Analyzing single-molecule dynamics with both complex types of motion and complex transition kinetics: Benchmarking of ExaTrack

Single-particle tracking (SPT) is a tool of growing importance which enables biologists to better understand the dynamics of protein interactions at the single-molecule level and in vivo. However, the stochastic nature of the motion of single molecules, the wide variety of types of motion that they can experience and complex transition kinetics between the different states of motion are challenging factors that complicate the interpretation of SPT data. This article presents and benchmarks the tool ExaTrack. Like previous tools, it can handle particles moving in one or multiple states of motion with transitions between states. Its unique feature is that it can simultaneously handle a wide range of complex types of motion such as diffusive motion, directed motion and confined motion while also managing a variety of transition kinetics such as memoryless first-order transitions or more complex time-dependent state transitions. This manuscript focuses on the benchmarking of ExaTrack on simulated data.