The microstructure and mineralogy of any system define its chemical and physical properties. The heterogeneity of shale exists across multiple scales making accurate characterization difficult at any scale. In addition, heterogeneity has made linking variance in measured physical properties to the observed microstructural characteristics equally problematic. Because of the nano-scale components of shale, scanning electron microscopy (SEM) has proven invaluable as a tool for understanding microstructural and physical properties such as storage, storage partitioning between organic and inorganic phases, and fluid flow dynamics of shale. However, until recently, the restricted field of view of the SEM has limited its utility in yielding representative analysis of these complex rocks. The emergence of automated high-resolution imaging and stitching software permits bridging 7 orders of magnitude of scale using a single instrument. The collection of large images with nanometer-scale resolution is utilized to image and quantify microstructural characteristics from different shale plays. Image analysis on the stitched mosaic provides quantitative measurements of key microstructural elements. These features include, organic content, organic and inorganic porosity. In addition, mineralogy will be quantified using FTIR as well as an EDS-based approach for automated identification of the spatial mineralogy of each sample. The results of this detailed microstructural and mineralogical analysis are presented in the context of petrophysical measurements made on the same samples. Key petrophysical measurements include helium porosity, and NMR for porosity, TOC and pyrolysis for organic maturity as well as nano-indentation for defining mechanical properties of the samples.