Summary Microstructural MRI techniques are unique among neuroimaging modalities because they probe tissue features at the micron scale that are invisible using other methods. This class of MRI methods is therefore promising to address the unmet needs for neuroimaging in Alzheimer’s disease (AD) and related dementias: 1. early detection of subtle cellular and protein alterations and 2. delineation of comorbid pathologies in AD. In particular, diffusion MRI (dMRI) is sensitive to alterations in cellularity, cell morphology, and other microstructural changes and relaxometery MRI (rMRI) is sensitive to macromolecular content. Both of these microstructural MRI techniques are relevant for detecting AD pathology, namely beta-amyloid (Ab) plaques and Tau tangles, as well as comorbid pathologies such as Lewy body disease (LBD), hippocampal sclerosis (HS) and TDP-43 proteinopathy. While studies in humans have begun to use some of these approaches, there is a need to understand the radiologic-pathologic correspondence of MRI changes with the underlying tissue pathology and also to determine which of the more advanced dMRI and rMRI methods are the most promising for translation to human studies. In order to meet these challenges, we propose a “bottom-up” study using MRI microscopy to image post-mortem temporal lobe and brainstem tissue from humans with and without a clinical diagnosis of AD in life. Our first aim is the identification of dMRI and rMRI markers of AD pathology in which we will optimize and apply acquisition, processing and analysis strategies for post-mortem tissue for diffusion tensor MRI (DTI), mean apparent propagator MRI (MAP-MRI), q-space trajectory imaging (QTI), bound pool fraction (BPF) and myelin water fraction (MWF) mapping. Then the tissue will be stained for phosphorylated Tau (pTau) and Ab and undergo neuropathologic review and scoring as well as quantitative histology. Correlation statistics will be performed between MRI metrics and neuropathologic outcomes to identify radiologic- pathologic relationships. In our second aim, we will investigate comorbid pathologies by the additional staining and scoring of a-synuclein and TDP-43. Similar correlation analysis will be used to determine the dMRI and rMRI metric profiles associated with LBD and TDP-43 proteinopathy. Our final aim will then compare these radiologic-pathologic signatures in different temporal lobe structures (e.g. hippocampus, amygdala, cortex and white matter) and in brainstem regions (locus coeruleus, dorsal raphe nucleus and white matter tracts). Overall, our goal is to establish initial findings about the most promising MRI methods for further development and translation of improved MRI markers for AD research and diagnosis.