An x-ray imaging system data acquisition and image reconstruction system and method are disclosed which enable optimizing the image parameters based on multiple tomographic volumes of the sample that have been captured using an x-ray microscopy system. This enables the operator to control the image contrast, for example, of selected slices, and apply the information associated with optimizing the contrast of the selected slice to all slices in two or more tomographic volume data sets. This creates a combined volume with optimized image contrast throughout. Also, the system enables navigation within the volumes through functional annotation, improvements in volume registration and improvements in noise suppression both within the volumes and within slice histograms of the sample.