title: Optimal processing for gel electrophoresis images: Applying Monte Carlo Tree Search in GelApp.
abstract: In biomedical research, gel band size estimation in electrophoresis analysis is a routine process. To facilitate and automate this process, numerous software have been released, notably the GelApp mobile app. However, the band detection accuracy is limited due to a band detection algorithm that cannot adapt to the variations in input images. To address this, we used the Monte Carlo Tree Search with Upper Confidence Bound (MCTS-UCB) method to efficiently search for optimal image processing pipelines for the band detection task, thereby improving the segmentation algorithm. Incorporating this into GelApp, we report a significant enhancement of gel band detection accuracy by 55.9 ± 2.0% for protein polyacrylamide gels, and 35.9 ± 2.5% for DNA SYBR green agarose gels. This implementation is a proof-of-concept in demonstrating MCTS-UCB as a strategy to optimize general image segmentation. The improved version of GelApp-GelApp 2.0-is freely available on both Google Play Store (for Android platform), and Apple App Store (for iOS platform).
authors.affiliation: Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
authors.forename: Phi-Vu
authors.initials: PV
authors.lastname: Nguyen
authors.affiliation: Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
authors.forename: Ali
authors.initials: A
authors.lastname: Ghezal
authors.affiliation: Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
authors.forename: Ya-Chih
authors.initials: YC
authors.lastname: Hsueh
authors.affiliation: Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.|Sorbonne Universités, Paris, France.|UPMC Univ. Paris 06, UJF, CNRS, IMT, NUS, Image and Pervasive Access Lab (IPAL), Singapore.
authors.forename: Thomas
authors.initials: T
authors.lastname: Boudier
authors.affiliation: Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.|p53 Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
authors.forename: Samuel Ken-En
authors.initials: SK
authors.lastname: Gan
authors.affiliation: Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.|Sorbonne Universités, Paris, France.|UPMC Univ. Paris 06, UJF, CNRS, IMT, NUS, Image and Pervasive Access Lab (IPAL), Singapore.|Department of Computer Science, National University of Singapore (NUS), Singapore.
authors.forename: Hwee Kuan
authors.initials: HK
authors.lastname: Lee
mesh_terms: D000465:Algorithms; D004587:Electrophoresis, Agar Gel / Q000379:methods; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D009010:Monte Carlo Method; D012984:Software
keywords: Band size estimation; Gel electrophoresis; Image processing; Image segmentation; Monte Carlo Tree Search with Upper Confidence Bound