Researchers from the Mark and Mary Stevens Neuroimaging and Informatics Institute ( Stevens INI ) at the Keck School of Medicine of USC have developed a new, noninvasive way to examine how blood flow and cellular organization align across the layers of the living human brain.
The study, published in Nature Communications , introduces the cerebral blood flow–cell-body staining intensity similarity index, or CCSI. It may help scientists understand how blood vessels, cells, and energy-producing machinery work together to support brain function. The hope is that CCSI may eventually offer insight into early signs of disease and potential treatments.
The cerebral cortex, the brain's folded outer layer, contains layers with different numbers and types of cells. These cells need a continuous supply of oxygen and nutrients, but researchers have had limited tools for studying how blood flow matches their distribution in the living brain.
"The brain has almost no ability to store energy, so its cells depend on a constant and carefully regulated supply from the bloodstream," said Fanhua Guo, co-first author of the study and a researcher at the Stevens INI. "Our new measure gives us a way to study how well that energy supply is positioned to meet cellular demands in different parts of the cortex."
Mapping blood flow across cortical layers
The researchers used arterial spin labeling, or ASL, a noninvasive MRI technique that magnetically labels water in the blood and tracks it into brain tissue. A powerful 7 Tesla MRI scanner measured blood flow throughout the brain at a resolution of one cubic millimeter. The study included 30 healthy adults; 14 returned for a second scan to test the consistency of the measurements.
The team divided the cortex into 360 regions and examined blood flow at multiple depths. They compared those patterns with cell-body staining data from BigBrain, a detailed three-dimensional digital reconstruction of a human brain that maps how densely cells are packed throughout the cortex.
"Conventional brain imaging often averages information across the full thickness of the cortex, but the cortex is not a uniform sheet," said Chenyang Zhao, co-first author of the study and a researcher at the Stevens INI. "By imaging blood flow at very high resolution, we can begin to see how perfusion changes from the outer surface of the cortex to its deeper layers."
"Neuroscience is entering an era where we can combine advanced brain imaging with detailed maps of the brain's cells, gene expression, and metabolism," said Ravi R. Bhatt, PhD, a postdoctoral scholar at the Stevens INI. "Each map provides a different view of the brain, and together they reveal patterns that would otherwise remain hidden."
The resulting CCSI score measured how closely blood flow and cellular density followed the same pattern across cortical depth. Higher scores indicated that cell-dense layers tended to receive more blood flow. Blood flow and cellular organization aligned in most cortical regions, meaning that within a given region, blood flow tended to be highest in the layers with the most cells, although the strength varied across the brain. Alignment was strongest in primary visual and sensorimotor areas, which support vision, movement, and touch.
Connecting blood flow to the brain's energy system
To clarify what CCSI represents biologically, the researchers compared it with maps of mitochondrial activity, cell types, and gene expression.
Mitochondria convert nutrients and oxygen into usable energy. Regions where blood flow and cellular organization aligned more strongly also had greater mitochondrial respiratory capacity, the maximum rate at which mitochondria can produce energy, suggesting they may be better equipped to meet local energy demands.
The relationship involved mitochondrial capacity, not simply the number of mitochondria. Total blood flow did not show the same association, suggesting CCSI reveals metabolic organization that standard blood-flow measurements may miss.
"Blood flow tells us how much blood reaches a region, but it does not tell us how that supply is distributed in relation to the cells that need it," said Danny JJ Wang, PhD , senior and corresponding author of the study, professor of neurology, and director of imaging technology innovation at the Stevens INI. "CCSI adds that missing spatial information and may provide a more biologically meaningful picture of how vascular supply supports energy use across cortical layers."
CCSI was also associated with capillary endothelial cells, which line the smallest blood vessels and help regulate how blood reaches surrounding tissue. It was also associated with mature oligodendrocytes, brain cells that produce the protective myelin coating around nerve fibers. Because oligodendrocytes also support nerve fibers' metabolism, the finding suggests they may help connect vascular supply with neurons' energy needs.
Gene activity further linked CCSI to energy metabolism, blood vessel development, vascular organization, and healthy mitochondria. Together, the findings suggest that the alignment of blood flow and cellular structure reflects a coordinated system involving blood vessels, supporting cells, and energy production.
Helping explain the brain's most complex regions
The researchers also asked whether CCSI could help explain the relationship between brain structure and function. That connection is usually close in sensory and motor regions but less direct in higher-order association regions, which support memory, reasoning, and attention.
The researchers tested this using structural-functional coupling analysis that predicts brain function from the cortex's structural features. Adding CCSI significantly improved the models' ability to predict function in these higher-order regions. The findings suggest that metabolic and vascular factors shape brain function in ways cellular structure alone cannot explain.
"This study bridges several levels of brain organization, from blood vessels and mitochondria to cells, cortical layers, and gene expression," said Arthur W. Toga, PhD , director of the Stevens INI. "By bringing these sources of information together, the researchers have created a new framework for investigating how the living brain supports its extraordinary energy demands."
The study does not establish that stronger alignment causes more efficient energy use. Its molecular and cellular comparisons relied on reference atlases from a limited number of postmortem donors, and CCSI currently measures groups rather than individuals. Future studies will test larger, more varied populations and explore changes linked to aging and neurological or psychiatric conditions.
Disruptions in blood flow, metabolism, and oligodendrocyte function occur in Alzheimer's disease, multiple sclerosis, schizophrenia, and epilepsy. CCSI could eventually help researchers study how these systems become disconnected.
"Understanding the healthy relationship between vascular supply and cellular organization is an important first step," said Neda Jahanshad, PhD , professor of neurology and biomedical engineering at the Stevens INI. "The long-term goal is to determine whether changes in this relationship can reveal early signs of disease or help us evaluate treatments aimed at restoring brain metabolism and vascular health. The hope is that CCSI may eventually offer insight into early signs of disease and potential treatments.
About the study
In addition to Guo, Zhao, and Wang, other study authors include Ravi R. Bhatt, Zixuan Liu, Zidong Yang, Kay Jann, Xingfeng Shao, and Neda Jahanshad of the Stevens INI; Mara Mather and Andy Jeesu Kim of the USC Leonard Davis School of Gerontology, USC Department of Psychology, and USC Department of Biomedical Engineering; and Siyi Xu of the University of Washington.
The research was supported by the National Institutes of Health under grants UF1-NS100614, S10-OD025312, R01-EB032169, RF1-AG084072, R01-MH134004 and R01-NS134712.
