Damage to the tiny clusters of cells inside can be catastrophic, but the dense architecture of that region has long thwarted attempts to map it in detail.

The importance of ANCHOR lies not simply in producing another anatomical map, but in uniting two worlds that have largely remained separate: medical scanning, which shows the brain as a whole, and cellular pathology, which reveals it cell by cell.

“We are seeing a visionary program that puts India at the international forefront,” says Shubha Tole, an Indian neuroscientist at the Tata Institute of Fundamental Research, who describes the project as an “unprecedented integration” of engineering, neuroscience and medicine.

Doctors typically begin by examining the entire brain in an autopsy or tissue removed during neurosurgery. An adult brain weighs between 1.2 and 1.5 kg, and its folds and major structures can reveal important clues before microscopic examination begins.

“As a neuropathologist, I start by examining the entire brain with the naked eye before looking at small segments under the microscope,” says Rebecca Folkerth, who is affiliated with Harvard Medical School and New York University and collaborated with the SGBC center team.

“For Alzheimer’s disease, we would be examining only 15 to 20 sections, just a fraction of 1% of the entire organ.”

That has been the practice since the pioneering work of Spanish neuroscientist Santiago Ramón y Cajal more than a century ago. Modern MRI scans reveal the entire brain but lack cellular detail; Microscopes reveal individual cells but only in isolated slices.

“What the Indian center has created is essentially what I dreamed of at the beginning of my career; that brain scans match the microscopic anatomy of the brain,” Rebecca Folkerth, who has studied thousands of brains over more than three decades, told the BBC.

ANCHOR seeks to close that gap.

Users can zoom in from the image of the entire brainstem to view each individual neuron without losing their precise spatial relationships. The researchers have made the atlas online free, hoping it will become a reference tool for neuroscientists, neurologists and neurosurgeons around the world.

Its applications could also extend beyond anatomy.

By comparing maps of a healthy brainstem with diseased tissue, scientists could better understand everything from Parkinson’s disease and stroke to Alzheimer’s disease and sudden infant death syndrome (SIDS). More accurate maps could also help neurosurgeons navigate one of the brain’s most delicate regions with greater confidence.

ANCHOR is not a diagnostic tool. Instead, its greatest value lies in the questions it could help answer.

Partha Mitra, a brain scientist at the prestigious Cord Spring Laboratory in New York who has worked with the SGBC, says that detailed brain atlases like this one could have a “transformative impact” on the study of neurological diseases by revealing, cell by cell, how brains that are affected by diseases like Alzheimer’s or autism differ from those that are healthy.

They could also help explain how infections, including Covid-19, can trigger long-term neurological damage, Mitra told the BBC.

Taking stroke as an example, Folkerth says the atlas has revealed new features that could help doctors preserve damaged but still recoverable brain tissue, potentially improving a patient’s prognosis. Other scientists say the atlas could also help neurosurgeons navigate the brainstem more safely.

Part of the appeal of this atlas is in its simplicity. Having been prepared from high-resolution images of thin sections of post-mortem brain tissue, it allows detailed mapping at the cellular level at a modest cost.

That, says Mitra, has made it possible to map the brain stem at an unprecedented level.

The achievement reflects a broader transformation of neuroscience, in which progress increasingly depends on engineering and computing as much as biology.

Around 20 scientists spent 18 months at the SGBC manually analyzing more than 200 brain sections, combining MRI scans, microscopic anatomy and 3D reconstruction into a unique digital atlas. The center now brings together more than 200 researchers, engineers and technicians working with collaborators around the world.

The result serves to fill a surprising gap in neuroscience.

Scientists have mapped the brains of several animal species in astonishing detail, but the human brain has been comparatively little explored because detailed studies of human brain tissue are scarce, Mohanasankar Sivaprakasam, director of the SGBC, told the BBC.

That doesn’t mean scientists haven’t had brain atlases. “Different atlases do different things,” Mitra said.

MRI-based atlases capture the overall structure of the brain, but not individual cells. Histological atlases map their architecture at cellular resolution using microscopic images of tissue sections. New molecular techniques go a step further, detecting the precise identity of each cell.

But scientists still know little about how the brain’s nearly 20,000 proteins are distributed across different regions and cell types, a frontier that will likely define the next generation of brain mapping.

“Every brain,” Folkerth maintains, “is a treasure chest of new knowledge.”

The SGBC now plans to scan more than 100 whole human brains across different stages of life and with different neurological disorders, including Alzheimer’s disease and dementia, to create a reference library that could reveal how these pathologies restructure the brain cell by cell.

The new atlas will not solve the mysteries of the human brain. But by giving scientists a more detailed map, it could help them ask—and ultimately answer—better questions.

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