Open source software for the analysis of intracellular particle motility and cytoskeletal polarity
By Russell S. Hamilton & Ilan Davis
Department of Biochemistry, University of Oxford

Contact:
darogan -@- gmail.com

Abstract
The study of dynamic cellular processes in living cells is central to biology and is particularly powerful when the motility characteristics of individual objects within cells can be determined and analysed statistically. However, commercial programs only offer a very limited range of inflexible analysis modules and there are currently no open source programs for extensive analysis of particle motility. Here, we describe ParticleStats (www.ParticleStats.com), a web server and open source programs, which input the X,Y co-ordinate positions of objects in time, and outputs novel analyses, graphical plots and statistics for motile objects. ParticleStats comprises three separate analysis programs. Firstly ParticleStats:Directionality, for the global analysis of polarity, for example microtubule plus end growth in Drosophila oocytes. Secondly, ParticleStats:Compare for the analysis of saltatory movement in terms of runs and pauses. This can be applied to chromosome segregation and molecular motor based movements. Thirdly, ParticleStats:Kymographs for the analysis of kymograph images, for example as applied to separation of chromosomes in mitosis. These analyses have provided key insights into molecular mechanisms that are not possible from qualitative analysis alone and are widely applicable to many other cell biology problems.
News
Date Program Affected Details
08/04/14 ParticleStats Source Code Source code now hosted on GitHub for the latest additions and bug fixes
Web Server
ParticleStats is now available as a web service. The interface provides all the features of the command line version in an easy to use graphical format.

[Use ParticleStats Online]

ParticleStats:Directionality ParticleStats:Compare ParticleStats:Kymographs

Features
ParticleStats:Compare:
The dynamics of particle movement, such as in the case of motor driven transport, can be explored through the calculation of runs and pauses in the movement. Statistical comparisons can be made between different populations of particles such as in the case of a wild type Vs mutant.

ParticleStats:Directionality:
The directionality of a set of tracked particles is determined using directional statistics. The windmaps are a novel way of visualising bias in the travel direction of particles. Further evidence is provided with rose diagrams and radial histograms.

ParticleStats:Kymographs:
Analysis of the dynamics of separating kinetochores as displayed in kymographs
Publications
ParticleStats Publication:

  • Hamilton, R.S., Parton, R.M., Oliveira, R.A., Ball, G., Vendra, G., Nasmyth, K. & Davis, I. (2010) ParticleStats: Open source software for the analysis of intracellular particle motility and cytoskeletal polarity. Nucleic Acids Research (Web Server Edition) [DOI]

    Publications utilising ParticleStats:

  • Oliveira, R.A., Hamilton, R.S., Pauli, A., Davis, I., Nasmyth, K. (2010) Cohesin cleavage and Cdk inhibition trigger formation of daughter nuclei. Nature Cell Biology, 12, 185-192 [DOI]

  • Vendra, G., Hamilton, R.S. & Davis, I. (2007) Dynactin suppresses the retrograde movement of apically localized mRNA in Drosophila blastoderm embryos. RNA, 13, 1-8. [DOI]
      Supplemental Materials: Figures and Movies can be found here

  • Parton, R.M., Hamilton, R.S., Ball, G., Yang, L., Cullen, F., Lu, W., Ohkura, H. & Davis, I. (2011) A PAR-1 dependent orientation gradient of dynamic microtubules establishes cell polarity in the Drosophila oocyte. Journal of Cell Biology, 194, 121-135. [DOI]

  • Hartswood. E., Brodie, J., Vendra, G., Davis, I. and Finnegan. D.J. (2012) RNA:RNA interaction can enhance RNA localization in Drosophila oocytes. RNA, 18, 1-9. [DOI]
  • Documentation
    The ParticleStats User Guide has been significantly updated and is available in PDF format
    [ParticleStats_UserGuide.pdf]

  • Now includes a trouble-shooting gude for data import
  • Installation instructions are now part of the User Guide
  • Download
    Most up to date ParticleStats version is available on GitHub, and includes additional features and bug fixes from the published version. Alternatively the stable version of the source code can be downloaded directly below
    Source Code Python Package Windows
    Latest Release:
    [GitHub] N/A N/A
    Stable Release:
        Version 0.3 [.tar.gz] [.tar.gz] [.exe]
    ROI Tool Only:
        Version 0.1: [.tar.gz] [.tar.gz] [.exe]
    License
    Open Source
    GNU License