One of the principal challenges when applying X-ray microscopy to solve academic and industrial problems is a compromise one needs to make between imaging throughput and image quality. High resolution 3D X-ray microtomography acquisition times can be on the order of several hours, which can lead to challenging return-on-investment (ROI) calculations when weighing the relative advantage of high accuracy 3D analysis with cheaper, less capable analytical techniques.

To tackle this issue, optimization of each step in the production of actionable information from these microscopes is required. For 3D X-ray microtomography, these steps typically consist of sample mounting, scan setup, 2D-projection image acquisition, 2D to 3D image reconstruction, image post-processing and segmentation, and final analysis.