DefocusTracker: A modular toolbox for defocusing-based, single-camera, 3D particle tracking

TL;DR

DefocusTracker is an open-source, modular MATLAB toolbox for single-camera 3D particle tracking using defocusing principles, facilitating accessible and adaptable biomedical imaging analysis.

Contribution

It introduces a flexible, user-friendly software toolbox based on GDPT principles, enabling widespread adoption of defocusing-based 3D particle tracking.

Findings

Open-source MATLAB implementation available

Modular design allows easy integration of new methods

Parallel Python version under development

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.