UmUTracker: A versatile MATLAB program for automated particle tracking of 2D light microscopy or 3D digital holography data

TL;DR

UmUTracker is a versatile MATLAB tool that automatically detects and tracks particles in 2D and 3D from microscopy and holography videos, enabling detailed analysis of particle dynamics and microfluidic flows.

Contribution

The paper introduces a novel, fast MATLAB program with an isosceles triangle transform and Rayleigh-Sommerfeld model for accurate 2D and 3D particle tracking from microscopy data.

Findings

Achieves 5 frames per second processing speed on standard desktop.

Accurately tracks particles in both synthetic and real holographic data.

Successfully profiles microfluidic flow consistent with CFD simulations.

Abstract

We present a versatile and fast MATLAB program (UmUTracker) that automatically detects and tracks particles by analyzing video sequences acquired by either light microscopy or digital in-line holographic microscopy. Our program detects the 2D lateral positions of particles with an algorithm based on the isosceles triangle transform, and reconstructs their 3D axial positions by a fast implementation of the Rayleigh-Sommerfeld model using a radial intensity profile. To validate the accuracy and performance of our program, we first track the 2D position of polystyrene particles using bright field and digital holographic microscopy. Second, we determine the 3D particle position by analyzing synthetic and experimentally acquired holograms. Finally, to highlight the full program features, we profile the microfluidic flow in a 100 micrometer high flow chamber. This result agrees with computational fluid dynamic simulations. On a regular desktop computer UmUTracker can detect, analyze, and track multiple particles at 5 frames per second for a template size of 201 x 201 in a 1024 x 1024 image. To enhance usability and to make it easy to implement new functions we used object-oriented programming. UmUTracker is suitable for studies related to: particle dynamics, cell localization, colloids and microfluidic flow measurement.