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BiofilmScanner: A Computational Intelligence Approach to Obtain Bacterial Cell Morphological Attributes from Biofilm Image

Desulfovibrio alaskensis G20 (DA-G20) is utilized as a model for sulfate-reducing bacteria (SRB) that are associated with corrosion issues caused by microorganisms. SRB-based biofilms are thought to be responsible for the billion-dollar-per-year bio-corrosion of metal infrastructure. Understanding the extraction of the bacterial cells' shape and size properties in the SRB-biofilm at different growth stages will assist with the design of anti-corrosion techniques. However, numerous issues affect current approaches, including time-consuming geometric property extraction, low efficiency, and high error rates. This paper proposes BiofilScanner, a Yolact-based deep learning method integrated with invariant moments to address these problems. Our approach efficiently detects and segments bacterial cells in an SRB image while simultaneously invariant moments measure the geometric characteristics of the segmented cells with low errors. The numerical experiments of the proposed method demonstrate that the BiofilmScanner is 2.1x and 6.8x faster than our earlier Mask-RCNN and DLv3+ methods for detecting, segmenting, and measuring the geometric properties of the cell. Furthermore, the BiofilmScanner achieved an F1-score of 85.28% while Mask-RCNN and DLv3+ obtained F1-scores of 77.67% and 75.18%, respectively.

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