IIT Madras Unveils ANCHOR, a Cellular 3D Map of the Human Brainstem

More Than 500 Sections Reveal the Brainstem in Detail

Scientists at the Sudha Gopalakrishnan Brain Centre (SGBC) at the Indian Institute of Technology, Madras (IIT Madras), have unveiled ANCHOR, a digital atlas that brings together more than 500 tissue sections from foetal, childhood and adult brains. The researchers describe it as the world's most detailed 3D atlas of the human brainstem at cellular resolution.

ANCHOR, short for the Atlas of Neurochemical Characterisation of the Human Brainstem with 3D Reconstruction, combines MRI scans, microscopic tissue images and eight chemical markers. It identifies more than 200 clusters of nerve cells and nerve pathways, allowing researchers to move from a view of the brainstem on a scan to individual cells while retaining their positions within the larger structure.

The atlas was unveiled during the 3rd BRICS Neuroscience Symposium 2026, held at IIT Madras from June 5 to June 7. Its public release gives researchers a shared reference for studying a small, densely packed part of the brain that controls breathing, heartbeat, sleep and other functions essential to life.

The project addresses a longstanding problem in brain research: scientists can examine the whole organ through medical scans or inspect individual cells under a microscope, but connecting those views has been difficult. A pathologist investigating Alzheimer's disease typically examines only a handful of tissue samples from a brain containing roughly 86 billion neurons. ANCHOR seeks to make more of that hidden anatomy visible and navigable.

The work has been released as a bioRxiv preprint and is awaiting peer review. ANCHOR is a research resource, with potential applications in disease studies and surgical planning, rather than a diagnostic tool currently used to identify illness in patients.

Why Such a Small Region Matters

The brainstem sits at the base of the brain and connects it to the spinal cord. It regulates breathing, heartbeat, blood pressure, sleep, wakefulness, body temperature and movement. Damage to even a small cluster of cells can have catastrophic consequences because so many essential functions are concentrated in this limited space.

Dr. Mihail Bota, a senior scientist at SGBC and one of the project's lead researchers, described the brainstem 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 contributes to autonomic functions, emotional regulation and purposeful behaviour. Autonomic functions are the processes the body manages automatically, such as maintaining a heartbeat.

Thousands of nerve cells and fibre pathways are tightly packed together here. Different nuclei, meaning clusters of nerve cells, and control centres appear and disappear across very short distances. That variation makes reconstructing the region much harder than drawing a simple outline of its shape.

Researchers studying its microscopic structure depend on tissue collected after death, thin sections, chemical stains, imaging and computational reconstruction because taking brainstem biopsies from living patients is unsafe. Each stage demands careful handling, which has limited the scale and detail of earlier maps.

Scientists have mapped several animal brains in considerable detail, while comparable studies of human tissue remain scarce. Every human brain is different, and ethical, technical and logistical difficulties complicate studies involving many brains. ANCHOR provides a detailed reference drawn directly from human tissue.

How Thin Slices Become a 3D Atlas

SGBC developed a platform for brain imaging and computing that can process large amounts of tissue data and turn whole human brains into databases with cellular resolution. Work begins with collecting and processing a donated brain within carefully controlled time windows.

Prof. Mohanasankar Sivaprakasam, head of SGBC, described the brainstem as roughly the shape of a carrot. Researchers cut it into sections only 10 to 20 microns thick. The explanation accompanying the project compares a micron to about one fifth of the width of a human hair, conveying the extremely fine scale of the cuts.

The sections undergo chemical and biological processing before being digitally mapped and annotated. Artificial intelligence imaging tools and powerful computing systems align the slices, enabling the team to reconstruct the original brainstem in three dimensions.

Around 20 scientists spent 18 months manually analysing more than 200 brain sections and combining MRI, microscopic anatomy and 3D reconstruction into one atlas. The resource as a whole incorporates more than 500 tissue sections across foetal, childhood and adult brains.

Preserving the tissue was a major part of the work. The team developed specialised protocols to maintain its integrity and remove blood residues that could interfere with imaging. Neuroscientists, neuroanatomists, histology specialists, imaging specialists and computational scientists contributed to the process. Histology is the study of tissue under a microscope.

