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UmUTracker: A versatile MATLAB program for automated particle tracking of 2D light microscopy or 3D digital holography data
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

We present a versatile and fast MATLAB program (UmUTracker) that automatically detects and tracks particles by analyzing long video sequences acquired by either light microscopy or digital holography microscopy. Our program finds the 2D particle center position using an isosceles triangle transform and the axial position by a fast implementation of Rayleigh-Sommerfeld numerical reconstruction algorithm using a one dimensional radial intensity profile. To validate the accuracy of our program we test each module individually in controlled experiments. First, we determine the lateral position of polystyrene particles recorded under bright field microscopy and digital holography conditions. Second, we reconstruct the axial position of the same particles by analyzing synthetic and experimentally acquired holograms. Thereafter, as a proof of concept, we profile the fluid 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 a single particle 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 object-oriented programming. UmUTracker is suitable for studies related to: particle dynamics, cell localization, colloids and microfluidic flow measurement.

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Computer Vision and Robotics (Autonomous Systems) Other Physics Topics
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URN: urn:nbn:se:umu:diva-131047DOI: arxiv.org/abs/1701.08025Archive number: arXiv:1701.08025OAI: oai:DiVA.org:umu-131047DiVA: diva2:1071237
Available from: 2017-02-03 Created: 2017-02-03 Last updated: 2017-02-03

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Zhang, HanqingStangner, TimWiklund, KristerRodrigues, AlvaroAndersson, Magnus
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Computer Vision and Robotics (Autonomous Systems)Other Physics Topics

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