of its internal anatomy (yolk sac, eye, notocord, and more), together with body regions of the pinnacle, trunk, and tail.

For every of those objects, the software measures the morphology (area, length, and shape) and may detect fluorescence in associated color channels. Each fluorescence intensity and spot/structure detection inside specific anatomy are supported.

The software is fitted to a broad range of researchers and accepts multiple image format types output from nearly all microscope manufacturers.

Click here for a free 14-day trial of Athena Zebrafish software, available for download from the IDEA Bio-Medical website. 

What benefits does this method have over alternative techniques? 

Athena is the one automated software dedicated to zebrafish microscopy, offering several benefits:

• Automation: It allows experimental scale-up while eliminating subjective human bias or error and permitting direct comparison of results between different labs.
• Intuitive and user-friendly interface: Users can quickly and simply adapt Athena for his or her research. 
• Versatile and versatile AI: Widely applicable for a lot of forms of screens involving zebrafish, as described by Athena customers on the IDEA Bio-Medical YouTube page. 
• Customer support with personalized recent user onboarding to make sure the success of our customers. 

What’s the Flexible Pay-Per-Use license you might be offering, and what are its benefits? 

IDEA Bio-Medical recognizes that annual software licenses may be expensive, especially if images aren’t consistently analyzed all year long. Hence, we provide Athena on a pay-per-use basis in order that zebrafish researchers can adapt their license to research images once they need it.

We provide three reasonably priced packages for various throughput needs. With an efficient price between $0.15 and $0.29 USD per image, any Zebrafish lab or researcher can use Athena and enhance their evaluation workflows. 

Licenses may be purchased monthly or quarterly, in response to need. This flexibility allows labs to regulate their licenses to suit their changing projects, students, grant submissions and other dynamics of educational research.

Source: IDEA Bio-Medical Ltd.

 

What support does IDEA Bio-Medical provide to Athena software users?

Analyzing microscopy images is complex, requiring skill and experience. Together with an intuitive software interface, we provide personalized customer support to enable any user of any skill level to develop into independent and productive with Athena.

We at IDEA Bio-Medical take pride in working closely with our clients and their unique needs. Latest users can receive a one-on-one onboarding session with a professional product specialist to walk through the software using their very own data and ensure a smooth, positive first experience.

Additional Athena support can be available by reaching out to IDEA Bio-Medical directly.

What’s the long run direction of your Athena software, and who would profit from using it? 

Athena is a wealthy application-based image evaluation software for simple and quick evaluation of microscope images. The complete Athena package is currently integrated into the Hermes platform, IDEA Bio-Medical’s flagship high content screening (HCS) microscope.

In the long run, the total Athena software, relevant for microscopy images of 2D and 3D cell culture, might be offered as a stand-alone platform, allowing all biology researchers to perform image evaluation on the push of a button. 

About Dr. Otterstrom

Dr. Otterstrom obtained a Bachelor of Arts in Applied Physics on the University of Utah. As a Ph.D. student at Harvard University, he studied the biophysics of membrane fusion as mediated by influenza virus hemagglutinin protein using single-molecule microscopy techniques. He went on to acquire a Marie Curie fellowship to utilize super-resolution imaging to check chromatin fine-packing structures on the Institute of Photonic Sciences (ICFO) near Barcelona, Spain.

As an application scientist for IDEA Bio-Medical, he supports clients with adapting their diverse experiments and assays to be performed within the context of automated microscopy on the corporate’s flagship product, the WiScan Hermes.

About IDEA Bio-Medical Ltd.

IDEA Bio-Medical was founded in 2007 through a partnership between YEDA (the Weizmann Institute’s commercialization arm) and IDEA Machine Development (an innovation hub).

The corporate focuses on automated imaging systems and image evaluation software, offering a broad range of biological applications based on the corporate’s unique algorithms library. 

The WiScan Hermes system incorporates probably the most advanced technologies currently available within the machine vision field, integrated with engineering methodologies of high reliability and quality at the extent of semi-conductors and digital printing industries, that are the specialty of the mother company, IDEA Machine Development Design and Production Ltd.