Stochastic Neural Networks for Automatic Cell Tracking in Microscopy Image Sequences of Bacterial Colonies

We describe an automated analysis method to quantify the detailed growth dynamics of a population of bacilliform bacteria. We propose an innovative approach to frame-sequence tracking of deformable-cell motion by the automated minimization of a new, specific cost functional. This minimization is implemented by dedicated Boltzmann machines (stochastic recurrent neural networks). Automated detection of cell divisions is handled similarly by successive minimizations of two cost functions, alternating the identification of children pairs and parent identification. We validate this automatic cell tracking algorithm using recordings of simulated cell colonies that closely mimic the growth dynamics of \emph{E. coli} in microfluidic traps. On a batch of 1100 image frames, cell registration accuracies per frame ranged from 94.5\% to 100\%, with a high average. Our initial tests using experimental image sequences of \emph{E. coli} colonies also yield convincing results, with a registration accuracy ranging from 90\% to 100\%.