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We present a versatile and fast MATLAB program (UmUTracker) thatautomatically detects and tracks particles by analyzing video sequencesacquired by either light microscopy or digital in-line holographic microscopy.Our program detects the 2D lateral positions of particles with an algorithmbased on the isosceles triangle transform, and reconstructs their 3D axialpositions by a fast implementation of the Rayleigh-Sommerfeld model using aradial intensity profile. To validate the accuracy and performance of ourprogram, we first track the 2D position of polystyrene particles using brightfield and digital holographic microscopy. Second, we determine the 3D particleposition by analyzing synthetic and experimentally acquired holograms. Finally,to highlight the full program features, we profile the microfluidic flow in a100 micrometer high flow chamber. This result agrees with computational fluiddynamic simulations. On a regular desktop computer UmUTracker can detect,analyze, and track multiple particles at 5 frames per second for a templatesize of 201 x 201 in a 1024 x 1024 image. To enhance usability and to make iteasy to implement new functions we used object-oriented programming. UmUTrackeris suitable for studies related to: particle dynamics, cell localization,colloids and microfluidic flow measurement.

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