The environmental sciences are undergoing an accelerating data revolution. The excitement at the capacity for next-generation sequencing, transcriptomic profiling and remote sensing of our environment has led to an unparalleled expansion in the types and amount of data available. X-ray computed tomography (x-ray CT) has established itself as a standard tool for extracting Synchrotron-equivalent resolution of three-dimensional ecological trait data. Within the discipline of environmental science, these images are extracted in an ad hoc basis across different laboratories. The discipline hop needed is generalisable pre-filtering software that can extract comparable metrics regardless of the original scanning protocols. Removing such measurement bias would open up appropriate comparative analysis on rapidly developing tools.