q&more
My watch list
my.chemie.de  
Login  

News

Machine learning algorithm automatically sorts zebrafish eggs

© Fraunhofer IPA

Prototype of the automated fish egg sorter.

06-Sep-2018: Zebrafish possess almost all of the same genes we humans do - and that makes their eggs the perfect model organisms for use in genetic and drug research. Previously, samples have had to be prepared manually, which is a very time-consuming task. Now, however, a clever machine learning algorithm will be able to separate and sort the fish eggs automatically.

The zebrafish, or danio rerio, has long been popular as a model organism for cell and molecular biologists. Measuring just six centimeters in length when adult, these tiny creatures hatch out of transparent eggs spawned by the mother fish. The fish is extremely valuable to researchers because its eggs remain transparent right into the early larval stage, which allows scientists to observe the developing cells and organs under the microscope without damaging the embryos. A mature female can lay several hundred eggs each week, which can then be used in the lab for genetic and drug research: toxicology studies of cancer drugs for instance or the investigation of heart diseases. The zebrafish genome is a 70-percent match for the human genome, and some of the most important organ systems are also the same - making it extremely valuable for biomedical research.

Working toward a high-throughput analysis system

If there is one difficulty with preparing fish egg samples, it is that a specialist is required to manually inspect each egg, determine its stage of fertilization, classify it under the microscope and then place it on a microtiter plate. It currenly takes a trained lab technician around 12 minutes to fill a standard 96-well microtiter plate - with the monotony of the task only increasing the rate of error. Researchers at Fraunhofer IPA in Stuttgart wanted to speed up this process, and now a new automated solution is expected to classify three eggs a second and sort fertilized eggs into a 96-well microtiter plate in under two minutes.

The goal is to establish a high-throughput analysis process that can be incorporated into a fully automated system, thereby further increasing sample processing rates. The initiative is funded by Baden-Württemberg’s State Ministry of Economic Affairs, Labour and Housing Construction as part of a project entitled “Laboratory 4.0 Application Center - The Cloud Laboratory.”

“Not only does this technology take the strain off the lab technicians who have to prepare the samples, it’s also a way to bypass the choke point in the process chain, cut staffing costs and increase the speed with which products such as new medicines can be developed,” says Bastian Standfest, a researcher in Technology and Device Development within Fraunhofer IPA’s department for Laboratory Automation and Biomanufacturing Engineering. Together with group leader Martin Thoma and colleagues Xi Chen and Sascha Getto from the department of Image and Signal Processing, Standfest is responsible for developing the automated fish egg sorter that is now available in prototype form. The core of the solution is a camera system that identifies the stage of fertilization using a machine learning algorithm.

A self-learning system

A rotating syringe sucks the mixture of fertilized and unfertilized eggs out of a ventilated container, adding them to a transfer liquid so that in the next step they can be directed into a fluidic channel and separated there.

Optical sensors monitor the entire process. After that, the camera system uses a deep learning algorithm trained to recognize various stages of cell development so as to determine the eggs’ stage of fertilization. “We’re training the algorithm using a database of images of classified fish eggs. The algorithm learns to identify the various markers of the different stages of cell development as it goes, and this is what allows it to determine whether an egg is fully fertilized or not,” explains Standfest. The fertilized eggs are placed in the wells of the microtiter plate by means of a pressure pulse generated by the fluidic chip. Initial testing has gone well, with an extremely low false positive rate - only in 0.2 percent of cases was an unfertilized egg erroneously classified as fertilized. The research team anticipates being able to process several thousand eggs an hour.

At the moment, Standfest and his colleagues are busy at work maximizing the speed of the process and optimizing the algorithm. “The newly recorded images are constantly being fed back into the system, gradually improving it until, we hope, we have a self-learning system,” says Standfest. “On top of that, we can potentially adapt the system to other macroscopic sorting processes, including automated separation and classification of other organisms.”

The current design represents a first use case for an intelligent and self-learning system of this type. This platform technology is the first step toward bio-intelligent systems, and it can potentially be adapted to other areas of application. Projects of this type moreover support the biological transformation of manufacturing at the interface between the life sciences and engineering.

The researchers will be presenting their solution from November 6-8, 2018 at the VISION trade show in Stuttgart (joint Fraunhofer booth, Hall 1, Booth G42).

Facts, background information, dossiers

  • zebrafish
  • model organisms
  • machine-learning

More about Fraunhofer-Institut IPA

  • News

    Producing vaccines without the use of chemicals

    Producing vaccines is a tricky task – especially in the case of inactivated vaccines, in which pathogens must be killed without altering their structure. Until now, this task has generally involved the use of toxic chemicals. Now, however, an innovative new technology developed by Fraunhofe ... more

    Automation to ensure quality in 3D printing

    The genuine hope for Industry 4.0 is pinned on 3D-printed parts, but there are still no quality standards in place for additive manufacturing. Fraunhofer IPA has developed an automated system that enables quality to be automatically checked during printing. Industry partners can test and fu ... more

    Cleanroom on demand

    “Clean Multipurpose Cover” is the world’s first flexible cleanroom system The smallest degree of contamination can lead to major quality issues across many industries. Should, for example, any impurities occur on microchips, space probes and lenses, this can lead to defects or faulty end d ... more

More about Fraunhofer-Gesellschaft

  • News

    Fraunhofer presents high-speed microscope with intuitive gesture control

    The Fraunhofer Institute for Production Technology IPT in Aachen has developed a high-speed microscope for quality control of large-area objects for the semiconductor and electronics industries or for rapid testing of biological samples. The microscope digitizes samples with up to 500 frame ... more

    Pocket-size food scanner

    According to a study by the environmental organization WWF Germany, ten million metric tons of food are thrown in the garbage every year in Germany despite still being edible. A mobile food scanner will allow consumers and supermarket operators in the future to test whether food items have ... more

    Producing vaccines without the use of chemicals

    Producing vaccines is a tricky task – especially in the case of inactivated vaccines, in which pathogens must be killed without altering their structure. Until now, this task has generally involved the use of toxic chemicals. Now, however, an innovative new technology developed by Fraunhofe ... more

q&more – the networking platform for quality excellence in lab and process

The q&more concept is to increase the visibility of recent research and innovative solutions, and support the exchange of knowledge. In the broad spectrum of subjects covered, the focus is on achieving maximum quality in highly innovative sectors. As a modern knowledge platform, q&more offers market participants one-of-a-kind networking opportunities. Cutting-edge research is presented by authors of international repute. Attractively presented in a high-quality context, and published in German and English, the original articles introduce new concepts and highlight unconventional solution strategies.

> more about q&more

q&more is supported by:

 

Your browser is not current. Microsoft Internet Explorer 6.0 does not support some functions on Chemie.DE