An example from the Nano-CT system based on Excillum’s NanoTube at the Technical University of Munich, where the anatomical structures in cortex of the mouse kidney sample was studied with the eosin-based staining method. The compatibility of this new staining method to high resolution Micro-CT and Nano-CT have been studied. The Nano-CT images, together with the eosin-based staining method, gain a good comparison to conventional histological data, which reveal very detailed views into the 3D anatomical structure of the stained soft tissue with significantly high contrast and spatial resolution down to 200 nm. Moreover, the Nano-CT images also provide a good conjunction to the Micro-CT images to form a multi-scale CT data zooming from whole organ to small tissues. The achievement in this work indicates the future applicability of non-destructive, time-efficient virtual histology method in diagnostic screening of 3D tissue samples based on the laboratory Micro/ Nano-CT and eosin-based staining technique.