TRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data [version 1; peer review: 1 approved, 1 approved with reservations]

• Published in: F1000 research Vol. 10; p. 838
• Main Authors: Reina, Francesco, Wigg, John M.A, Dmitrieva, Mariia, Lefebvre, Joël, Rittscher, Jens, Eggeling, Christian
• Format: Journal Article
• Language: English
• Published: England 2021
• Subjects: Algorithms; Computer Simulation; Diffusion; Software; Data analysis; Simulation; Microscopy; Single Particle Tracking; Diffusion; Graphical User Interface; Python
• ISSN: 2046-1402; 2046-1402
• DOI: 10.12688/f1000research.54788.1

Single particle tracking (SPT) is one of the most widely used tools in optical microscopy to evaluate particle mobility in a variety of situations, including cellular and model membrane dynamics. Recent technological developments, such as Interferometric Scattering microscopy, have allowed recording of long, uninterrupted single particle trajectories at kilohertz framerates. The resulting data, where particles are continuously detected and do not displace much between observations, thereby do not require complex linking algorithms. Moreover, while these measurements offer more details into the short-term diffusion behaviour of the tracked particles, they are also subject to the influence of localisation uncertainties, which are often underestimated by conventional analysis pipelines. we thus developed a Python library, under the name of TRAIT2D (Tracking Analysis Toolbox - 2D version), in order to track particle diffusion at high sampling rates, and analyse the resulting trajectories with an innovative approach. The data analysis pipeline introduced is more localisation-uncertainty aware, and also selects the most appropriate diffusion model for the data provided on a statistical basis. A trajectory simulation platform also allows the user to handily generate trajectories and even synthetic time-lapses to test alternative tracking algorithms and data analysis approaches. A high degree of customisation for the analysis pipeline, for example with the introduction of different diffusion modes, is possible from the source code. Finally, the presence of graphical user interfaces lowers the access barrier for users with little to no programming experience.