Detailed Mouse Brain Maps in Simple Pictures

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Detailed mouse brain map created with off-the-shelf microscope

07 May 2025

Simple-enlarging trick helps researchers to untangle brain connectivity using readily available equipment.


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Animated sequence from a video of a colourised partial reconstruction of 658 neuronal structures.
Researchers used an artificial-intelligence model to reconstruct neural circuits in brain samples imaged using a light microscope.Credit: Tavakoli, Lyudchik et al./Nature

Scientists have found a way to map the intricate patterns of cells in mouse brain tissue with an off-the-shelf light microscope, using a trick that inflates a tiny sample to 16 times its original size.

Until now, charting the tangled forest of neurons in the brain to build a map of connections known as the connectome required an electron microscope. These are powerful but expensive machines that cannot generate coloured images.

A milestone map of mouse-brain connectivity reveals challenging new terrain for scientists

The approach described in Nature on 7 May1 uses gels that swell when soaked in water. These space out the tightly packed neurons in a piece of mouse brain, making the details visible under standard light microscopes down to individual synapses — the junctions between neurons. Using artificial intelligence (AI) models to trace individual neurons, the researchers created colourful maps that show how brain cells connect, which molecules they use to communicate and whether their signals excite or silence other cells.

“The hope is that we’re going to be able to do exactly what electron microscopy does, but faster, cheaper and in some sense more creative, with the use of colour,” says Mariela Petkova, a neuroscientist at Harvard University in Cambridge, Massachusetts, who was not involved in the work.

Supersized sample:

Light microscopes are cheap, fast and found in almost all biology laboratories, but they lack the resolution needed to map the fine branches of neurons and synapses in the brain. The neural circuits of worms2, flies, mice and humans have all been mapped using electron microscopy.

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https://www.nature.com/articles/d41586-024-01096-3

15 April 2024


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A milestone map of mouse-brain connectivity reveals challenging new terrain for scientists

A pioneering ‘connectomics’ collaboration has successfully reconstructed one cubic millimetre of brain tissue, but researchers are still just scratching the surface of the complexity it contains.

Neural processes of four distinctly coloured neurons mapped by the Machine Intelligence from Cortical Networks project. Credit: MICrONS Explorer

A cubic millimetre is a tiny volume — less than a teardrop but a cubic millimetre of mouse brain is densely packed with tens of thousands of neurons and other cells in a staggeringly complex architectural weave.