Fig 1.
(A) Schematic of the experimental setup used for the biofilm culturing as well as the region of the tubular reactor used for biofilm imaging. (B) Schematic of the configuration used for the X-ray scans where the distances SOD and STD represent the source-to-object (SOD) and the source-to-detector distance (STD).
Table 1.
Information relative to the different scans and datasets used in this work as well as the corresponding details concerning the data analysis.
Fig 2.
(A) raw projection image (unfiltered). (B) Lorentz filtered image of (A) using α = 1.5 ⋅ 10−7. (C) Lorentz filtered image of A using α = 1.5 ⋅ 10−8. The same dynamic range was used for (A), (B) and (C) for the sake of comparison. (D) displays horizontal normalized profiles at the location of the dashed line in (A), and (B) and (C) as well as for additional values of α. The inset shows a magnification of the gray value profile at the center of the tubular reactor. The scale bar in (A) is also valid on (B) and (C).
Fig 3.
Slices from the FeSO4 (A) and LFeSO4 (C) datasets.
For the sake of comparison, both images were normalized with 0.4% of the pixels saturated. The two red resp. blue arrows indicate the location and direction at which the gray value profiles are extracted. The scale bar represents 1 mm. Gray value profile for the first (P1, (D) and the second location P2, (B)). The profiles are labeled with the different phases observed.
Fig 4.
Middle slices (filtered prior to segmentation according information in Table 1) for the LFeSO4 (A) and BaSO4 (B) datasets.
The corresponding 8 bit gray value histograms are shown in C) for the BaSO4 (blue) dataset and for the LFeSO4 (red) dataset after contrast enhancement and application of the 3D curvature-driven diffusive filter. For the LFeSO4 dataset, the vertical dashed lines in yellow, purple and green correspond to isosurface values of 64, 73 and 82 used for the segmentation and the corresponding sensitivity analysis. The peaks corresponding to the different phases are annotated. (D) and (E) show the segmented datasets where the solid, liquid and biofilm phases are color coded in white, blue and green respectively. The scale bar represents 1 mm.
Fig 5.
Three-dimensional renderings of the solid phase (left), of the sample imaged with FeSO4 (center) and barium suflate (right) as a contrast-enhancing agents.
Fig 6.
Profiles of the volumetric fractions (S: solid, L: liquid, BF: biofilm) obtained for the different datasets (BaSO4: small dashes, FeSO4: longer dashes).
The shaded region is defined by the results obtained for the threshold sensitivity analysis. For the sake of clarity, the results of this sensitivity analysis are not added to the liquid phases. The average volumetric fractions (in percent) for the different phases (Solid VS, Liquid VL, Biofilm VBF) obtained with the two different contrast-enhancing agents is given in the legend.
Table 2.
Conditioned probabilities that a given phase in the FeSO4 data locally belongs to the same phase in the BaSO4 data computed for the solid (S), liquid (L) and biofilm (BF) phases for the registered Lorentz filtered FeSO4 and BaSO4 datasets.
Fig 7.
Schematic of biofilm detachment mechanisms during BaSO4 injection.
Table 3.
Evaluation of the presented method and another existing one for imaging biofilms in porous media.