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7 Tesla MRI followed by histological 3D reconstructions in whole-brain specimens

posted on 14.09.2020, 11:35 by J.M. Alkemade, Kerrin Pine, Evgeniya Kirilina, Max Keuken, Martijn J. Mulder, Rawien Balesar, Josephine M Groot, Ronald L. A. W. Bleys, Robert Trampel, Nikolaus Weiskopf, Andreas Herrler, Harald Möller, Pierre-Louis Bazin, Birte Forstmann

Here you can download blockface movies of subjects:






Post mortem magnetic resonance imaging (MRI) studies on the human brain are of great interest for the validation of in vivo MRI. It facilitates a link between functional and anatomical information available from MRI in vivo and neuroanatomical knowledge available from histology/immunocytochemistry. However, linking in vivo and post mortem MRI to microscopy techniques poses substantial challenges. Fixation artifacts and tissue deformation of extracted brains, as well as co registration of 2D histology to 3D MRI volumes complicate direct comparison between modalities. Moreover, post mortem brain tissue does not have the same physical properties as in vivo tissue, and therefore MRI approaches need to be adjusted accordingly.

Here, we present a pipeline in which whole-brain human post mortem in situ MRI is combined with subsequent tissue processing of the whole human brain, providing a 3-dimensional reconstruction via blockface imaging. To this end, we adapted tissue processing procedures to allow both post mortem MRI and subsequent histological and immunocytochemical processing. For MRI, tissue was packed in a susceptibility matched solution, tailored to fit the dimensions of the MRI coil. Additionally, MRI sequence parameters were adjusted to accommodate T1 and T2* shortening, and scan time was extended, thereby benefitting the signal-to-noise-ratio that can be achieved using extensive averaging without motion artifacts. After MRI, the brain was extracted from the skull and subsequently cut while performing optimized blockface imaging, thereby allowing three-dimensional reconstructions. Tissues were processed for Nissl and silver staining, and co-registered with the blockface images. The combination of these techniques allows direct comparisons across modalities.


This research is financially supported by STW/NWO (BUF, MM, AA), NWO VICI (BUF), the European Research Council (BUF and NW [n° 616905]), the BMBF (01EW1711A & B to NW), the Brain Foundation of the Netherlands (BUF, AA), Stichting Internationaal Parkinson Fonds (BUF, AA).


Retention period


Research priority area

  • Brain & Cognition



University of Amsterdam / Amsterdam University of Applied Sciences