D tomographic data at various scales is increasingly available through the wide adoption of CT (Micro Computed Tomography) and FIB-SEM (Focused Ion Beam - Scanning Electron Microscopy) technologies. However, upscaling these observations is very challenging. This paper provides a template of an upscaling protocol between FIB-SEM data on a micron sized sample and CT data on the same sample region but at millimeter- scale. We use a Devonian North American shale rock fragment in our study. Due to the large scale variations in the pore structure and drastic petrophysical property heterogeneity, shale rocks are very challenging and costly to study as compared to rock samples from conventional reservoirs. Using CT with voxel resolution of tens of microns, we are able to identify different rock heterogeneities. A smaller sample from each distinct heterogeneity region is then digitized using FIB-SEM 3D imaging with voxel resolution of a few nanometers. Stokes flow at pore-scale is used to model the absolute permeability tensor, an intrinsic rock property associated with each rock heterogeneity. Afterwards, multiphase porous medium flow at Darcy-scale is conducted on the CT data, constrained by the permeability tensor and the porosity calculated from FIB-SEM data that correspond to each heterogeneity identified from the CT data previously.