Eight Chemical Markers Add Another Layer

ANCHOR uses eight complementary immunostains to distinguish different neurochemical cell types. These markers act like filters, making particular biological features visible so researchers can separate cell populations that might otherwise be difficult to tell apart.

The team overlaid the staining information across tissue sections and combined it with MRI, block-face imaging and histology at cellular resolution. Block-face images record the exposed surface of tissue during sectioning, helping connect the physical specimen with the series of thin slices.

Researchers can examine a location in the brainstem at several resolutions and through different staining methods. The atlas therefore shows both where a structure sits and some of the chemical features of its cells, rather than providing an anatomical outline alone.

The approach uses microscope images with high resolution instead of the costlier methods used in molecular atlases. The researchers present this as a way to make detailed mapping at cellular resolution more affordable and easier to expand.

Connecting Medical Scans With Individual Cells

MRI provides a view of the whole brain but cannot show individual cells in the detail available through microscopy. Microscopes reveal those cells, yet an isolated tissue slice can lose its relationship to the surrounding brain. ANCHOR connects the two scales while keeping structures in their positions.

A researcher can move from the brainstem as it appears on MRI to individual neurons and examine how they fit into nearby nuclei and pathways. This connection between medical imaging and cellular pathology is central to the atlas's design.

Dr. Rebecca Folkerth, a neuropathologist affiliated with Harvard Medical School and New York University, collaborated with SGBC. Having examined thousands of brains over more than three decades, she described the resource as fulfilling an ambition from early in her career:

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, a neuroscientist at the Tata Institute of Fundamental Research, called the programme an "unprecedented integration" of engineering, neuroscience and medicine. She said it 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 atlases could transform the study of neurological disease. They could allow researchers to compare brains affected by conditions such as Alzheimer's disease or autism with healthy brains, cell by cell.

What Researchers Hope to Learn About Disease

Parkinson's disease, stroke, Alzheimer's disease and sudden infant death syndrome (SIDS) are among the conditions researchers hope to investigate using more precise brainstem maps. Comparing reference anatomy with tissue affected by disease could help reveal which cell populations and pathways change.

Parkinson's disease involves the gradual loss of nerve cells that produce dopamine in the substantia nigra, a structure within the brainstem. Alzheimer's disease has also been associated with changes in brainstem regions. A detailed map gives scientists a common framework for locating and comparing such changes.

Stroke can injure brain tissue in ways that are still incompletely understood. Folkerth said the atlas had revealed new features that could help doctors preserve tissue that is injured but not yet beyond repair, potentially improving patient outcomes.

Mitra also pointed to infections, including COVID-19, as an area where brain atlases could help explain lasting neurological damage. Because the brainstem controls breathing and arousal, examining how viruses or inflammation affect its cells could support research into conditions that persist after infection.

Sleep medicine, developmental disorders and changes associated with ageing are other possible applications. The brainstem starts developing very early in embryonic growth and rapidly establishes crucial neural connections while the fetus is still in the womb. Later in life, several brainstem structures begin losing neurons.

Researchers need to understand those normal developmental and ageing changes before identifying what goes wrong in disease. The atlas may also help neurosurgeons navigate this delicate region with greater confidence by providing anatomical detail beyond that available on conventional scans.

A Public Launch at the BRICS Symposium

The June symposium brought neuroscientists, clinicians, academics and researchers from BRICS nations to IIT Madras. Prof. Ajay Kumar Sood, Principal Scientific Adviser to the Government of India, attended the launch as chief guest.

Kris Gopalakrishnan, co-founder of Infosys and a major supporter of SGBC, was also present, alongside Prof. V. Kamakoti, Director of IIT Madras, and Sivaprakasam. The event presented ANCHOR as both a scientific milestone and part of India's growing role in international neuroscience.

Sood said the maps could help identify specific cell populations affected by brainstem lesions, or areas of damaged tissue, which may be critical for clinical applications. He praised the centre's work across institutions, countries and disciplines, and described the framework:

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.

Chemo-architecture refers to the arrangement of cells and structures according to their chemical features. In ANCHOR, that information sits alongside the shapes visible in tissue and the broader view provided by MRI.

