Indian Scientists Unveil ANCHOR, the World’s Most Detailed 3D Atlas of the Human Brainstem

Mapping the Brain’s Hidden Control Center

For more than a century, neuroscientists have studied the human brain much as early cartographers mapped unknown lands, piecing together a vast landscape from scattered observations. Even today, a pathologist diagnosing Alzheimer’s disease typically inspects only a handful of tissue samples from an organ that contains roughly 86 billion neurons. That small window leaves much of the brain unseen.

Scientists at the Sudha Gopalakrishnan Brain Centre (SGBC) at the Indian Institute of Technology, Madras (IIT-M), believe they have taken a major step toward filling that gap. They have produced what they describe as the world’s most detailed 3D atlas of the human brainstem at cellular resolution. Named ANCHOR, short for the Atlas of Neurochemical Characterisation of the Human Brainstem with 3D Reconstruction, the digital map lets researchers travel from MRI scans of the whole brain to individual nerve cells while keeping every structure in its exact place.

The atlas combines more than 500 tissue sections from foetal, childhood and adult brains. Eight chemical markers, known as immunostains, help distinguish different neurochemical cell types. The result identifies more than 200 clusters of brain cells and nerve pathways across the brainstem. Unlike costlier molecular atlases, ANCHOR is built from high resolution microscope images, making detailed cell resolution mapping more affordable and easier to scale.

The project was unveiled during the 3rd BRICS Neuroscience Symposium 2026 at IIT-Madras, attended by leaders from government, academia and philanthropy. The launch signaled both a scientific milestone and a growing role for India in global neuroscience.

Why the Brainstem Has Remained Neuroscience’s Last Frontier

The brainstem occupies only a small sliver at the base of the brain, yet it keeps people alive. It connects the brain to the spinal cord and governs breathing, heartbeat, blood pressure, sleep, wakefulness, body temperature and movement. Damage to tiny clusters of cells within it can be catastrophic, but the region’s densely packed architecture has long frustrated efforts to map it in detail.

Dr. Mihail Bota, a senior scientist at SGBC and one of the lead researchers behind the project, noted that the brainstem also serves as the vital bridge between the brain and the rest of the body through the spinal cord. It contains ten of the twelve cranial nerves and plays a major role in autonomic functions, emotional regulation and purposeful behavior.

Mapping this region is particularly challenging because thousands of nerve cells and fiber pathways are tightly packed into a small space. The structure is highly heterogeneous. Different nuclei and control centers appear and disappear across very small distances. Because researchers cannot safely biopsy the brainstem in living patients, they must rely on postmortem tissue, thin sections, stains, imaging and computational reconstruction. This slow, careful work has limited the scale and detail of previous maps.

Scientists have mapped the brains of several animal species in remarkable detail, but the human brain remains comparatively under-charted because detailed studies of human brain tissue are scarce. Each human brain is unique, and ethical, technical and logistical barriers make large-scale human studies difficult. ANCHOR helps address that gap by providing a high resolution reference built directly from human tissue.

Building ANCHOR: From 500 Slices to a Digital Atlas

The ANCHOR team developed a high throughput brain imaging and computing platform that transforms whole human brains into 3D cell resolution databases. The process begins after a donated brain is collected and processed within carefully controlled time windows. The brainstem, which Prof. Mohanasankar Sivaprakasam, head of SGBC, described as roughly the shape of a carrot, is sliced into sections just 10 to 20 microns thick. A micron is about one-fifth the width of a human hair, so each cut is extraordinarily fine.

The slices then undergo chemical and biological processing before being mapped and annotated digitally. Advanced artificial intelligence imaging tools and high-performance computing align the sections so precisely that the original brainstem can be reconstructed in three dimensions. Around 20 scientists spent 18 months manually analyzing more than 200 brain sections and combining MRI scans, microscopic anatomy and 3D reconstruction into a single atlas.

