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

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 µm 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 × 201 in a 1024 × 1024 image. To enhance usability and to make it easy to implement new functions we used objectoriented programming. UmUTracker is suitable for studies related to: particle dynamics, cell localization, colloids and microfluidic flow measurement. Nature of problem: 3D multi-particle tracking is a common technique in physics, chemistry and biology. However, in terms of accuracy, reliable particle tracking is a challenging task since results depend on sample illumination, particle overlap, motion blur and noise from recording sensors. Additionally, the computational performance is also an issue if, for example, a computationally expensive process is executed, such as axial particle position reconstruction from digital holographic microscopy data. Versatile robust tracking programs handling these concerns and providing a powerful post-processing option are significantly limited. PROGRAM SUMMARY Friday, April 21, 2017Manuscript 2 Solution method: UmUTracker is a multi-functional tool to extract particle positions from long video sequences acquired with either light microscopy or digital holographic microscopy. The program provides an easy-to-use graphical user interface (GUI) for both tracking and post-processing that does not require any programming skills to analyze data from particle tracking experiments. UmUTracker first conduct automatic 2D particle detection even under noisy conditions using a novel circle detector based on the isosceles triangle sampling technique with a multi-scale strategy. To reduce the computational load for 3D tracking, it uses an efficient implementation of the Rayleigh-Sommerfeld light propagation model. To analyze and visualize the data, an efficient data analysis step, which can for example show 4D flow visualization using 3D trajectories, is included. Additionally, UmUTracker is easy to modify with user-customized modules due to the object-oriented programing style.

3D printed water-soluble scaffolds for rapid production of PDMS micro-fluidic flow chambers

“…We position the image plane ≈5 µm below the bottom coverslip and image 1500 particles in a 272 µm × 272 µm ( x , y ) field of view. After image analysis using UmUTracker 23 , we calculate the mean speed and mean spatial position ( x , y , z ) for each particle from their respective trajectory. To visualize the flow profile in a cross section perpendicular to the flow direction, we interpolate the discrete point cloud to obtain a homogeneous surface representation without changing the information content and color-code the data according to the particle speed (Fig.…”

Integrated automated particle tracking microfluidic enables high‐throughput cell deformability cytometry for red cell disorders

“…We couple our microfluidic device with the UmUTracker, a highly accurate particle detection program that can be run on a standard desktop, to detect the velocity profiles of large numbers of individual RBCs under various conditions as they traverse an artificial microfluidic capillary system . The UmUTracker is a MATLAB based computational tool that automatically detects and tracks particles by analyzing video sequences acquired by light microscopy . The program can both track cells over the course of their entire transit and differentiate between the edges of cells and the constricting microchannels.…”

Step-by-step guide to reduce spatial coherence of laser light using a rotating ground glass diffuser

“…The whole setup is built in a temperature controlled room at (296 ± 1) K to ensure long-term stability and to reduce thermal drift effects [27]. For image analysis, we use the software UmUTracker [28].…”