Scintillator defect correction in x-ray microscopy

An X-ray microscopy system, comprising:

• an X-ray source subsystem of generating X-rays;
• an object stage subsystem for holding a sample in the X-rays;
• a detector subsystem for detecting the X-rays after interaction with the sample;
• and
• a computer for receiving projections from the detector subsystem and controlling the system to collect a normal geometry projection and shifted geometry projection with a detector for each defect of the detector such that each projection pair (normal and shifted) are acquired so that they visualize the portion of a sample with and without detector defect obstruction, training a machine learning system using the pairs of the normal geometry projection and the shifted geometry projection, and correcting tomographic projection datasets and/or tomographic volume sets using the trained machine learning system.