In this interview, NewsMedical talks to Jason Otterstrom about the role of AI-based Athena Zebrafish software in investigating zebrafish imaging results and its importance in biomedical research using zebrafish models. Athena Now available for download with a flexible, pay-as-you-go license.
How could high-content imaging of zebrafish revolutionize the biomedical research field?
Zebrafish (Danio Lelio) are promising emergent model systems for biomedical research and may enable fast, high-throughput studies of human disease in living vertebrates.
Humans and zebrafish have almost identical organs, share 70% of the same genes, and 84% of genes associated with human diseases have zebrafish counterparts.
Zebrafish embryos are transparent, can be manipulated at the single-cell stage, and rapidly develop into larvae in a few days. This physiological development can be microscopically imaged using thousands of individual fish to directly visualize the effects of treatments on organ systems, development, and physiology.
Currently, there are no other well-characterized biological model systems that can offer these advantages.
Dr. Otterstrom: “We offer three affordable license packages to suit your different throughput needs. At an effective price of $0.15 to $0.29 per image, zebrafish labs and researchers can use Athena software to enhance their analytical workflows. ” Image credit: IDEA Bio-Medical Ltd.
How are zebrafish images used and why are they important to researchers?
Analyze microscopic images of zebrafish to extract numerical or quantitative information about embryos and larvae. The animal’s transparent body allows much of the fish’s internal structure to be observed, even with simple brightfield imaging.
Through genetic manipulation, fluorescent proteins can be inserted into living zebrafish for tissue-specific imaging and analysis.
Life science researchers then analyze zebrafish images to study and measure the biological and physiological changes occurring in different anatomical regions of living fish. For example, organ development and cell proliferation or cell death associated with pharmacokinetics, toxicity, cancer, and genetic alterations can be directly observed and measured.
How can AI help with these investigations?
Analyzing zebrafish images is a time-consuming bottleneck in screening studies. Images can be easily interpreted by humans, but conventional image analysis algorithms cannot easily detect fish and their anatomy. Instead, measurements are performed manually using a single image.
IDEA Bio-Medical learned about this challenge from a client and created a new deep learning AI (artificial intelligence) algorithm to automatically analyze zebrafish images.
The AI training process is complex, error-prone, and requires substantial time and effort that biology-focused clients cannot do on their own. The AI we developed can now reliably identify objects that are clearly visible to humans, such as the outline of a zebrafish and its internal structure.
Now, we want to make this tool available to all zebrafish researchers, regardless of the microscope they use.
Athena software analyzes zebrafish without parameters using simple bright-field images, capturing the outline of the fish and much of its internal anatomy (yolk sac, eyes, notochord, etc.), including the head, trunk, and tail. can be extracted along with body regions. Image credit: IDEA Bio-Medical Ltd.
Why do you need information about zebrafish anatomy to interpret fluorescence signals?
Many processes investigated using zebrafish originate or initiate in specific organs or regions within the body. They can be marked with fluorescent labels to image tissues or cells of interest. However, these should be distinguished from unwanted signals and autofluorescence.
For example, in zebrafish larvae, hematopoietic stem cells (HSCs) originate from a specific region of the tail, also known as tail hematopoietic tissue (CHT). It resembles mammalian fetal liver and is associated with human leukemia. Studies looking at proliferation of GFP-labeled HSCs should focus specifically on the tail and ignore fluorescent signals present elsewhere, such as autofluorescence in circulating cells and the yolk sac.
Athena is currently the only available software that enables high content screening in this context. It enables automated cell counting in only specific parts of the fish, maximizing both throughput and extracted data.
This is in contrast to common approaches such as a simple intensity threshold that ignores visible anatomy. Instead, all fluorescence is collected together, regardless of its origin, producing noisy data. Manually selecting tails improves quality but severely limits achievable throughput.
Athena is the first of its kind Automated image analysis software for zebrafish microscopy. Image credit: IDEA Bio-Medical Ltd.
What is Athena image analysis software and how can I use it?
athena zebrafish Standalone software developed and delivered by IDEA Bio-Medical to empower every zebrafish researcher. This enables true high-content imaging in zebrafish for the first time.
