Summary: Researchers developed an AI-based method to track neurons in moving and deforming animals, a significant advancement in neuroscience research. This convolutional neural network (CNN) method overcomes the challenge of tracking brain activity in organisms like worms, whose bodies constantly change shape.
By employing ‘targeted augmentation’, the AI significantly reduces the need for manual image annotation, streamlining the neuron identification process. Tested on the roundworm Caenorhabditis elegans, this technology has not only increased analysis efficiency but also deepened insights into complex neuronal behaviors.
Key Facts:
- Innovative AI Technique: The CNN method automatically synthesizes annotations, learning internal brain deformations to adapt to new postures.
- Efficiency in Analysis: This approach triples the analysis throughput compared to full manual annotation, dramatically saving time and effort in research.
- Application and Findings: Applied to the neuron-rich roundworm Caenorhabditis elegans, the method revealed complex interneuron behaviors and responses to stimuli.
Source: EPFL
Recent advances allow imaging of neurons inside freely moving animals. However, to decode circuit activity, these imaged neurons must be computationally identified and tracked. This becomes particularly challenging when the brain itself moves and deforms inside an organism’s flexible body, e.g. in a worm. Until now, the scientific community has lacked the tools to address the problem.
Now, a team of scientists from EPFL and Harvard have developed a pioneering AI method to track neurons inside moving and deforming animals. The study, now published in Nature Methods, was led by Sahand Jamal Rahi at EPFL’s School of Basic Sciences.
The new method is based on a convolutional neural network (CNN), which is a type of AI that has been trained to recognize and understand patterns in images. This involves a process called “convolution”, which looks at small parts of the picture – like edges, colors, or shapes – at a time and then combines all that information together to make sense of it and to identify objects or patterns.
The problem is that to identify and track neurons during a movie of an animal’s brain, many images have to be labeled by hand because the animal appears very differently across time due to the many different body deformations. Given the diversity of the animal’s postures, generating a sufficient number of annotations manually to train a CNN can be daunting.
To address this, the researchers developed an enhanced CNN featuring ‘targeted augmentation’. The innovative technique automatically synthesizes reliable annotations for reference out of only a limited set of manual annotations. The result is that the CNN effectively learns the internal deformations of the brain and then uses them to create annotations for new postures, drastically reducing the need for manual annotation and double-checking.
The new method is versatile, being able to identify neurons whether they are represented in images as individual points or as 3D volumes. The researchers tested it on the roundworm Caenorhabditis elegans, whose 302 neurons have made it a popular model organism in neuroscience.
Using the enhanced CNN, the scientists measured activity in some of the worm’s interneurons (neurons that bridge signals between neurons). They found that they exhibit complex behaviors, for example changing their response patterns when exposed to different stimuli, such as periodic bursts of odors.
The team have made their CNN accessible, providing a user-friendly graphical user interface that integrates targeted augmentation, streamlining the process into a comprehensive pipeline, from manual annotation to final proofreading.
“By significantly reducing the manual effort required for neuron segmentation and tracking, the new method increases analysis throughput three times compared to full manual annotation,” says Sahand Jamal Rahi.
“The breakthrough has the potential to accelerate research in brain imaging and deepen our understanding of neural circuits and behaviors.”
News
Sleep Deprivation Triggers a Strange Brain Cleanup
When you don’t sleep enough, your brain may clean itself at the exact moment you need it to think. Most people recognize the sensation. After a night of inadequate sleep, staying focused becomes harder [...]
Lab-grown corticospinal neurons offer new models for ALS and spinal injuries
Researchers have developed a way to grow a highly specialized subset of brain nerve cells that are involved in motor neuron disease and damaged in spinal injuries. Their study, published today in eLife as the final [...]
Urgent warning over deadly ‘brain swelling’ virus amid fears it could spread globally
Airports across Asia have been put on high alert after India confirmed two cases of the deadly Nipah virus in the state of West Bengal over the past month. Thailand, Nepal and Vietnam are among the [...]
This Vaccine Stops Bird Flu Before It Reaches the Lungs
A new nasal spray vaccine could stop bird flu at the door — blocking infection, reducing spread, and helping head off the next pandemic. Since first appearing in the United States in 2014, H5N1 [...]
These two viruses may become the next public health threats, scientists say
Two emerging pathogens with animal origins—influenza D virus and canine coronavirus—have so far been quietly flying under the radar, but researchers warn conditions are ripe for the viruses to spread more widely among humans. [...]
COVID-19 viral fragments shown to target and kill specific immune cells
COVID-19 viral fragments shown to target and kill specific immune cells in UCLA-led study Clues about extreme cases and omicron’s effects come from a cross-disciplinary international research team New research shows that after the [...]
Smaller Than a Grain of Salt: Engineers Create the World’s Tiniest Wireless Brain Implant
A salt-grain-sized neural implant can record and transmit brain activity wirelessly for extended periods. Researchers at Cornell University, working with collaborators, have created an extremely small neural implant that can sit on a grain of [...]
Scientists Develop a New Way To See Inside the Human Body Using 3D Color Imaging
A newly developed imaging method blends ultrasound and photoacoustics to capture both tissue structure and blood-vessel function in 3D. By blending two powerful imaging methods, researchers from Caltech and USC have developed a new way to [...]
Brain waves could help paralyzed patients move again
People with spinal cord injuries often lose the ability to move their arms or legs. In many cases, the nerves in the limbs remain healthy, and the brain continues to function normally. The loss of [...]
Scientists Discover a New “Cleanup Hub” Inside the Human Brain
A newly identified lymphatic drainage pathway along the middle meningeal artery reveals how the human brain clears waste. How does the brain clear away waste? This task is handled by the brain’s lymphatic drainage [...]
New Drug Slashes Dangerous Blood Fats by Nearly 40% in First Human Trial
Scientists have found a way to fine-tune a central fat-control pathway in the liver, reducing harmful blood triglycerides while preserving beneficial cholesterol functions. When we eat, the body turns surplus calories into molecules called [...]
A Simple Brain Scan May Help Restore Movement After Paralysis
A brain cap and smart algorithms may one day help paralyzed patients turn thought into movement—no surgery required. People with spinal cord injuries often experience partial or complete loss of movement in their arms [...]
Plant Discovery Could Transform How Medicines Are Made
Scientists have uncovered an unexpected way plants make powerful chemicals, revealing hidden biological connections that could transform how medicines are discovered and produced. Plants produce protective chemicals called alkaloids as part of their natural [...]
Scientists Develop IV Therapy That Repairs the Brain After Stroke
New nanomaterial passes the blood-brain barrier to reduce damaging inflammation after the most common form of stroke. When someone experiences a stroke, doctors must quickly restore blood flow to the brain to prevent death. [...]
Analyzing Darwin’s specimens without opening 200-year-old jars
Scientists have successfully analyzed Charles Darwin's original specimens from his HMS Beagle voyage (1831 to 1836) to the Galapagos Islands. Remarkably, the specimens have been analyzed without opening their 200-year-old preservation jars. Examining 46 [...]
Scientists discover natural ‘brake’ that could stop harmful inflammation
Researchers at University College London (UCL) have uncovered a key mechanism that helps the body switch off inflammation—a breakthrough that could lead to new treatments for chronic diseases affecting millions worldwide. Inflammation is the [...]
