A deep learning pipeline for segmentation of Proteus mirabilis colony patterns

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.