Neuroscientists at the Allen Institute for Brain Science have released the third version of their Allen Mouse Brain Common Coordinate Framework (CCFv3).
Wang et al built a detailed map of the mouse brain from tiny virtual 3D blocks, or voxels. Image credit: Benedicte Rossi.
A mouse brain contains approximately 100 million cells across hundreds of different regions.
As neuroscience datasets grow larger and more complex, a common spatial map of the brain becomes more critical, as does the ability to precisely co-register many different kinds of data into a common 3D space to compare and correlate.
“In the old days, people would define different regions of the brain by eye. As we get more and more data, that manual curation doesn’t scale anymore,” said Dr. Lydia Ng, senior director of technology at the Allen Institute for Brain Science.
“Just as we have a reference genome sequence, you need a reference anatomy.”
The CCFv3 atlas builds on a partial version released in 2016 that mapped the entire mouse cortex, the outermost shell of the brain.
Previous versions of the atlas were lower resolution 3D maps, while CCFv3’s resolution is fine enough that it can pinpoint individual cells’ locations.
To make the atlas, Dr. Ng and colleagues 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 1,700 different animals.
The researchers 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 at the Allen Institute over the past several years — the atlas’s backbone of different types of data makes it unique among reference brain atlases,” they said.
Historically, brain atlases were drawn in 2D, taking sheet-like views of the brain at different depths and lining them up. For some types of data, this form of brain mapping works well.
But for modern neuroscience studies looking at neuron activity or cell characteristics across the entire brain, a 3D atlas gives better context.
Future iterations of the atlas will likely rely on machine learning or other forms of automation, rather than the laborious manual curation that went into the current version.
“As we know now, atlases should be evolving and living resources, because as we learn more about how the brain is organized, we will need to make updates,” said Dr. Julie Harris, associate director of neuroanatomy at the Allen Institute for Brain Science.
“Building atlases in an automatic, unbiased way is where the field is likely moving.”
The scientists describe their work in a paper published today in the journal Cell.
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Quanxin Wang et al. The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Cell, published online May 7, 2020; doi: 10.1016/j.cell.2020.04.007
This article is based on text provided by the Allen Institute.
