Background Micro-CT (X-ray computed tomographic) allows for 3D visualization of an entire structure, both internally and externally. The different materials are identified based on the differences in their ability to attenuate X-ray, with the differences being converted into a range of grey values. Low-density plant tissues with limited differences in grey values create a challenge in differentiating the cellular structures. In addition, internal movements due to autolysis, degradation, and shrinkage during dehydration of the tissues during scanning give rise to blurry images. Results In this study, oats and wheat were scanned using micro-CT to optimize the use of micro-CT in low-density plants. With the assistance of chemical fixing, phosphotunstate and a chemical drying agent, we were able to visualize microstructures of cereal stems. These preparation steps allow us to create 3D micrographs of low-density stem nodes suggesting key structural differences that are correlated with lodging resistance. Conclusion Micro-CT is a valuable tool to create 3D structural images of low-density material. Multiple steps to prepare the samples to stop autolysis, increase the contrast during scanning and eliminate internal movement are described in this paper. This process allowed for visualization of the stem nodal region suggesting morphology related to lodging resistance.