Athena allows you to analyze zebrafish without parameters using simple brightfield images. Automatically detect zebrafish embryos and larvae up to 5 days of age (dpf), showing the outline of the fish and many of its internal structures (yolk sac, eyes, notochord, etc.) and the body regions of the head, trunk, and tail. Extract with .
For each of these objects, the software can measure morphology (area, length and shape) and detect fluorescence in the associated color channel. Both fluorescence intensity and spot/structure detection within specific anatomical structures are supported.
The software is suitable for a wide range of researchers and accepts multiple image format types output from almost any microscope manufacturer.
Click here for a free 14-day trial of Athena Zebrafish software that can be downloaded from the IDEA Bio-Medical website.
What advantages does this method have over alternative techniques?
athena is It is the only automated software dedicated to zebrafish microscopy and offers several advantages.
- automation: It eliminates subjective human biases and errors and allows for direct comparison of results between different laboratories while allowing experimentation to be scaled up.
- Intuitive and easy-to-use interface: Users can quickly and easily adapt Athena to their research.
- Versatile and Flexible AI: It is widely applicable to many types of screens, including zebrafish, as explained by an Athena customer on the IDEA Bio-Medical YouTube page.
- customer support Ensure your success with personalized new user onboarding.
What is flexible, pay-as-you-go licensing that you offer and what are the benefits?
IDEA Bio-Medical recognizes that annual software licenses can be expensive. Especially if the images have not been analyzed consistently throughout the year. That’s why we offer Athena on a pay-as-you-go basis so that zebrafish researchers can adapt the license to analyze images when they need it.
We offer three affordable packages for different throughput needs. At an effective price of US$0.15-0.29 per image, zebrafish labs and researchers can use Athena to enhance their analytical workflows.
Licenses can be purchased monthly or quarterly, depending on your needs. This flexibility allows laboratories to adjust licenses to match changing projects, students, grant submissions, and other dynamics of academic research.
Source: IDEA Bio-Medical Ltd.
What kind of support does IDEA Bio-Medical provide to Athena software users?
Analysis of microscopic images is complex and requires skill and experience. In addition to an intuitive software interface, it offers personalized customer support, enabling users of all skill levels to be independent and productive with Athena.
At IDEA Bio-Medical, we pride ourselves on working closely with our clients and their unique needs. New users can undergo her one-on-one onboarding session with a certified product specialist to walk them through the software with their own data, ensuring a smooth and positive first experience.
Additional Athena support is also available by contacting IDEA Bio-Medical directly.
What is the future direction of Athena software and who will benefit from using it?
Athena is a rich application-based image analysis software for easy and fast analysis of microscopy images. The complete Athena package is now integrated into IDEA Bio-Medical’s flagship high-content screening (HCS) microscope, the Hermes platform.
In the future, the full Athena software associated with microscopy imaging of 2D and 3D cell cultures will be offered as a standalone platform, enabling all biologists to perform image analysis at the push of a button.
About Dr. Otterstrom
Dr. Otterstrom holds a BS in Applied Physics from the University of Utah. A Harvard student for his PhD, he used single-molecule microscopy techniques to study the biophysics of membrane fusion mediated by the influenza virus hemagglutinin protein. He then received his fellowship with Marie Curie at the Institute for Photonic Science (ICFO) near Barcelona, Spain to study the fine packing structure of chromatin using super-resolution imaging.
As an application scientist at IDEA Bio-Medical, he helps clients adapt a wide variety of experiments and assays performed in the context of automated microscopy for the company’s flagship product, WiScan Hermes.
About IDEA Bio-Medical Ltd.
IDEA Bio-Medical was founded in 2007 through a partnership between YEDA (the commercialization arm of the Weizmann Institute) and IDEA Machine Development (the innovation hub).
The company specializes in automated image processing systems and image analysis software, offering a wide range of biological applications based on proprietary algorithm libraries.
The WiScan Hermes system incorporates the most advanced technology currently available in the machine vision field, delivering high reliability and quality at the level of the semiconductor and digital printing industries, the areas of expertise of parent company IDEA Machine Development. The engineering methodology to achieve is integrated.Design and Production Co., Ltd.
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