This dataset contains a micro X-ray Computed Tomography (micro-XRCT) data set (projection, reconstructed, and segmented images) from a sintered glass beads column packing with enzymatically induced carbonate precipitation. The prepared sintered glass beads column sample has a diameter of about 5 mm and a length of 10 mm. It consists of glass beads with a diameter of about 180 µm which were sintered. For the subsequent mineralization procedure, the sample was sealed on the side with a shrink tube and glued into the center of a cylindrical, 3D-printed plastic mold using epoxy resin. For further details, see Gehring et al. (2022).

For the carbonate precipitation, the sample was put into a sample holder with three separate inlets: one for pressure measurement and two for separate injection of the urease solution (at 5 kg/m³) and the mineralization solution (containing calcium and urea at 333 mol/m³ concentrations each) and one outlet. The pressure was measured to monitor the progress of mineralization. Mineralization was carried out at 60°C to increase the reaction rates of urea hydrolysis and calcium carbonate precipitation. The reaction solutions were injected into the sample at a rate of 5 µl/s each using syringe pumps with a total volume of 5 ml, necessitating refilling of the syringes between injection periods. Mineralization was continued until the maximum pressure of 8 bar was reached. During the mineralization, the applied injection rates of both solutions and the measured pressure were recorded and are provided as *.csv file ("Column3_mediumMineralization_20200128.csv").

The micro-XRCT scan shows the inlet section of the sample located at the top side of the glass beads column. Image stack counting from top to bottom.

Based on the reconstructed gray-values data set ("reconstructed.tar.gz"), a segmentation ("segmentedPNGs.tar.gz") into three phases was performed: glass beads, precipitated calcium carbonate, and pore space.

For this, first, the software ilastik was used to get a distribution of the probabilities of identification of each voxel to those three phases, which were expressed as color values: red = glass beads, blue = precipitated calcium carbonate, and green = pore space.

In a second step, based on the output by ilastik ("probabilities.tar.gz"), the software Matlab (see the Matlab script "column3_postprocess.m" in "segmentedPNGs.tar.gz") was used to finalize the segmentation assigning each voxel to a single-phase and to crop out an inner subvolume undisturbed by irregularities at the outer edges of the sample. The resulting binarized stacks of images of each of the phases are given: glass beads ("segmentedPNGs.tar.gz", subfolder "red_sand"), precipitated calcium carbonate ("segmentedPNGs.tar.gz", subfolder "blue_precip"), pore space ("segmentedPNGs.tar. gz", subfolder "green_void"), as well as precipitate and pore space representing the initial, unmineralized pore space, ("segmentedPNGs.tar.gz", subfolder "precip_plus_void"), in which white signifies the presence of the respective phase at the location and black absence of the respective phase.

Ruf, M. and Hommel, J. contributed equally.