UvA scientists perform highly detailed 3D reconstructions of the human brain

Complete mapping of the human brain has been an important goal in neuroanatomy from the start. Non-invasive imaging techniques such as magnetic resonance imaging allow examination of the living brain, albeit with a limited amount of anatomical detail. More details can be obtained by looking at the brain under a microscope, but this is only possible with the brains of the deceased. It turns out to be a powerful scientific journey to combine MRI and microscopy. UvA scientists, along with an international team, have successfully bridged this gap. The result is a 3D image of two whole brains with an unprecedented level of detail. The results were published Wednesday, April 27 in the journal Science Advances.

UvA researchers have collaborated for more than five years to bridge the gap between ultra-high-field MRI and microscopy methods to create images of the brain. Two sets of human brains donated to science were placed in an MRI scanner for 21 hours, then sliced ​​and examined under a microscope. Study data from magnetic resonance imaging and microscopy were combined, resulting in images of the brain that allow study at a level of detail of 200 mm (0.2 mm).

Virtual brain anatomy
“We are excited about the new initiatives that will make our results possible,” says Anneke Alkemade, UvA team member. Teachers can use data sets, for example, to train neuroanatomy and virtual brain anatomy. The ability to compare MRI results with specific proteins visualized by microscopy gives researchers more insight into poorly understood MRI observations, as well as providing more anatomical detail in small brain structures.

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picture by picture
The researchers used a 7Tesla high-field magnetic resonance imaging system. It contains a magnet that is stronger than MRI systems commonly used in hospitals. The MRI software was specifically programmed by the researchers for the study to take into account the differences between living tissue and preserved tissue. During tissue sectioning, each brain slice was imaged individually so that it could later be used to digitally correct tissue distortion on microscopy slides. Brain slices were pulled into specially arranged glass slides and processed with custom laboratory equipment.

After digitizing all microscopy data, the researchers developed new algorithms to correct tissue distortion caused by cutting and tissue staining. After weeks of continuous calculations, the team was finally able to create full 3D reconstructions of the two sets of donated brains.

Open Science
In keeping with open science principles, the team made all data freely available. Scientists and interested research institutions from around the world can now travel through 3D reconstructions of the human brain.

Watch the 3D reconstruction

Post details
Anneke Alkemade, Pierre-Louis Bazin, Rawien Balesar, Kerrin Pine, Evgeniya Kirilina, Harald Moller, Robert Trampel, Johan Kros, Max Keuken, Ronald Bleys, Dick Swaab, Andreas Herrler, Nikolaus Weiskopf and Birte Forstmann’s 3D map: Microscopic architecture and magnetic resonance imaging of the human brain, in: Science Advances (April 27, 2022). DOI: 10.1126 / sciaadv.abj7892

This article is a submission and is not the responsibility of the editors.

Megan Vasquez

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