RT Journal Article
SR Electronic
T1 u-track 3D: measuring and interrogating dense particle dynamics in three dimensions
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.11.30.404814
DO 10.1101/2020.11.30.404814
A1 Philippe Roudot
A1 Wesley R. Legant
A1 Qiongjing Zou
A1 Kevin M. Dean
A1 Tadamoto Isogai
A1 Erik S. Welf
A1 Ana F. David
A1 Daniel W. Gerlich
A1 Reto Fiolka
A1 Eric Betzig
A1 Gaudenz Danuser
YR 2022
UL http://biorxiv.org/content/early/2022/07/18/2020.11.30.404814.abstract
AB Particle tracking is a ubiquitous task in the study of dynamic molecular and cellular processes through microscopy. Light-sheet microscopy has opened a path to acquiring complete cell volumes for investigation in 3-dimensions (3D). However, hypothesis formulation and quantitative analysis have remained difficult due to fundamental challenges in the visualization and the verification of large and dense sets of 3D particle trajectories. Here we describe u-track 3D, a software package that addresses these two challenges. Building on the established framework of particle association in space and time implemented for 2D time-lapse sequences, we first report a complete and versatile pipeline for particle tracking in 3D. 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 which defines a score for every trajectory, thereby overcoming the challenges of trajectory validation by visual inspection. With these combined strategies, u-track 3D provides a framework for the unbiased study of molecular processes in complex volumetric sequences.Competing Interest StatementThe authors have declared no competing interest.