3D Atlas – Scientists have 3D mapped a mouse’s brain

Hyperaxion May 8, 2020

Researchers hope that the structure will serve as a reference point for the scientific community, facilitating studies on the neurological system of these animals.

A study published Thursday in the journal Cell contains the most complete “map” ever made of a mouse’s brain. The “3D Atlas”, as it was called, took three years to complete and is the result of CT scans carried out on 1675 animals.

3D Atlas - Scientists have 3D mapped a mouse's brain
(Credit: Allen Institute for Brain Science).

The researchers hope that the structure will serve as a point of reference for the scientific community, which uses rodents frequently to conduct studies. “By making our atlas and related tools open access, new data and data types generated across our community can be more easily integrated and compared in the same spatial context,” said Lydia Ng, one of the researchers, in a statement to the press.

A mouse’s brain contains approximately 100 million cells that are divided into different regions – which is precisely why mapping it digitally is so important. According to the researchers, 3D Atlas works like a GPS: instead of searching for information manually, a process that can take a long time and result in errors, scientists will be able to search for the data they need quickly and effectively.

(Credit: Allen Institute for Brain Science).

According to Ng, in the past, scholars defined different regions of the brain with the naked eye. But, with the volume of information you find today, this is no longer possible. “Just as we have a reference genome sequence, you need a reference anatomy,” completes the researcher, referring to the new atlas.


To create the map, the researchers aligned different sets of data obtained from previous research and new analyzes. This allowed them to label more than 800 brain structures, some of which had never been described before.

(Credit: Allen Institute for Brain Science).

To create the atlas, the researchers divided the brain into small 3D blocks, known as voxels, and assigned each block a unique coordinate, drawing “boundaries” between different areas. “We are now using this atlas as the common anatomical reference space for many large-scale projects, including whole-brain circuit mapping, single-cell reconstructions, and the generation of a comprehensive brain cell-type census,” said Julie Harris, co-author of the research.

(Credit: Allen Institute for Brain Science).


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