summary: A new AI-powered atlas called NextBrain allows researchers to visualize the human brain in unprecedented detail, down to hundreds of tiny subregions previously invisible to MRI scans. Constructed from 10,000 microscopic slices of post-mortem brains and coordinated with AI, the atlas accurately maps 333 brain regions in 3D.
When tested on thousands of MRI scans, it quickly and consistently identified complex brain structures, outperforming previous tools. The open access atlas will accelerate global research into aging, neurodegenerative diseases, and brain development, paving the way for early diagnosis and new treatments.
important facts
- Unprecedented precision: NextBrain maps 333 brain regions and reveals cellular-level details with live MRI scans.
- AI integration: Artificial intelligence arranges microscopy and MRI data from 10,000 tissue slices into a single 3D atlas.
- Clinical promise: Identifying subtle structural changes enables early detection of neurological diseases such as Alzheimer’s disease.
sauce: UCL
A new AI-assisted brain atlas that helps visualize the human brain in unprecedented detail has been developed by UCL researchers, marking a major step forward in neuroscience and neuroimaging.
The human brain is made up of hundreds of interconnected areas that drive our thoughts, emotions, and actions. Existing brain atlases can identify key structures such as the hippocampus, which support memory and learning, in MRI scans, but its more subtle subregions remain difficult to detect.
These distinctions are important because subregions of regions such as the hippocampus, for example, are affected differently during the progression of Alzheimer’s disease.
Examination of the brain at the cellular level can be done using microscopy (histology), but it cannot be done on living individuals, which limits the possibility of understanding how the human brain changes during development, aging, and disease processes.
Published in naturea new study introduces NextBrain, an atlas of the entire adult brain that can be used to analyze MRI scans of living patients in minutes and at a level of detail previously impossible.
The authors of the freely available atlas hope it will ultimately help accelerate discoveries in brain science and apply them to better diagnosis and treatment of conditions such as Alzheimer’s disease.
How was the AI-assisted brain atlas developed?
The atlas took a team of researchers six years to build, a painstaking process similar to completing a jigsaw puzzle. However, it was not made using post-mortem tissue from five human brains.
Each brain was painstakingly dissected, divided into 10,000 pieces, stained to identify brain structures, photographed under a microscope, and reassembled into a 3D digital model. Before starting this process, the researchers conducted an MRI scan of the brain to see how they could put the brain back together, similar to the photo on the front of the jigsaw puzzle box.
AI was used to help align the microscopic images and MRI scans, taking into account the differences between the two techniques and ensuring there were no overlapping parts or gaps.
A total of 333 brain regions were then labeled on digital 3D models of each of the five brains. This process has been greatly accelerated by AI. Researchers say this would take decades if done manually.
Dr. Juan Eugenio Iglesias, senior author of the study from UCL Medical Physics and Biomedical Engineering and Massachusetts General Hospital/Harvard Medical School, said: “NextBrain is the culmination of years of efforts to bridge the gap between microscopic imaging and MRI.
By combining high-resolution tissue data with advanced AI techniques, we have created a tool that allows researchers to analyze brain scans at a level of detail previously unattainable. This opens new possibilities for the study of neurodegenerative diseases and aging. ”
The resulting atlas is an “average” of the five brain models and can be generalized to all adults. This means it can be used to automatically infer details from MRI scans of living or dead subjects.
Brain Atlas accuracy tested over thousands of scans
NextBrain has been successfully tested on thousands of MRI datasets and has been demonstrated to reliably identify brain regions across a variety of imaging conditions and scanner types.
In one experiment, the team used the atlas to automatically label brain regions in publicly available ultra-high resolution MRI scans. This closely matched manually labeled regions, even for small regions such as subregions of the hippocampus.
In another experiment, the researchers applied NextBrain to more than 3,000 MRI scans of living individuals to examine age-related changes in brain volume. The atlas allows for a more detailed analysis of aging patterns than is possible using existing tools.
Dr Zain Jaunmukhtan, study author from the UCL Queen Square Institute of Neurology and the Queen Square Neurological Disease Brain Bank, said: “Our goal in building this atlas was to preserve the fine-grained anatomical accuracy of the microscopy data while enabling researchers to “NextBrain’s level of anatomical detail is astonishing, and its public availability means researchers around the world can immediately benefit from it.”
“NextBrain provides an unparalleled map of the cellular structure of the brain. The infrastructure built into the Atlas enables rapid, accurate and accessible analysis of brain images in living individuals, opening the door to detecting early signs of neurological diseases such as Alzheimer’s disease long before symptoms appear, improving our ability to understand, monitor and ultimately prevent these devastating diseases.”
All underlying data, tools, and annotations used in NextBrain, along with visualization tools and educational resources, are openly released through the FreeSurfer neuroimaging platform.
Funding: This research was supported by the European Research Council, the Alzheimer’s Association, the Lundbeck Foundation, and the National Institutes of Health (USA).
Answers to key questions:
A: NextBrain is a new AI-assisted brain atlas that can map the living human brain in MRI scans with microscopic precision, bridging the gap between histology and neuroimaging.
A: Researchers combined MRI and microscopy images from five postmortem human brains divided into 10,000 slices to reconstruct 3D models of 333 brain regions that were aligned and labeled using AI.
A: NextBrain enables scientists and clinicians to identify subtle changes in the brains of living people, enabling early detection of diseases such as Alzheimer’s disease and advancing our understanding of brain aging and disease.
About this AI/brain mapping research news
author: matt migley
sauce: UCL
contact: Matt Midgley – UCL
image: Image credited to Neuroscience News
Original research: Open access.
“Probabilistic Histological Atlas of the Human Brain for MRI Segmentation” by Juan Eugenio Iglesias et al. nature
abstract
Probabilistic histological atlas of the human brain for MRI segmentation
In human neuroimaging, brain atlases are essential for segmenting regions of interest (ROIs) and comparing subjects in a common coordinate system.
State-of-the-art atlases derived from histology provide sophisticated three-dimensional cytoarchitectural maps but lack brain-wide probabilistic labels, i.e., the probability that each location belongs to a particular ROI.
Here we introduce NextBrain, a probabilistic histological atlas of the entire human brain.
We developed an artificial intelligence-enabled method that aligns approximately 10,000 tissue sections from across the five hemispheres of the brain into a three-dimensional volume and generates depictions of 333 ROIs on these sections. We also created a companion Bayesian tool for automatic segmentation of these ROIs in magnetic resonance imaging (MRI) scans.
We present two applications of the atlas: ultra-high resolution ex vivo MRI segmentation and volumetric analysis of Alzheimer’s disease using in vivo MRI. We make publicly available the raw aligned data, online visualization tools, atlases, segmentation tools, and high-resolution extracorporeal hemisphere ground truth depictions used for validation.
By enabling researchers around the world to automatically analyze brain MRI with greater granularity, NextBrain promises to increase the specificity of findings and accelerate the quest to understand the human brain in health and disease.
