Molecular Mapping of 8 Million Cells Brings Cerebral Architecture into Focus

Researchers on UC Irvine’s brain procurement study included (from left) Pedro Adolfo Sequeira Mendieta, Hannah Park, John Crawford, Edwin Monuki, Todd Holmes, Xiangmin Xu, Robert Edwards, Jessica Diaz and Martha Mardueno Pangan. Steve Zylius / UC Irvine

• UC Irvine researchers mapped about 8 million cells in brain regions involved in movement and behavior, identifying 60 distinct types and revealing how they form cellular communities.
• The atlas provides a reference for investigating why certain brain cells are more vulnerable to Parkinson’s and Huntington’s diseases.
• A second UC Irvine-led study details the human brain donation and tissue preparation program supporting this large-scale mapping effort.

Irvine, Calif., Nov. 12, 2026 — University of California, Irvine researchers have mapped approximately 8 million cells in regions deep within the human brain, identifying 60 distinct types and revealing how they form cellular communities. The work offers a foundational reference for investigating brain systems affected by Parkinson’s disease, Huntington’s disease and other neurological and psychiatric disorders.

The atlas focuses on the basal ganglia, a group of interconnected structures involved in movement, motivation, habits and decision-making. By examining both the molecular characteristics of cells and their locations, scientists are building a more precise picture of how these areas are organized and creating a basis for exploring what changes in disease.

The study, appearing in Cell, is one of two led by UC Irvine’s Center for Neural Circuit Mapping in a coordinated publication package from the BRAIN Initiative Cell Atlas Network, an international project funded by the National Institutes of Health under the Brain Research Through Advancing Innovative Neurotechnologies Initiative. The university’s team also contributes to four additional Cell papers on brain cells’ molecular features and their similarities across species.

Directing UC Irvine’s participation is Xiangmin Xu, Chancellor’s Professor of anatomy and neurobiology in the School of Medicine and director of the Center for Neural Circuit Mapping, which brings together campus expertise in neuroscience, genomics, engineering and computational sciences to foster collaborative research on brain organization, function and neurological disorders.

“Knowing which cells exist in the brain is only part of the story,” Xu said. “We also need to know where those cells are located, which other cells surround them and how they’re organized within specific brain structures.”

Single-cell sequencing has transformed scientists’ ability to distinguish brain cell types by examining gene activity. The process generally separates cells from their original positions, removing information about their surroundings.

The UC Irvine-led team used spatial transcriptomics, which measures gene activity while retaining information about where cells sit in tissue. Combining two technologies, MERFISH+ and Stereo-seq, researchers analyzed brain samples from four neurotypical donors to connect molecular cell identities with the anatomy of the human basal ganglia.

The study showed that different cell types occupy distinct areas within the basal ganglia. Some supporting cells clustered along the borders between compartments, while certain kinds of neurons that are more abundant in primates were found only within particular compartments.

For Xu, a central advance is the ability to probe cellular communities: the combinations of cells found together in particular locations. These relationships provide insights that a list of cell types alone cannot capture.

Among the many contributors to UC Irvine’s brain cell mapping study were Bereket Tesfay Berackey, Sujan Das, Zhiqun Tan, Ginny Wu, Todd Holmes, Pedro Adolfo Sequeira Mendieta and Xiangmin Xu. Steve Zylius / UC Irvine

UC Irvine researchers led large-scale data generation, computational analysis and the integration of molecular findings with anatomical organization. Bereket Tesfay Berackey, Zhiqun Tan, Ginny Wu and Sujan Das are among the study’s major authors. Bogdan Bintu, an assistant professor at UC San Diego, was a key collaborator in technology development, experimental design and data analysis.

The resulting reference gives scientists a framework for comparing tissue from people with and without brain disorders. Researchers could use it to investigate why particular cell populations are vulnerable to disease while others remain relatively resistant — and whether surrounding cells help explain those differences.

Over time, that work could support more precise experimental models and aid in identifying potential therapeutic targets. The multiscale spatial atlas itself is a foundational research resource; its clinical value depends on the studies that follow.

Read more about UC Irvine’s second lead study in the full press release in UC Irvine News.