UmUTracker: A versatile MATLAB program for automated particle tracking of 2D light microscopy or 3D digital holography data
This provides a versatile tool for researchers in fields like particle dynamics and microfluidics, though it is incremental as it builds on existing tracking methods with new implementations.
The authors tackled the problem of automated particle tracking in microscopy data by developing UmUTracker, a MATLAB program that detects and tracks particles in 2D or 3D with an accuracy validated against simulations and experiments, achieving a processing speed of 5 frames per second on a desktop computer.
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.