DefocusTracker: A Modular Toolbox for Defocusing-based, Single-Camera, 3D Particle Tracking. (23rd July 2021)

• Record Type: Journal Article
• Authors: Barnkob, Rune; Rossi, Massimiliano
• Is Part Of: Journal of open research software. Volume 9(2021)
• Publication Date: 2021-07-23
• Subjects: particle tracking -- velocimetry -- PTV -- general defocusing particle tracking -- fluid dynamics -- MATLAB -- Python; Computer software -- Reusability -- Periodicals; Open source software -- Periodicals; 005
• DOI: 10.5334/jors.351
• Languages: English
• ISSNs: 2049-9647

Abstract

The need for single-camera 3D particle tracking methods is growing, among others, due to the increasing focus in biomedical research often relying on single-plane microscopy imaging. Defocusing-based methods are ideal for a wide-spread use as they rely on basic microscopy imaging rather than requiring additional non-standard optics. However, a wide-spread use has been limited by the lack of accessible and easy-to-use software. DefocusTracker is an open-source toolbox based on the universal principles of General Defocusing Particle Tracking (GDPT) relying solely on a reference look-up table and image recognition to connect a particle's image and its respective out-of-plane depth coordinate. The toolbox is built in a modular fashion, allowing for easy addition of new image recognition methods, while maintaining the same workflow and external user interface. DefocusTracker is implemented in MATLAB, while a parallel implementation in Python is in the preparation.