Eight complementary immunostains were overlaid across the tissue sections. These chemical markers act like filters, highlighting different neurochemical cell types. The result is a multimodal resource that combines MRI, block-face imaging and cellular resolution histology. Researchers can examine any given point in the brainstem across multiple resolutions and staining methods, revealing anatomical and chemical details that would otherwise stay hidden.

Brains intended for this kind of cellular resolution mapping must be collected and processed under strict conditions. The team had to develop specialized protocols to preserve tissue integrity and remove blood residues that could interfere with imaging. The work required expertise from neuroscientists, neuroanatomists, histology specialists, imaging specialists and computational scientists.

Bridging the Gap Between Whole Brain Scans and Single Cells

Modern neuroscience has long operated across two separate worlds. MRI reveals the whole brain but lacks cellular detail. Microscopes reveal individual cells, yet only in isolated slices. The spatial relationship between those slices and the larger structure is often lost. That gap has left clinicians and researchers unable to match the brain as it appears on a scan with the brain as it looks under a microscope.

ANCHOR attempts to close that divide. Users can zoom from the whole brainstem seen on MRI down to individual neurons while maintaining their precise spatial relationships. This integration is what makes the atlas unusual. It is not merely another anatomical diagram; it is a bridge between medical imaging and cellular pathology.

Dr. Rebecca Folkerth, a neuropathologist affiliated with Harvard Medical School and New York University, collaborated with the SGBC team. She has examined thousands of brains over more than three decades. She described the new resource as the realization of a long-held professional dream.

“What the Indian centre has created is essentially what I dreamed of early in my career – to have brain scans match the brain’s microscopic anatomy.”

Dr. Shubha Tole, an Indian neuroscientist at the Tata Institute of Fundamental Research, described the project as an “unprecedented integration” of engineering, neuroscience and medicine. She said the programme puts India at the international table.

Dr. Partha Mitra, a brain scientist at Cold Spring Harbor Laboratory who helped design and establish IIT Madras’s human brain histology programme, said detailed brain atlases could have a transformative impact on the study of neurological disease by revealing, cell by cell, how brains affected by conditions such as Alzheimer’s disease or autism differ from healthy ones.

From Parkinson’s Disease to Stroke: What ANCHOR Could Reveal

The atlas is not a diagnostic tool. Its greatest value lies in the questions it can help scientists ask. By comparing healthy brainstem maps with diseased tissue, researchers may better understand disorders ranging from Parkinson’s disease and stroke to Alzheimer’s disease and sudden infant death syndrome, or SIDS.

Parkinson’s disease is linked to the gradual loss of dopamine-producing nerve cells in the substantia nigra, a structure located within the brainstem. Stroke can injure tissue in ways that are not yet fully understood. Alzheimer’s disease has been associated with changes in brainstem regions. More precise maps could help neurosurgeons navigate one of the brain’s most delicate areas with greater confidence.

Dr. Folkerth used stroke as an example. She said the atlas has uncovered new features that could help doctors preserve brain tissue that is injured but not yet beyond repair, potentially improving patient outcomes.

Dr. Mitra also noted that atlases like ANCHOR could help explain how infections, including Covid-19, trigger long-term neurological damage. Because the brainstem controls functions such as breathing and arousal, understanding how viruses or inflammation affect its cells could open new avenues for research into post infectious conditions.

Other applications may include sleep medicine, developmental disorders and the study of age related changes. The brainstem begins developing very early in embryonic growth and rapidly establishes critical neural connections while the fetus is still in the womb. Later in life, several brainstem structures begin losing neurons. Understanding such normal developmental and aging changes is essential before researchers can identify what goes wrong in disease.

Open Science, Global Collaboration, and the BRICS Launch

ANCHOR was unveiled during the 3rd BRICS Neuroscience Symposium 2026, held from June 5 to June 7 at IIT Madras. The symposium brought together neuroscientists, clinicians, academicians and researchers from BRICS nations. The launch was attended by Prof. Ajay Kumar Sood, Principal Scientific Adviser to the Government of India, who served as chief guest. Also present were Kris Gopalakrishnan, co-founder of Infosys and a major supporter of SGBC; Prof. V. Kamakoti, Director of IIT Madras; and Prof. Mohanasankar Sivaprakasam, head of SGBC.

