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
The CDC buried a measles forecast that stressed the need for vaccinations
This story was originally published on ProPublica, a nonprofit newsroom that investigates abuses of power. Sign up to receive our biggest stories as soon as they’re published. ProPublica — Leaders at the Centers for Disease Control and Prevention [...]
Light-Driven Plasmonic Microrobots for Nanoparticle Manipulation
A recent study published in Nature Communications presents a new microrobotic platform designed to improve the precision and versatility of nanoparticle manipulation using light. Led by Jin Qin and colleagues, the research addresses limitations in traditional [...]
Cancer’s “Master Switch” Blocked for Good in Landmark Study
Researchers discovered peptides that permanently block a key cancer protein once thought untreatable, using a new screening method to test their effectiveness inside cells. For the first time, scientists have identified promising drug candidates [...]
AI self-cloning claims: A new frontier or a looming threat?
Chinese scientists claim that some AI models can replicate themselves and protect against shutdown. Has artificial intelligence crossed the so-called red line? Chinese researchers have published two reports on arXiv claiming that some artificial [...]
New Drug Turns Human Blood Into Mosquito-Killing Weapon
Nitisinone, a drug for rare diseases, kills mosquitoes when present in human blood and may become a new tool to fight malaria, offering longer-lasting, environmentally safer effects than ivermectin. Controlling mosquito populations is a [...]
DNA Microscopy Creates 3D Maps of Life From the Inside Out
What if you could take a picture of every gene inside a living organism—not with light, but with DNA itself? Scientists at the University of Chicago have pioneered a revolutionary imaging technique called volumetric DNA microscopy. It builds [...]
Scientists Just Captured the Stunning Process That Shapes Chromosomes
Scientists at EMBL have captured how human chromosomes fold into their signature rod shape during cell division, using a groundbreaking method called LoopTrace. By observing overlapping DNA loops forming in high resolution, they revealed that large [...]
Bird Flu Virus Is Mutating Fast – Scientists Say Our Vaccines May Not Be Enough
H5N1 influenza is evolving rapidly, weakening the effectiveness of existing antibodies and increasing its potential threat to humans. Scientists at UNC Charlotte and MIT used high-performance computational modeling to analyze thousands of viral protein-antibody interactions, revealing [...]
Revolutionary Cancer Vaccine Targets All Solid Tumors
The method triggers immune responses that inhibit melanoma, triple-negative breast cancer, lung carcinoma, and ovarian cancer. Cancer treatment vaccines have been in development since 2010, when the first was approved for prostate cancer, followed [...]
Scientists Uncover Hidden Protein Driving Autoimmune Attacks
Scientists have uncovered a critical piece of the puzzle in autoimmune diseases: a protein that helps release immune response molecules. By studying an ultra-rare condition, researchers identified ArfGAP2 as a key player in immune [...]
Mediterranean neutrino observatory sets new limits on quantum gravity
Quantum gravity is the missing link between general relativity and quantum mechanics, the yet-to-be-discovered key to a unified theory capable of explaining both the infinitely large and the infinitely small. The solution to this [...]
Challenging Previous Beliefs: Japanese Scientists Discover Hidden Protector of Heart
A Japanese research team found that the oxidized form of glutathione (GSSG) may protect heart tissue by modifying a key protein, potentially offering a novel therapeutic approach for ischemic heart failure. A new study [...]
Millions May Have Long COVID – So Why Can’t They Get Diagnosed?
Millions of people in England may be living with Long Covid without even realizing it. A large-scale analysis found that nearly 10% suspect they might have the condition but remain uncertain, often due to [...]
Researchers Reveal What Happens to Your Brain When You Don’t Get Enough Sleep
What if poor sleep was doing more than just making you tired? Researchers have discovered that disrupted sleep in older adults interferes with the brain’s ability to clean out waste, leading to memory problems [...]
How to prevent chronic inflammation from zombie-like cells that accumulate with age
In humans and other multicellular organisms, cells multiply. This defining feature allows embryos to grow into adulthood, and enables the healing of the many bumps, bruises and scrapes along the way. Certain factors can [...]
Breakthrough for long Covid patients who lost sense of smell
A breakthrough nasal surgery has restored the sense of smell for a dozen long Covid patients. Experts at University College London Hospitals NHS Foundation Trust successfully employed a technique typically used for correcting blocked nasal passages, [...]