Histology to MRI registration quality of ex vivo human brain blocks fixed with solutions used in anatomy laboratories

Post-mortem brain tissue is obtained from brain banks that provide small samples that are fixed with neutral-buffered formalin (NBF), while gross anatomy laboratories could become a source of complete brains for neuroscientists. These are preserved with solutions developed for dissection, such as a saturated-salt-solution (SSS) or an alcohol-formaldehyde solution (AFS). Histology remains the gold standard in neuroscientific research, while MRI is the most common imaging modality. Thus, MRI-histology registration quality needs to be assessed in human brains fixed with NBF, SSS and AFS. To this end, we used 12 human brain blocks fixed in our anatomy laboratory (SSS=4; AFS=4; NBF=4). The blocks were scanned using a 7T Bruker animal MRI scanner with a T2-TurboRARE sequence and cut into 40μm sections, which were stained with histochemistry and immunohistochemistry. Stained sections were imaged using a slide scanner microscope and segmented with masks using Display, and the sections were manually registered to the T2-TurboRare images using landmarks in Register (MINCToolKit). Our results showed that more landmarks were needed to achieve proper alignment of the histology to MRI images for the SSS-fixed blocks. These blocks also showed a lower percentage of overlap between the good histology quality masks and the MRI masks. We conclude that our MRI and registration protocols are suitable for brains fixed with solutions used in gross anatomy laboratories, although more challenging when fixed with SSS. These results are promising for neuroscientists interested in using full brains from anatomy laboratories, either using MRI, histology or registration of both modalities to study normal aging and neurodegenerative conditions.