@inproceedings{01J9R5K6ZVZA2BAC31K3CG6WWA,
  abstract     = {{1. Introduction 
Biofilms are microbial communities colonizing objects at the surface and in the pore space. Their growth affects material properties, impacting e.g. industrial processes, the environment, or healthcare. It is essential to image these biofilms in situ to understand their impact. Micro-computed tomography (µCT) could visualize biofilms but is hindered by a low contrast with water. Contrast-enhancing staining agents (CESAs) can be applied, but existing ones mainly stain the solution and often precipitate. Previous research by Schröer et al. [1] tested novel CESAs for directly staining biofilms. It showed that Isotonic Lugol (IL) and Hf-WD 1:2 POM revealed cyanobacterial biofilms on a stone surface. This research examined if these CESAs can image biofilms within the pore space using sand filter samples, which are relevant for drinking water production. 

2. Materials and Methods  
Biofilms were present in sand filters retrieved from water treatment plants. Triplicates were scanned at UGCT using CoreTOM (TESCAN XRE) before and after adding IL or Hf-WD 1:2 POM. For each CESA, an extra sample was scanned at TESCAN XRE using spectral CT. Moreover, the biofilms were imaged using Scanning Electron Microscopy (SEM) as a ground truth. 

3. Results and Discussion 
Before adding CESAs, biofilms were (nearly) invisible (Fig. A, C). Both CESAs increased the attenuation and contrast of the biofilms and the surrounding solution. IL-stained biofilms had an attenuation that was often higher than the grains (Fig. B), while Hf-WD 1:2 POM had a moderate effect (Fig. D). Biofilms imaged with µCT matched the SEM data. Challenges remained to segment the biofilm due to the heterogeneous attenuation of the sand grains and the biofilm. Image registration was not possible due to grain movements between scans. However, segmentation was successful using WEKA in Fiji [2]. Spectral CT localized high concentrations of I in the IL-stained biofilms, but detecting Hf and W was more difficult after using HfWD 1:2 POM. Spectral CT proved the affinity of the CESAs for biofilms. For IL, it allowed distinguishing between biofilms and grains with similar attenuation values. The acquired spectral data could enhance training data to segment biofilms using WEKA. 

4. Conclusion 
IL and Hf-WD 1:2 POM enabled biofilm imaging in the pore space by increasing the attenuation of the biofilm. Spectral CT could enhance its segmentation when identification remains difficult.}},
  author       = {{Schröer, Laurenz and Balcaen, Tim and Folens, Karel and Boon, Nico and Dewanckele, Jan and De Kock, Tim and Kerckhofs, Greet and Cnudde, Veerle}},
  booktitle    = {{ICTMS 2024, 6th International Conference on Tomography of Materials and Structures, Abstracts}},
  language     = {{eng}},
  location     = {{Cape Town, South Africa}},
  pages        = {{1}},
  title        = {{Enhanced imaging of biofilms in pore spaces with absorption and spectral CT}},
  year         = {{2024}},
}