Abstract
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 benefiting 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.
Highlights
Magnetic resonance imaging (MRI) is today’s leading technique in the study of the human brain (Bandettini, 2009)
We have developed a pipeline in which we processed an entire human brain combining ultrahigh fields (UHF) MRI with cryosectioning, followed byhistological processing and subsequent 3D reconstructions
One advantage of the pipeline is that MRI is performed before brain extraction, preventing major tissue deformations at this stage, facilitating registration to available brain atlases
Summary
Magnetic resonance imaging (MRI) is today’s leading technique in the study of the human brain (Bandettini, 2009). An additional challenge when aiming to bridge the gap between histological and/or immunocytochemical techniques and MRI research is the preparation of the tissue so that it accommodates both optimal MRI acquisition as well as it preserves the tissue properties required for reliable analyses using microscopy approaches. Tissue processing for microscopy purposes, causes substantial tissue deformation, caused by brain extraction, as well as the preparation of slides for histology and/or immunocytochemistry These deformations need to be accommodated in co-registrations of post mortem and in vivo MRI, as well as MRI to histology. The obtained individual sections can be used for histological processing to perform anatomical validation of MRI results visualizing small anatomical structures which can be reconstructed providing a detailed account of the 3D microstructure of the human brain. The protocol description presented here can be used as a guide to set up the required collaborations
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