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Imaging Complex Brains in 3D at Micron Resolution
A new high-throughput 3D fluorescence imaging technique can produce a 3D mapping of an entire monkey brain at micron resolution.

The brain is made up of billions of nerve cells, interconnected by synapses. In order to understand how the brain functions, it is vital to have a high-resolution map showing how the different nerve cells are organised and linked to each other.

With our current technology, it takes days to produce a 3D image of a mouse’s whole brain at micron resolution. However, when we scale up 200 times to the brain of larger non-human primates like the rhesus monkey, such high-resolution brain mapping is hindered by the sheer size of the monkey brain.

To overcome this technical challenge, researchers led by Professors Bi Guoqiang and Lau Pakming from the University of Science and Technology of China and Shenzhen Institute of Advanced Technology and collaborators developed a high-throughput 3D fluorescence imaging technique called the Volumetric Imaging with Synchronous on-the-fly-scan and Readout (VISoR).

Unlike the usual 3D optical imaging techniques, VISoR is able to capture images of a sample in continuous motion without blur, allowing the method to achieve a speed more than 10 times faster than other 3D imaging techniques.

Apart from the size, another difficulty of imaging the monkey brain stems from the complicated folding structures and low tissue transparency. To address this, the scientists had to cut a portion of the isolated brain into 0.3mm slices and formulated reagents to achieve transparency.

With their improved VISoR system, the 3D imaging of a whole macaque brain was completed in 100 hours at micron resolution. The total volume of raw image data from two macaque brains was more than 1 petabyte, or 1000 terabyte.

On top of the speed and resolution of their new technique, the scientists also developed efficient algorithms and software to achieve automated 3D imaging reconstruction and semi-automated long-distance tracking of individual neuronal axon fibres. This revealed new axonal characteristics and surprising fibre patterns in the cortical folds not previously known.

This work has been praised by Professor David C. Van Essen from Washington University in St. Louis as a “technical tour de force that marks a stunning advance in our ability to map long-distance connectivity accurately and efficiently throughout the entire brain of the macaque monkey.”

Given the importance of non-human primates in modelling human diseases, Bi, Lau and colleagues’ work could have a widespread application in the imaging of other organs that will allow us to understand its detailed 3D structures and how they change in different disease conditions, thereby improving medical diagnostics and drug developments.

“Hopefully, this technology will be further improved for broader and larger-scale applications, to make important contributions to the mapping and understanding of primate and eventually the human brain,” said Professor Duan Shumin from Zhejiang University.

Source: Xu et al. (2021). High-throughput mapping of a whole rhesus monkey brain at micrometer resolution. Nature Biotechnology, 1-8.

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