200508 mouse brain

A mouse’s brain, mapped out

After three years of data gathering and drawing, the third iteration of the Allen Mouse Brain Common Coordinate Framework, or CCFv3, was completed and released.

CCFv3 is based on an average of the inherent fluorescence in the brains of mice imaged using serial two-photon tomography. This is a semi-transparent top-down view of the average template, revealing many striking anatomical features. Credit: Allen Institute for Brain Science.

Now, in a paper in the journal Cell, researchers from Allen Institute in the US describe how they created a high-res, 3D map of the brain of the laboratory mouse.

“In the old days, people would define different regions of the brain by eye. As we get more and more data, that… doesn’t scale anymore,” says Lydia Ng, one of the paper’s senior authors. “Just as we have a reference genome sequence, you need a reference anatomy.”

The whole-brain CCFv3 builds on a partial version released in 2016 that mapped the entire mouse cortex, the outermost shell of the brain. Its resolution is fine enough that it can pinpoint individual cells’ locations. 

To make it, the researchers broke up the brain into tiny virtual 3D blocks, known as voxels, and assigned each block a unique coordinate. The data that fed into that 3D construction came from the average brain anatomy of nearly 1700 different animals. 

The team then assigned each of those voxels to one of hundreds of different known regions of the mouse brain, drawing careful borders between distinct areas. The datasets that fed into these two aspects of the atlas came from several different kinds of experiments conducted over several years.

The researchers say future iterations will likely rely on machine learning or other forms of automation, rather than the laborious manual curation that went into the current version.

This video depicts a fusion of data in the CCF framework. The background grayscale image represents the average anatomy of 1675 individual specimens forming the basis for the common coordinate system. The coloured curved lines represented sampled streamlines.

This video depicts a fusion of data in the CCF framework. The background grayscale image represents the average anatomy of 1675 individual specimens forming the basis for the common coordinate system. The coloured curved lines represented sampled streamlines. Credit: Allen Institute for Brain Science.

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