Example of applications using the full range of available resolutions. (A)...
Example of applications using the full range of available resolutions. (A) Shape tensor analysis of the different sections at the 20-μm scale, recombined to the 200-μm space of the blockface image; (B) density maps of blood vessels detected from the background of the 20-μm sections realigned in 3D at 200 μm, projected, and averaged into MNI space at 0.5 mm.

Image source: Alkemade et al., Science Advances 2022 (CC BY 4.0)

News • Neuroanatomy

Researchers create high-res 3D map of the brain

An exhaustive map of the human brain has been a long-sought goal of neuroanatomists. Noninvasive imaging techniques such as magnetic resonance imaging (MRI) allow scientists to investigate the healthy living human brain but provide only limited anatomical detail.

A higher level of detail can be obtained by using microscopy on brains from deceased donors, generally focusing on small brain structures imaged in 2D. Now a team led by scientists from the University of Amsterdam (UvA), have combined MRI and microscopy to produce 3D images of two entire brains with a previously unmatched level of detail. Their findings have been published in the journal Science Advances.

Anatomical detail obtained from reconstructed human brains. Coronal (A) and axial view (B) for the three MRI contrasts, blockface images, and five microscopy stains.

Image source: Alkemade et al., Science Advances 2022 (CC BY 4.0)

The researchers used an ultra-high field 7 Tesla MRI system, which has a more powerful magnet than the MRI systems routinely used in hospitals. The MRI software was programmed specifically for these studies by the researchers to accommodate the differences between living and preserved tissue. During the cutting of the tissue, each section was photographed individually, so that it could be used later to digitally correct tissue deformation in microscopy sections. Individual brain sections were placed on specially ordered glass slides, and processed with custom-built laboratory equipment. 

After digitisation of the individual microscopy slides, new algorithms were created by the researchers to correct for the tissue deformation resulting from the cutting and microscopy processing. After weeks of uninterrupted calculations, the researchers were finally able to create full reconstructions of two individual brains. 

Following Open Science principles, the researchers have made their data available free of cost as a service to the field. Scientists and other interested parties from around the world can now travel through the resulting 3D reconstructions of the human brain. 

Source: University of Amsterdam


Read all latest stories

Related articles


News • Brain tumour analysis

Glioblastoma '3D maps' help find new therapies

Researchers at the Universitat Autònoma de Barcelona obtained a highly accurate recreation of human glioblastoma’s features using a novel 3D microscopy analysis. The study, published in the…


News • In-depth view at neurodegeneration

New 3D imaging approach looks into earliest stages of Alzheimer's

Novel 3D imaging could comprehensively characterize a part of the brain that shows perhaps the earliest accumulation of tau protein, an important biomarker for the development of Alzheimer's disease.


News • Potential of nigrosome imaging

Parkinson's: Misconception of 'swallow-tail'-sign rectified

A new understanding of the 'swallow-tail', an anatomical landmark in the brain, could pave the way for earlier detection of Parkinson's disease.

Related products

Magnetom Amira

1.5 Tesla

Siemens Healthineers · Magnetom Amira

Siemens Healthcare GmbH
32 Inch Height-Adjustable MRI LED Screen

Accessories / Complementary Systems

allMRI · 32 Inch Height-Adjustable MRI LED Screen

allMRI GmbH
3D printed pure tungsten anti-scatter grids

Accessories / Complementary Systems

Dunlee · 3D printed pure tungsten anti-scatter grids

Dunlee – Philips Medical Systems DMC GmbH
Accutron MR


Medtron AG · Accutron MR

Accutron MR3


Medtron AG · Accutron MR3

Advanced intelligent Clear-IQ Engine for MR

Artificial Intelligence

Canon · Advanced intelligent Clear-IQ Engine for MR

Canon Medical Systems Europe B.V.
Subscribe to Newsletter