Mougous, Joseph DWiggins, Paul ACutler, Kevin John2024-02-122024-02-122024-02-122023Cutler_washington_0250E_26462.pdfhttp://hdl.handle.net/1773/51242Thesis (Ph.D.)--University of Washington, 2023Until recently, the scientific community has lacked image segmentation tools that are precise, reliable, and general-purpose. Such tools are especially needed in applications to bacterial image cytometry, wherein single-pixel precision is needed, perfect segmentation must be achieved over thousands of cells over hundreds of time points, and the approach must be applicable to a diversity of cellular morphologies present in a single micrograph. In this document, I detail the challenges of bacterial image segmentation, the failures of prior approaches, and the use of machine learning to solve this problem in virtually any unilaminar cell imaging context.application/pdfen-USCC BY-NCaffinity graphsbacteriadeep neural networksinstance segmentationmachine learningphase contrastBiophysicsMicrobiologyPhysicsThesis