Description:The subcortex accounts for 25% of the entire human brain volume. Less than 10% of subcortical structures are included in commonly used MRI atlases. This translates to over 400 structures in the human subcortex that are still being systematically overlooked. We have invested in the development of both in vivo and post mortem approaches to improve the available anatomical tools to study the subcortex. Using 7 Tesla (functional) MRI at submillimeter resolutions in vivo, we have mapped the development of 17 individual subcortical brain structures across the adult lifespan (age 18-80y). These studies not only revealed location shifts of many structures across the lifespan, but also provide valuable information on the morphometry and neuroimaging properties of these subcortical structures. This knowledge can be used for the further refinement of neuroimaging parameters, and the resulting probabilistic maps of the structures can be reused by researchers to identify regions of interest in their fMRI studies. However, many subcortical structures are too small to visualize using MRI. We have developed a research pipeline that allows us to combine post mortem MRI and microscopy approaches. This pipeline provides us with a level of anatomical detail, that allows the mapping of subcortical structures that are not visible on MRI. To this end, we combined neuroanatomy, image processing, cognitive neuroscience, pathology, and physics to perform ultra-high field (7 Tesla) MRI scanning on human post mortem brain tissue. The scanned tissue was then processed for microscopy studies. The created detailed digital 3D reconstructions can be overlaid with the MRI scans. The openly available dataset represents a novel and rich resource for neuroscientists world-wide who wish to study the human brain at a 200mm level of detail, exploring a variety of image contrasts. These efforts together represent an incremental brain atlasing project in which data from different imaging modalities is combined in a shared 3 dimensional space. A major advantage of this approach is that the high numbers of observations in MRI studies, with limited anatomical detail can be combined with the low numbers obtained from microscopy approaches with unmatched detail. Combined these efforts provide a synergistic effect, and a valuable resource for researchers world-wide.
Bio: Anneke Alkemade, PhD, is an expert in human neuroanatomy working at the Brain and Cognition, Psychology Department at the University of Amsterdam. In her work she aims to uncover the functional neuroanatomy in health and disease, and to translate post mortem histological findings into information relevant for clinicians as well as other fields of neuroscience. Dr. Alkemade complements her in vivo atlasing efforts on 7 Tesla submillimeter MRI, with post mortem 3D reconstructions of human whole-brain specimens. Dr. Alkemade has developed a wide range of experimental protocols ranging from in vivo delineation protocols to tissue fixation procedures and blockface imaging during cutting procedures to staining protocols using histochemistry on thick sections, immunohistochemistry, as well classical radioactive isotope or chromogen labeled ribo-, oligo- and locked nucleic acid probes. Her work contributes to increase understanding of the pathogenesis underlying neurological disease and is focused on advancing microscopy techniques to allow the reconstruction of large tissue specimens into 3D volumes.
Twitter: @AlkemadeAnneke LinkedIn: Anneke Alkemade