u-track3D: Measuring, navigating, and validating dense particle trajectories in three dimensions.
Philippe Roudot, Wesley R Legant, Qiongjing Zou, Kevin M Dean, Tadamoto Isogai, Erik S Welf, Ana F David, Daniel W Gerlich, Reto Fiolka, Eric Betzig, Gaudenz Danuser
Author Information
Philippe Roudot: Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA; Aix Marseille University, CNRS, Centrale Marseille, I2M, Turing Centre for Living Systems, Marseille, France. Electronic address: philippe.roudot@univ-amu.fr.
Wesley R Legant: Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC, USA; Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA.
Qiongjing Zou: Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA.
Kevin M Dean: Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA.
Tadamoto Isogai: Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA.
Erik S Welf: Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA.
Ana F David: Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.
Daniel W Gerlich: Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.
Reto Fiolka: Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA.
Eric Betzig: Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
Gaudenz Danuser: Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA. Electronic address: gaudenz.danuser@utsouthwestern.edu.
We describe u-track3D, a software package that extends the versatile u-track framework established in 2D to address the specific challenges of 3D particle tracking. First, we present the performance of the new package in quantifying a variety of intracellular dynamics imaged by multiple 3D microcopy platforms and on the standard 3D test dataset of the particle tracking challenge. These analyses indicate that u-track3D presents a tracking solution that is competitive to both conventional and deep-learning-based approaches. We then present the concept of dynamic region of interest (dynROI), which allows an experimenter to interact with dynamic 3D processes in 2D views amenable to visual inspection. Third, we present an estimator of trackability that automatically defines a score for every trajectory, thereby overcoming the challenges of trajectory validation by visual inspection. With these combined strategies, u-track3D provides a complete framework for unbiased studies of molecular processes in complex volumetric sequences.
