title: Classification and Segmentation of Nanoparticle Diffusion Trajectories in Cellular Micro Environments.
abstract: Darkfield and confocal laser scanning microscopy both allow for a simultaneous observation of live cells and single nanoparticles. Accordingly, a characterization of nanoparticle uptake and intracellular mobility appears possible within living cells. Single particle tracking allows to measure the size of a diffusing particle close to a cell. However, within the more complex system of a cell's cytoplasm normal, confined or anomalous diffusion together with directed motion may occur. In this work we present a method to automatically classify and segment single trajectories into their respective motion types. Single trajectories were found to contain more than one motion type. We have trained a random forest with 9 different features. The average error over all motion types for synthetic trajectories was 7.2%. The software was successfully applied to trajectories of positive controls for normal- and constrained diffusion. Trajectories captured by nanoparticle tracking analysis served as positive control for normal diffusion. Nanoparticles inserted into a diblock copolymer membrane was used to generate constrained diffusion. Finally we segmented trajectories of diffusing (nano-)particles in V79 cells captured with both darkfield- and confocal laser scanning microscopy. The software called "TraJClassifier" is freely available as ImageJ/Fiji plugin via https://git.io/v6uz2.
authors.affiliation: Biomedical Imaging Group, Department of Informatics, University of Applied Sciences and Arts Dortmund, Dortmund, Germany.
authors.forename: Thorsten
authors.identifier: http://orcid.org/0000-0002-1550-8275
authors.initials: T
authors.lastname: Wagner
authors.affiliation: EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Kroll
authors.affiliation: Experimental Physics IV and Bayreuth Insitute for Macromolecular Research, University of Bayreuth, Bayreuth, Germany.
authors.forename: Chandrashekara R
authors.initials: CR
authors.lastname: Haramagatti
authors.affiliation: Biomedical Imaging Group, Department of Informatics, University of Applied Sciences and Arts Dortmund, Dortmund, Germany.
authors.forename: Hans-Gerd
authors.initials: HG
authors.lastname: Lipinski
authors.affiliation: IBE R&D gGmbH Institute for Lung Health, Münster, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Wiemann
mesh_terms: D003585:Cell Biology; D004058:Diffusion; D018613:Microscopy, Confocal; D008962:Models, Theoretical; D053758:Nanoparticles