U-Net Based Image Segmentation Techniques for Development of Non-Biocidal Fouling-Resistant Ultra-Thin Two-dimensional (2D) Coatings

• Published in: 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) pp. 3602 - 3604
• Main Authors: Gurung, Bichar Dip Shrestha, Devadig, Ramesh, Do, Tuyen, Gadhamshetty, Venkataramana, Gnimpieba, Etienne Z.
• Format: Conference Proceeding
• Language: English
• Published: IEEE 06.12.2022
• Subjects: 2D material; biofilms; Grain boundaries; Graphene; Image segmentation; microbial cells; Nickel; Nonhomogeneous media; Scanning electron microscopy; segmentation; Training; U-Net
• DOI: 10.1109/BIBM55620.2022.9995609

Bacterial adhesion to the metallic surfaces creates a complex biofilm network, resulting in many problems like corrosion and fouling. Precise quantitative analysis of the surface coverage of cells can be vital in decoding biofilm-related issues. We present a deep learning-based approach to automate the microbes' segmentation from the Scanning Electron Microscope (SEM) images of biofilm developed on coated multilayer graphene nickel samples. We collected SEM images from multilayer graphene nickel exposed to Oleidesulfovibrioalaskensis (OA-G20) for 30 days. Then we manually annotated the microbes with the help of subject expertise and trained a deep-learning U-Net architecture. In order to deal with larger image sizes, we perform patched-based image training and techniques for predicting segmentation masks over the larger image. Intersection over Union (IOU) was calculated for the evaluation of the performance of the model. After training the image for multiple epochs and extracting the optimal model parameters from the learning curve, we were able to get 70.64% mean IOU score. The patched-based technique for image training and image inference showed promising output during the segmentation.