Hospitals, Donors and Open Access

Indian medical institutions helped the team obtain brains from individuals of different ages and backgrounds. The collaborators included CMC Vellore, Government Kilpauk Medical College, Sri Ramachandra Institute of Higher Education and Research, and MediScan Systems.

Their involvement connected access to donated tissue with the engineering, imaging and neuroscience needed to build the atlas. Strict collection and preservation requirements made this cooperation essential to the project.

Researchers have made the ANCHOR digital atlas publicly accessible. The intention is for it to serve as shared research infrastructure, allowing scientists beyond SGBC to use the same reference rather than restricting it to an internal team.

Prof. Vidita A. Vaidya, senior professor and co-chairperson in the Department of Biological Sciences at the Tata Institute of Fundamental Research, said open access resources such as ANCHOR are crucial for international collaboration and faster discovery.

Vaidya sees India emerging as a major global hub for neuroscience research, with SGBC leading work in neuroanatomy and expanding into spatial transcriptomics. That approach would overlay molecular detail onto cellular maps, adding another way to investigate the tissue already being mapped.

From a Foetal Atlas to More Than 100 Brains

ANCHOR belongs to a wider SGBC programme to build comprehensive maps of the human brain at cellular resolution across stages of life and neurological conditions. The centre released DHARANI, an atlas of the developing foetal brain, in 2024.

Researchers are now preparing additional atlases covering the third trimester of pregnancy, early childhood and several neurological diseases. A detailed atlas of a brain affected by ischemic stroke is expected within the next year. Ischemic stroke involves an interruption to the blood supply reaching brain tissue.

The programme's main milestones and plans are:

• 2024: SGBC released DHARANI, its atlas of the developing foetal brain.
• June 5 to June 7, 2026: IIT Madras hosted the 3rd BRICS Neuroscience Symposium, during which ANCHOR was unveiled.
• Within the next year: The team expects to release an atlas of a brain affected by ischemic stroke.
• The broader programme: SGBC plans to image more than 100 whole human brains across the lifespan and neurological disorders, including Alzheimer's disease and dementia.

The planned reference library would let researchers study how disease reshapes the brain cell by cell, while also examining differences associated with development and ageing.

Sivaprakasam described ANCHOR as a scientific achievement with substantial potential benefits for medicine and clinical practice. He said clinicians can, for the first time, see the brainstem in detail at a resolution far higher than MRI or CT, and he expects applications in brain surgery among other fields.

The People and Funding Behind the Programme

SGBC receives its principal foundational funding from Kris Gopalakrishnan and his wife, Sudha Gopalakrishnan. Private institutions and philanthropic organisations provide grants, while the Government of India has supplied seed support.

The centre now has more than 200 researchers, engineers and technicians, working with collaborators from roughly 20 countries. The scale of that wider team supports a programme extending beyond the brainstem to whole brains, different ages and neurological disorders.

Sivaprakasam's account of the project's ambitions connects its scientific goals with the need for technology that can serve society:

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.

ANCHOR brings that ambition into a publicly accessible reference: MRI, microscopic anatomy and chemical markers connected in three dimensions. Its immediate contribution is to research, giving scientists a more detailed foundation for investigating how the human brainstem develops, ages and is affected by disease.

The Essentials

• IIT Madras's Sudha Gopalakrishnan Brain Centre has released ANCHOR, described by its researchers as the world's most detailed 3D human brainstem atlas at cellular resolution.
• The atlas combines more than 500 tissue sections from foetal, childhood and adult brains with MRI, microscopy and eight neurochemical markers.
• It identifies more than 200 brainstem nuclei and fibre tracts while preserving their positions across different imaging scales.
• The brainstem controls essential functions including breathing, heartbeat, blood pressure, sleep, wakefulness and movement.
• Potential research applications include Parkinson's disease, stroke, Alzheimer's disease, SIDS, sleep disorders and surgical planning.
• ANCHOR is publicly accessible, is currently a research resource rather than a diagnostic tool, and has been released as a bioRxiv preprint awaiting peer review.
• SGBC plans to image more than 100 whole human brains and expects an atlas of a brain affected by ischemic stroke within the next year.