Prof. Sood addressed the event and said the maps could help identify specific cell populations affected in brainstem lesions, which may be critical for clinical applications. He called the project a major achievement in neurobiology and praised the centre for spanning institutions, nations and disciplines.

“This is a significant accomplishment in the field of neurobiology. This is a multimodal framework integrating MRI, histology and detailed chemo-architecture. It will be the most detailed and comprehensive maps of the human brainstem, and will be made available publicly in digital form.”

The project also depended on Indian medical institutions for tissue access. CMC Vellore, Government Kilpauk Medical College, Sri Ramachandra Institute of Higher Education and Research, and MediScan Systems helped acquire brains from individuals of various ages and backgrounds. This collaboration between hospitals, engineers and neuroscientists was essential to the atlas’s creation.

The researchers have made ANCHOR publicly accessible through the website anchor.humanbrain.in. Open access is central to the project’s design. The team wants the atlas to become shared infrastructure rather than a limited internal resource.

The Larger Mission: Mapping 100 Brains Across Life and Disease

ANCHOR is part of a broader effort at SGBC to create comprehensive cell resolution maps of the human brain across different stages of life and neurological conditions. In 2024, the centre released DHARANI, a detailed atlas of the developing fetal brain. The researchers are now working on additional atlases covering the third trimester of pregnancy, early childhood and various neurological diseases.

One of the projects underway is a detailed atlas of a brain affected by ischemic stroke, which the team expects to release within the next year. The centre plans to image more than 100 whole human brains across the lifespan and neurological disorders, including Alzheimer’s disease and dementia, creating a reference library that could reveal how disease reshapes the brain cell by cell.

Prof. Sivaprakasam said the feat is both a scientific accomplishment and a development that medicine and clinical practice will benefit from greatly. For the first time, clinicians can know how a brainstem looks in detail at a resolution far higher than MRI or CT. He expects applications in brain surgery, among other fields.

The centre is primarily funded through foundational contributions by Infosys co-founder Kris Gopalakrishnan and his wife Sudha Gopalakrishnan. It also receives grants from private institutions and philanthropic organizations, plus seed support from the Government of India. The team now includes more than 200 researchers, engineers and technicians working with collaborators from roughly 20 countries.

“I hope this will make important contributions to neuroscience in the world. In India, we have the awareness of affordable science and affordable technology because ultimately technology must serve the society and the people.”

Prof. Vidita A. Vaidya, senior professor and co-chairperson in the Department of Biological Sciences at Tata Institute of Fundamental Research, said that open access research resources such as ANCHOR are crucial for advancing international collaboration and accelerating discovery. She sees India emerging as a significant global hub for neuroscience research, with SGBC leading in neuroanatomy and expanding into spatial transcriptomics to overlay molecular detail onto cellular maps.

The Essentials

• Researchers at IIT Madras’ Sudha Gopalakrishnan Brain Centre have released ANCHOR, a free 3D atlas of the human brainstem at cellular resolution.
• The atlas combines MRI, high resolution histology and eight neurochemical markers across more than 500 tissue sections from foetal, childhood and adult brains.
• It identifies more than 200 brainstem nuclei and fibre tracts, allowing scientists to move from whole brain scans down to individual nerve cells.
• The brainstem controls breathing, heartbeat, blood pressure, sleep, wakefulness and movement, making detailed maps essential for clinical research.
• Potential applications include studies of Parkinson’s disease, stroke, Alzheimer’s disease, sleep disorders, SIDS and neurosurgical planning.
• ANCHOR is currently a research resource, not a diagnostic tool, and the work has been released as a bioRxiv preprint awaiting peer review.
• SGBC plans to map more than 100 whole human brains across the lifespan and neurological diseases, building on earlier work such as the DHARANI fetal brain atlas.