A map of part of a mouse brain, which is expected to be generalisable to people, could help scientists understand behaviours, consciousness and even what it means to be human
By Helen Thomson
9 April 2025
An artistic representation of more than 1000 cells from a brain map, with each neuron a different colour
The Allen Institute
The largest and most comprehensive 3D map of a mammalian brain to date offers an unprecedented insight into how neurons connect and function. The new map, which captures a cubic millimetre of a mouse’s visual cortex, will allow scientists to study brain function in extraordinary detail, potentially revealing crucial insights into how neural activity shapes behaviour, how complex traits like consciousness arise, and even what it means to be human.
“Our behaviours ultimately arise from activity in the brain, and brain tissue shares very similar properties in all mammals,” says team member Forrest Collman at the Allen Institute for Brain Science in Seattle. “This is one reason we believe insights about the mouse cortex can generalise to humans.”
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The achievement – something that biologist Francis Crick said in 1979 was “impossible” – took seven years to complete and involved 150 researchers from three institutions. It began with a team recording neural activity from a portion of a mouse’s visual cortex, that was no bigger than a grain of sand, as it watched movies and YouTube clips.
Next, a second group dissected that same brain region, dividing it into layers 1/400th the width of a human hair, and took pictures of each slice. Due to the delicate nature of the structure, the slicing process couldn’t be stopped for long, so the team took shifts. “We spent 12 days and 12 nights sectioning this millimetre cube of tissue into almost 30,000 layers,” says team member Nuno da Costa, also at the Allen Institute.
From there, a third team used AI to trace all the cells and reconstruct each slice into a 3D map. “It was like asking AI to do the world’s hardest colouring book,” says Collman. “You have 100 million images in three dimensions and every single cell has to get coloured with a different crayon. The AI has to decide where one cell starts and the next one stops.”