Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Neural networks let microscopists see more

07.12.2018

Researchers develop a method to overcome the limitations of microscopes

Modern microscopes can record many hours of 3D time-lapse movies of every cell as an organism develops. Just as for regular photography, fluorescence microscopy requires enough light to avoid dark and noisy images. However, the light necessary for such movies can easily reach levels that harm frequently studied model organisms such as worms, fish, and mice.


Noisy fluorescence microscopy image of cell nuclei of the planaria Schmidtea mediterranea (top) and the result after applying CARE (bottom)

© Martin Weigert, Tobias Boothe, and Deborah Schmidt / MPI-CBG, CSBD


Noisy fluorescence microscopy image of cell nuclei of the planaria Schmidtea mediterranea (top) and the result after applying CARE (bottom)

© Martin Weigert, Tobias Boothe, and Florian Jug / MPI-CBG, CSBD

To date, the only option to avoid this “ultimate sunburn” is to record shorter movies or reduce the amount of light used. As a consequence, many biologists are forced to work with very noisy images that are hard to interpret.

Researchers around Florian Jug and Eugene W. Myers at the Center for Systems Biology Dresden (CSBD) and the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), have now developed a content-aware image restoration method – CARE – that solves this dilemma.

This self-learning software is based on artificial neural networks and reveals the content hidden in low-light microscopy images. CARE networks are able to restore high-quality microscopy images, even if acquired with up to 60 times less laser power.

Hence, CARE enables imaging experiments that were previously impossible. This new method is freely available and designed to be used and adapted by anyone.

Fluorescence microscopy has become an indispensable tool to answer fundamental questions in the biomedical sciences. It visualizes the position of fluorescently labeled cellular building blocks in biological tissues and organisms.

In living samples, dynamic processes can be imaged over the course of many hours, enabling researchers to investigate how cells form tissues and organs during embryonic development.

However, the quality of the obtained images strongly depends on the amount of light used during acquisition. Light levels leading to high-quality images can, unfortunately, cause undesired side effects.

These side effects, known as phototoxicity, lead to changes in cellular behavior and can even be lethal for cells. Additionally, some organisms react with muscle flinching to even moderate amounts of light, also leading to unusable data. In order to avoid this “ultimate sunburn”, researchers have to limit the total amount of light used during imaging, which results in low-quality images that are hard to analyze.

An interdisciplinary group of researchers at the CSBD and MPI-CBG in Dresden, have now developed a method to get high-quality images despite using up to 60 times less light.

The novel approach – CARE – is a self-learning Content-Aware image REstoration software based on artificial neural networks. The scientists reasoned that, although one cannot acquire a long movie of high-quality images without running into the phototoxicity trap, it would be possible to obtain pairs of image snapshots: one in low-light quality and the other one with sufficient light to generate clean images.

These pairs of snapshots are used to train CARE networks that later help to make the “hidden” content in even very noisy images visible. In their study, recently published in Nature Methods, the researchers show that CARE can be successfully applied to many different microscopes, experiments, and organisms.

Martin Weigert, first author and Myers lab member, says: “One of the main applications of our method will be to enable the observation of cell or tissue dynamics under highly challenging conditions by improving the quality of the acquired images.”

Former Myers group member and co-author, Loïc Royer, who recently started his own research group at the Chan Zuckerberg Biohub in San Francisco, adds, “Imaging living organisms often requires compromises. With CARE, biologists won’t need to make such drastic compromises anymore. Our method makes previously impossible imaging experiments possible.”

“CARE is a prime example for the type of break-through technology that a truly interdisciplinary campus like ours here in Dresden-Johannstadt can produce. Computer scientists, physicists, biologists, and chemists from the CSBD, the MPI-CBG, and DRESDEN-concept institutions collaborated closely.

Everyone brought their special expertise to make this fundamental advance!”, says Florian Jug, who was a key driver behind the work. He concludes, “CARE is now opening windows through which we can better observe the biological processes that govern life. We are excited to see what creative minds around the world will do with CARE.”

Wissenschaftliche Ansprechpartner:

Dr. Florian Jug
+49 (0) 351 210 2486
jug@mpi-cbg.de

Originalpublikation:

Martin Weigert et al.: Content-aware image restoration: pushing the limits of fluorescence microscopy, Nature Methods, volume 15, pages 1090–1097 (2018), Veröffentlicht 26. November 2018 https://doi.org/10.1038/s41592-018-0216-7

Weitere Informationen:

http://www.csbdresden.de

Anja Glenk | Max-Planck-Institut für molekulare Zellbiologie und Genetik

More articles from Life Sciences:

nachricht Plant breeders of the University of Göttingen und Agrecol test Open Source Seed (OSS) Licence
07.12.2018 | Georg-August-Universität Göttingen

nachricht Artificial synapses made from nanowires
06.12.2018 | Forschungszentrum Juelich

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Researchers develop method to transfer entire 2D circuits to any smooth surface

What if a sensor sensing a thing could be part of the thing itself? Rice University engineers believe they have a two-dimensional solution to do just that.

Rice engineers led by materials scientists Pulickel Ajayan and Jun Lou have developed a method to make atom-flat sensors that seamlessly integrate with devices...

Im Focus: Three components on one chip

Scientists at the University of Stuttgart and the Karlsruhe Institute of Technology (KIT) succeed in important further development on the way to quantum Computers.

Quantum computers one day should be able to solve certain computing problems much faster than a classical computer. One of the most promising approaches is...

Im Focus: Substitute for rare earth metal oxides

New Project SNAPSTER: Novel luminescent materials by encapsulating phosphorescent metal clusters with organic liquid crystals

Nowadays energy conversion in lighting and optoelectronic devices requires the use of rare earth oxides.

Im Focus: A bit of a stretch... material that thickens as it's pulled

Scientists have discovered the first synthetic material that becomes thicker - at the molecular level - as it is stretched.

Researchers led by Dr Devesh Mistry from the University of Leeds discovered a new non-porous material that has unique and inherent "auxetic" stretching...

Im Focus: The force of the vacuum

Scientists from the Theory Department of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science (CFEL) in Hamburg have shown through theoretical calculations and computer simulations that the force between electrons and lattice distortions in an atomically thin two-dimensional superconductor can be controlled with virtual photons. This could aid the development of new superconductors for energy-saving devices and many other technical applications.

The vacuum is not empty. It may sound like magic to laypeople but it has occupied physicists since the birth of quantum mechanics.

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

EGU 2019 meeting: Media registration now open

06.12.2018 | Event News

Expert Panel on the Future of HPC in Engineering

03.12.2018 | Event News

Inaugural "Virtual World Tour" scheduled for december

28.11.2018 | Event News

 
Latest News

Engineers demonstrate mechanics of making foam with bubbles in distinct sizes

07.12.2018 | Materials Sciences

Researchers develop method to transfer entire 2D circuits to any smooth surface

07.12.2018 | Materials Sciences

UC San Diego researchers develop sensors to detect and measure cancer's ability to spread

06.12.2018 | Health and Medicine

VideoLinks
Science & Research
Overview of more VideoLinks >>>