We used Bruker's inbuilt acquisition software (ParaVision 360, version 3.4) to process all the proton MRI images acquired and obtain the subsequent DICOM files. From the DICOM images, we defined the ROIs required (i.e. scaffold and container region) using ImageJ (version 2.14.0) and generated binary masks from them. At this point, we processed all the data using custom-made Python scripts (version 3.10.9) to extract pixel intensity values and compute region averages or sums from individual ROIs. All the data and scripts generated for the processing are available in the GitHub repository ScaffoldsDifPerfPaper_2023.