High image resolution ([approximately]1.3 m/pixel) and precision positioning capability make the Xradia X-ray microscopy an attractive platform on which to study X-ray opacity variations. It can complement precision radiography (PR) as an instrument with much higher spatial resolution. PR measures X-ray transmission intensity variations down to 0.01% at 100-m resolution. Since the requirement to differentiate minute lateral variations in X-ray transmission intensity scales inversely with the spatial resolution, an X-ray imaging microscope such as the Xradia MicroXCT can be useful if it measures the transmission intensity variations to <1%. In normal practice, a number of imaging artifacts limit the intensity measurement to only [approximately]2% precision. Such artifacts include the thermal drift and the illumination uniformity of the X-ray source, as well as thickness variations in the scintillator plate and the beryllium X-ray tube window. The conventional flat-fielding technique is not effective against the dynamic interaction between the beryllium window texture and the moving shadow cast by a moving X-ray spot. We have modified the image processing routine so that the lateral variations in the transmitted intensity can be measured to [approximately]0.3% precision on low-Z samples. This technique can be used to record microstructure variations in beryllium samples. Currently, the beryllium microstructures are characterized by ultrasmall angle X-ray scattering on a synchrotron source, which is not commonly accessible, is expensive, and has a long turnaround time. This Xradia-based method has the potential to make it a routine measurement.