X-ray submicron computed tomography (submicron CT) is a powerful method for 3D visualization and inspection of many types of samples. This non-destructive method provides sufficient resolution and contrast to evaluate any microstructural features, with the ability to resolve structures even below one micron. Moreover, this method requires minimal/no sample preparation, eliminating complicated tasks such as embedding, coating or thin slicing required with other high-resolution methods. The Rigaku nano3DX represents state-of-the-art laboratory-based nanoscale X-ray imaging. This device, when used with deep learning methods, is an unmatched tool for the plant science.