Imaging Zebrafish? Here's a software you must know

Dr. Jason Otterstrom talks about the role of AI-based Athena Zebrafish software in exploring Zebrafish imaging results and its importance for bio-medical research using Zebrafish models. With an effective price of $0.29 USD per image or less, any Zebrafish lab or researcher can use Athena and enhance their analysis workflows.  Athena Zebrafish is now available for download with a flexible pay-per-use license. 

Why is high-content Zebrafish imaging such a breakthrough, and how will it revolutionize bio-medical research

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 most of the same organs, share 70% of the same genes, and 84% of the genes associated with human disease have zebrafish counterparts.  Embryos are transparent and can be manipulated at the single-cell stage, then quickly grow to larvae in a matter of days.  This physiological development can be imaged with a microscope using thousands 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 able to offer these advantages. 

How are zebrafish images used and why are they important for researchers? 

Zebrafish images are analyzed to extract numerical or quantitative information about the embryos and larvae.  Because they are transparent, much of the fish’s internal anatomy is clearly observable even with simple bright-field imaging. Genetic manipulation permits the insertion of fluorescent proteins into the live zebrafish for tissue-specific imaging and analysis.  Life science researchers then analyze images of zebrafish to study and measure biological and physiological changes happening in different anatomical regions within a living fish.  For example, organ development and cellular proliferation or death in relation to pharmacokinetics, toxicity, cancer and genetic changes can be directly observed and measured. 

How can AI help in Zebrafish based research? 

The zebrafish image analysis is a time-consuming bottleneck in screening studies.  While the images may be easily interpretable to a human, conventional image analysis algorithms do not readily detect the fish or its anatomy.  Instead, 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 automatically analyze their images for them. The AI training process is complex and error-prone, requiring substantial time and effort that our biology-focused clients were not able to do themselves. The AI we have developed is now able to robustly identify objects like the zebrafish contour and its  internal anatomy that are clearly visible to us humans.  We now want to make this tool available to all zebrafish researchers.

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Many processes investigated using zebrafish take place or begin in specific organs or regions within the body.  They can be marked with fluorescence labeling to image the tissue or cells of interest. But these must be distinguished from undesired signals and autofluorescence.

For example, in the zebrafish larva, hematopoietic stem cells (HSC) originate in a specific area within the tail termed the caudal hematopoietic tissue (CHT).  It is analogous to the mammalian fetal liver and relevant to leukemia in humans.  Studies looking at proliferation of GFP-labeled HSC need to focus specifically on the tail and ignore those fluorescent signals present elsewhere, such as circulating cells and yolk sac autofluorescence.  

Athena is currently the only software enabling high-content screening in this context.  It permits automated cell counts exclusively within specific parts of the fish to maximize both throughput and data extracted.  It stands in contrast to common approaches such as simple intensity thresholding, which ignores the visible anatomy.  Instead, all fluorescence is gathered together, irrespective of its origin, producing noisy data.  Manual selection of the tail would improve quality, but severely limit achievable throughput.  

What is Athena image analysis software, and how can it be 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 first time.

Athena permits parameter-free zebrafish analysis using simple brightfield images.  It automatically detects zebrafish embryos and larvae up to 5 days old (dpf), extracting the fish contour and much of its internal anatomy (yolk sac, eye, notocord and more), along with body regions of the head, trunk and tail.  For each of these objects, the software measures the morphology (area, length, and shape) and can detect fluorescence in associated color channels. Both fluorescence intensity and spot/structure detection within specific anatomy are supported.  The software is suited for a broad range of researchers and accepts multiple image format types output from nearly all microscope manufacturers.  

A free 14-day trial version of Athena Zebrafish is available for download by new users from the IDEA Bio-Medical website

What advantages does this method have over alternative techniques? 

Athena is the only automated software dedicated to zebrafish microscopy, offering several advantages:

  • Automation: allows experimental scale-up while eliminating subjective human bias or error; reproducibility permits direct comparison of results between different labs.
  • Intuitive and user-friendly software interface: facilitates users to quickly and easily adapt Athena for their research. 
  • Versatile and flexible AI algorithm: widely applicable for many types of screens involving zebrafish, as described by Athena customers on the IDEA Bio-Medical YouTube page. 
  • Customer support with new user on-boarding to ensure the success of our customers. 

What is the Flexible Pay-Per-Use license you are offering and what are its advantages? 

IDEA Bio-Medical recognizes that annual software licenses can be expensive, especially if images are not consistently analyzed throughout the year.  Hence, we offer Athena on a pay-per-use basis so that zebrafish researchers can adapt their license to analyze images when they need it.

We offer 6 affordable packages for different throughput needs. With an effective price of $0.29 USD per image or less, any Zebrafish lab or researcher can use Athena and enhance their analysis workflows. 

Packages are valid for 12 months and can be purchased according to needs. This flexibility allows labs to adjust their licenses to fit their changing projects, students, grant submissions and other dynamics of academic research. 

Athena Packages

Flexible Pay-Per-Use License

We offer six license packages for different throughput requirements.
Choose the best package that fits your needs.
Number Of Images:
500 Starter
1,000 Advanced
5,000 Pro
10,000 Expert
25,000 Elite
50,000 Enterprise
Price per image: 0.2
Order Now
*All purchased packages are valid for 12 months post installation

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

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

We at IDEA Bio-Medical take pride in working closely with our clients and their unique needs.  New users can receive a one-on-one on-boarding session with a qualified product specialist to walk through the software using their own data and ensure a smooth, positive first experience.  Additional Athena support is also available by reaching out to IDEA Bio-Medical directly.  

Dr. Otterstrom: "We offer six affordable license packages for different throughput needs. With an effective price between $0.15 and $0.29 USD per image analyzed, any Zebrafish lab or researcher can use Athena software to enhance their analysis workflows."

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.