Indian scientists create world's most detailed 3D human brainstem atlas

Indian scientists create world's most detailed 3D human brainstem atlas

Researchers at the Sudha Gopalakrishnan Brain Centre (SGBC) at the Indian Institute of Technology, Madras (IIT-M) have developed what they describe as the world's most detailed three-dimensional atlas of the human brainstem at cellular resolution. The digital map, named Anchor (Atlas of Neurochemical Characterisation of the Human Brainstem with 3D Reconstruction), was unveiled earlier this month during the 3rd BRICS Neuroscience Symposium 2026.

The brainstem is an evolutionarily ancient structure that links the brain to the spinal cord and regulates autonomic processes including heartbeat, breathing, wakefulness, sleep, and thermoregulation. While it occupies only a sliver of the brain, damage to its tiny cell clusters can be catastrophic. Its densely packed architecture has historically made detailed mapping difficult.

Anchor integrates more than 500 tissue sections from adult, childhood, and foetal brains. By using eight chemical markers to distinguish cell types, the atlas identifies more than 200 nerve pathways and clusters of brain cells. The project was a multidisciplinary effort involving around 20 scientists who spent 18 months manually analysing more than 200 brain sections, combining 3D reconstruction, microscopic anatomy, and MRI scans.

Bridging Medical Imaging and Pathology

The primary innovation of Anchor is its ability to link medical imaging, which views the brain as a whole, with cellular pathology, which examines it one cell at a time. Users can zoom from a whole-brainstem MRI view down to individual neurons while maintaining precise spatial relationships.

According to Rebecca Folkerth, a collaborator affiliated with New York University and Harvard Medical School, traditional neuropathology often involves examining only 15 to 20 sections of an organ containing some 86 billion neurons when diagnosing Alzheimer's disease. Folkerth stated that the atlas achieves what she had dreamed of early in her career: to have brain scans match the brain's microscopic anatomy.

The atlas is not a diagnostic tool but a reference resource. It has been made freely available online for neurosurgeons, neurologists, and neuroscientists. By comparing diseased tissue with healthy maps, researchers may better understand conditions such as sudden infant death syndrome (SIDS), stroke, and Parkinson's disease.

Folkerth noted that the atlas has already uncovered new features regarding brain stroke that could help doctors preserve injured brain tissue that is not yet beyond repair.

Cost-Effective Innovation

Unlike newer molecular techniques, Anchor was built from high-resolution images of thin slices of post-mortem brain tissue. Partha Mitra of the Cold Spring Harbor Laboratory noted that this simpler approach made detailed, cell-level mapping affordable and possible at an unprecedented scale.

This effort is part of a larger project by IIT Madras to map the human brain across various life stages. This includes DHARANI, a high-resolution 3D imaging dataset of the human foetal brain featuring over 5,000 sections. According to the institute, this work was accomplished at less than one-tenth of the cost of similar Western projects. The initiative received backing from Fortis Healthcare, Premji Invest, the Office of the Scientific Adviser to the Government of India, and Infosys co-founder Kris Gopalakrishnan.

Prof. Mohanasankar Sivaprakasam, head of SGBC, told the BBC that the human brain remains under-charted compared to animal species because detailed human brain tissue is scarce.

Future Directions

The SGBC is continuing its expansion into comprehensive cellular-resolution maps. Current and future goals include:

• Imaging more than 100 whole human brains across different neurological disorders and life stages, including dementia and Alzheimer's disease.
• Developing additional atlases for early childhood and the third trimester of pregnancy.
• Releasing a detailed atlas of a brain affected by ischemic stroke within the next year.
• Exploring how infections, such as Covid-19, trigger long-term neurological damage, according to Partha Mitra.

The team continues to develop specialized protocols to preserve tissue integrity and remove blood residues during the collection of brains, which must be processed within strict time windows after death to maintain cellular resolution.