Deep segmentation of bacteria at different stages of the life cycle

Abstract

Segmentation of bacteria in live cell microscopy image sequences is a crucial task to gain insights into molecular processes. A main challenge is that some bacteria strongly change their appearance during the life cycle as response to fluctuations in environmental conditions. We present a novel deep learning method with shape-based weighting of the loss function to accurately segment bacteria during different stages of the life cycle. We evaluate the performance of the method for live cell microscopy images of Bacillus subtilis bacteria with strong changes during the life cycle.