{"id":29682168,"url":"https://github.com/thorstenwagner/traj","last_synced_at":"2025-07-23T02:08:28.764Z","repository":{"id":57730274,"uuid":"47341724","full_name":"thorstenwagner/TraJ","owner":"thorstenwagner","description":"Library for diffusion trajectory 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[![Build Status](https://travis-ci.org/thorstenwagner/TraJ.svg?branch=master)](https://travis-ci.org/thorstenwagner/TraJ)\n\u003cp align=\"center\"\u003e\n \u003cimg src=\"http://imagej.net/_images/a/a1/Trajlogo.png\" alt=\"TraJ logo\"/\u003e\n\u003c/p\u003e\n\n\n# TraJ\nJava library for diffusion trajectory (2D) analysis. \n\n# Features\n## Trajectory characterization\n- Diffusion coefficient via covariance estimator [1]\n- Diffusion coefficient via regression estimator \n- Hydrodynamic diameter by Stokes-Einstein converter\n- Aspect ratio\n- Asymmetry features [7][10]\n- Center of gravity\n- Efficency [6]\n- Elongation\n- Exponent in power law fit to MSD curve [4]\n- Fractal path dimension [2]\n- Gaussianity [9]\n- Kurtosis [6]\n- Maximum distance between two positions\n- Maximum distance for given timelag\n- Mean speed [11]\n- Mean squared displacment curve curvature [3]\n- Mean squared displacment\n- Short-time long-time diffusion coefficent ratio \n- Skeweness [6]\n- Spline curve analysis features according to [5]\n![Spline fit](https://dl.dropboxusercontent.com/u/560426/traj/splinefit.png \"Spline fit\")\n- Standard deviation in direction\n- Trapped probability [7]\n\n## Simulation\n- Brownian motion (free diffusion)\n- Active Transport\n- Confined diffusion\n- Anomalous diffusion with fixed obstacles (spheres)\n- Anomalous diffusion by weierstrass-mandelbrot approach [8]\n\n## Other\n- Global linear drift calculator\n- Static drift corrector\n- Trajectories are combineable\n\n  \n\n#Maven artifacts\nTraJ can be found on maven central:\n```\n\u003cdependency\u003e\n    \u003cgroupId\u003ede.biomedical-imaging.TraJ\u003c/groupId\u003e\n    \u003cartifactId\u003etraj\u003c/artifactId\u003e\n    \u003cversion\u003eMOST RECENT RELEASE\u003c/version\u003e\n\u003c/dependency\u003e\n```\n  \nReferences:\n\n[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.\n\n[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.\n\n[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.\n\n[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.\n\n[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.\n\n[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.\n\n[7] Saxton, M.J., 1993. Lateral diffusion in an archipelago. Single-particle diffusion. Biophysical Journal, 64(6), pp.1766–1780.\n\n[8] Guigas, G. \u0026 Weiss, M., 2008. Sampling the Cell with Anomalous Diffusion—The Discovery of Slowness. Biophysical Journal, 94(1), pp.90–94.\n\n[9] Ernst, D., Köhler, J. \u0026 Weiss, M., 2014. Probing the type of anomalous diffusion with single-particle tracking. Physical chemistry chemical physics : PCCP, 16(17), pp.7686–91.\n\n[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.\n\n[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.\n\nTo Do:\n- 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)\n- Simulation: Add anomalous diffusion with brownian motion obstacles and Ornstein-Uhlenbeck obstacles\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fthorstenwagner%2Ftraj","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fthorstenwagner%2Ftraj","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fthorstenwagner%2Ftraj/lists"}