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  1. The motility mechanisms of microorganisms are critical virulence factors, enabling their spread and survival during infection. Motility is frequently characterized by qualitative analysis of macroscopic colonies, yet the standard quantification method has mainly been limited to manual measurement. Recent studies have applied deep learning for classification and segmentation of specific microbial species in microscopic images, but less work has focused on macroscopic colony analysis. Here, we advance computational tools for analyzing colonies of Proteus mirabilis, a bacterium that produces a macroscopic bullseye-like pattern via periodic swarming, a process implicated in its virulence. We present a dual-task pipeline for segmenting (1) the macroscopic colony including faint outer swarm rings, and (2) internal ring boundaries, unique features of oscillatory swarming. Our convolutional neural network for patch-based colony segmentation and U-Net with a VGG-11 encoder for ring boundary segmentation achieved test Dice scores of 93.28% and 83.24%, respectively. The predicted masks at times improved on the ground truths from our automated annotation algorithms. We demonstrate how application of our pipeline to a typical swarming assay enables ease of colony analysis and precise measurements of more complex pattern features than those which have been historically quantified. An implementation of our work can be foundmore »on https://github.com/daninolab/proteus-mirabilis.« less
    Free, publicly-accessible full text available April 1, 2023
  2. Face detection and recognition benchmarks have shifted toward more difficult environments. The challenge presented in this paper addresses the next step in the direction of automatic detection and identification of people from outdoor surveillance cameras. While face detection has shown remarkable success in images collected from the web, surveillance cameras include more diverse occlusions, poses, weather conditions and image blur. Although face verification or closed-set face identification have surpassed human capabilities on some datasets, open-set identification is much more complex as it needs to reject both unknown identities and false accepts from the face detector. We show that unconstrained face detection can approach high detection rates albeit with moderate false accept rates. By contrast, open-set face recognition is currently weak and requires much more attention.