TraJ

Java library for diffusion trajectory (2D) analysis.

Features

Trajectory characterization

• Diffusion coefficient via covariance estimator [1]
• Diffusion coefficient via regression estimator
• Hydrodynamic diameter by Stokes-Einstein converter
• Aspect ratio
• Asymmetry features [7][10]
• Center of gravity
• Efficency [6]
• Elongation
• Exponent in power law fit to MSD curve [4]
• Fractal path dimension [2]
• Gaussianity [9]
• Kurtosis [6]
• Maximum distance between two positions
• Maximum distance for given timelag
• Mean speed [11]
• Mean squared displacment curve curvature [3]
• Mean squared displacment
• Short-time long-time diffusion coefficent ratio
• Skeweness [6]
• Spline curve analysis features according to [5]
• Standard deviation in direction
• Trapped probability [7]

Simulation

• Brownian motion (free diffusion)
• Active Transport
• Confined diffusion
• Anomalous diffusion with fixed obstacles (spheres)
• Anomalous diffusion by weierstrass-mandelbrot approach [8]

Other

• Global linear drift calculator
• Static drift corrector
• Trajectories are combineable

#Maven artifacts TraJ can be found on maven central:

<dependency>
    <groupId>de.biomedical-imaging.TraJ</groupId>
    <artifactId>traj</artifactId>
    <version>MOST RECENT RELEASE</version>
</dependency>

References:

[1] C. L. Vestergaard, P. C. Blainey, and H. Flyvbjerg, “Optimal estimation of diffusion coefficients from single-particle trajectories,” Phys. Rev. E - Stat. Nonlinear, Soft Matter Phys., vol. 89, no. 2, p. 022726, Feb. 2014.

[2] M. J. Katz and E. B. George, “Fractals and the analysis of growth paths,” Bull. Math. Biol., vol. 47, no. 2, pp. 273–286, 1985.

[3] S. Huet, E. Karatekin, V. S. Tran, I. Fanget, S. Cribier, and J.-P. Henry, “Analysis of transient behavior in complex trajectories: application to secretory vesicle dynamics.,” Biophys. J., vol. 91, no. 9, pp. 3542–3559, 2006.

[4] D. Arcizet, B. Meier, E. Sackmann, J. O. Rädler, and D. Heinrich, “Temporal analysis of active and passive transport in living cells,” Phys. Rev. Lett., vol. 101, no. 24, p. 248103, Dec. 2008.

[5] Spatial structur analysis of diffusive dynamics according to: B. R. Long and T. Q. Vu, “Spatial structure and diffusive dynamics from single-particle trajectories using spline analysis,” Biophys. J., vol. 98, no. 8, pp. 1712–1721, 2010.

[6] Helmuth, J.A. et al., 2007. A novel supervised trajectory segmentation algorithm identifies distinct types of human adenovirus motion in host cells. Journal of structural biology, 159(3), pp.347–58.

[7] Saxton, M.J., 1993. Lateral diffusion in an archipelago. Single-particle diffusion. Biophysical Journal, 64(6), pp.1766–1780.

[8] Guigas, G. & Weiss, M., 2008. Sampling the Cell with Anomalous Diffusion—The Discovery of Slowness. Biophysical Journal, 94(1), pp.90–94.

[9] Ernst, D., Köhler, J. & Weiss, M., 2014. Probing the type of anomalous diffusion with single-particle tracking. Physical chemistry chemical physics : PCCP, 16(17), pp.7686–91.

[10] Helmuth, J.A. et al., 2007., A novel supervised trajectory segmentation algorithm identifies distinct types of human adenovirus motion in host cells., Journal of structural biology, 159(3), pp.347–58.

[11] Meijering, Erik; Dzyubachyk, Oleh; Smal, Ihor (2012): „Methods for Cell and Particle Tracking“. In: Imaging and Spectroscopic Analysis of Living Cells - Optical and Spectroscopic Techniques., S. 183-200, DOI: 10.1016/b978-0-12-391857-4.00009-4.

To Do:

• Size distribution estimation for trajectory sets according to: J. G. Walker, “Improved nano-particle tracking analysis,” Meas. Sci. Technol., vol. 23, no. 6, p. 065605, Jun. 2012. (Already implemented in NanoTrackJ - I just have to port it)
• Simulation: Add anomalous diffusion with brownian motion obstacles and Ornstein-Uhlenbeck obstacles