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
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| 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. |
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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.
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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. |
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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. |
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ParticleStats:Kymographs: Analysis of the dynamics of separating kinetochores as displayed in kymographs |
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ParticleStats Publication:
Publications utilising ParticleStats:
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The ParticleStats User Guide has been significantly updated and is available in PDF format [ParticleStats_UserGuide.pdf]
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| Source Code | Python Package | Windows | |
| Latest Release: | |||
| Version 0.3 | .tar.gz | .tar.gz | |
| ROI Tool Only: | |||
| Version 0.1: | .tar.gz |
Open Source
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GNU License
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