Previous versions of the atlas were lower resolution 3-D maps, while CCFv3's resolution is fine enough that it can pinpoint individual cells' locations. The whole-brain CCFv3 builds on a partial version released in 2016 that mapped the entire mouse cortex, the outermost shell of the brain. Credit: Allen Institute for Brain Science "Just as we have a reference genome sequence, you need a reference anatomy."Īn angled view of the 3D Allen Mouse Brain Common Coordinate Framework (CCFv3), a high-resolution reference atlas parcellated into distinct brain regions using multiple types of data. As we get more and more data, that manual curation doesn't scale anymore," said Lydia Ng, Ph.D., Senior Director of Technology at the Allen Institute for Brain Science, a division of the Allen Institute, and one of the senior authors on the atlas paper along with Julie Harris, Ph.D., Associate Director of Neuroanatomy at the Allen Institute for Brain Science. "In the old days, people would define different regions of the brain by eye. With datasets in the thousands or millions of different pieces of information, that common set of coordinates-and pinpointing the corresponding brain landmarks for those coordinates-is crucial. Instead of manually searching for your location on a paper map based on what you see around you, the GPS (and the new brain atlas) tells you where you are. Think of it as the neuroscience equivalent of your phone's GPS. 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 3-D space to compare and correlate. Their brains contain approximately 100 million cells each across hundreds of different regions. Mice are widely used in biomedical research. The framework is meant to be a reference point for the neuroscience community, its creators said. In a paper published today in the journal Cell, the Allen Institute mapmakers describe this cartographical feat-the third iteration of the Allen Mouse Brain Common Coordinate Framework, or CCFv3 ( ), a complete, high-resolution 3-D atlas of the mouse brain. The complex terrain they charted, with all its peaks, valleys and borders, is only about half an inch long and weighs less than a jellybean: the brain of the laboratory mouse.
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