SpatTrack software

SpatTrack is a MatLab-based standalone software for quantitative analysis of vesicle distribution and motility in living cells. SpatTrack collects a variety of algorithms, has user friendly GUI’s for each function and allows for batch processing of large data sets. SpatTrack has been developed by Frederik W. Lund and Daniel Wüstner for reliable analysis of complex imaging data generated by fluorescence microscopy of living cells. The software and workflow is described in the paper Lund et al., Traffic, 2014.

Highlights of the SpatTrack program are:

  • Flexible multi-frame image denoising using a boxcar filter
  • Particle tracking from time-lapse sequences
  • Trajectory classification and analysis
  • Calculation of second-order statistics and fitting of various diffusion models to the mean square displacement
  • Assessment of fitting performance based on the parameter confidence interval and covariance matrix
  • Statistically valid selection of vesicle motion models based on the Bayesian information criterion
  • Simulation of diffusion of one and two vesicle populations according to the included motion models
  • Spatial statistics analysis using various measures including the nearest neighbor, distance-to-PM and the radial distribution function for particles in one channel
  • Spatial statistics for mutual analysis of particles in two channels
  • Object-based co-localization analysis for two-channel images, which is directly comparable to the two-color spatial statistics
  • Comparison of experimental data with Monte Carlo simulations of random particle distributions within the real cell geometry
  • User-friendly GUI’s collecting all algorithms under one main menu 

SpatTrack can be downloaded here (Unzip the archives to get two folders, one containing the program and the license agreement, the other containing test images to be used together with the User Guide located in the same folder). SpatTrack is compiled as 64-bit Windows version and does not require MatLab (The Mathworks Inc.) to be installed on your computer. However, you must download and install the MatLab compiler runtime (MCR) on your computer. The MCR can be found at

The required MCR for the compiled version of SpatTRack is 2015a (8.5)/ 64-bit for Windows. 

SpatTrack Dependencies

SpatTrack uses the following files developed by other MatLab users:
1. The tiffread MatLab function developed by Francois Nedelec at EMBL, Heidelberg, Germany, see
2. the ExportFig MatLab function developed by Oliver Woodford and freely available at
3. the Simple Tracker MatLab function developed by Jean-Yves Tinevez and freely available at

For help regarding SpatTrack contact Daniel Wüstner at