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A comprehensive understanding of mechanical and fluid flow properties in fine-grained geo-materials like shales requires imaging the microstructure at a range of scales as the microstructures are small and the samples are heterogeneous. Broad Ion Beam (BIB) milling followed by Scanning Electron Microscopy (SEM) imaging provides access to these microstructures at nanometre resolution and large cross sections of up to several mm2. Applying BIB-SEM on naturally and experimentally deformed or Wood’s Metal injected samples enables to resolve the related deformation processes and to image the pore connectivity, respectively. The pore fluid distribution, however, can be resolved by integrating BIB-SEM with cryogenic techniques. Examples of such integrated studies indicate calcite in shear fractures in Opalinus Clay and high connectivity in a fine-grained Boom Clay sample.