Open source software for the analysis of intracellular particle motility and cytoskeletal polarity.
[View latest version and code on GitHub]
ParticleStats was originally created by Russell Hamilton and Ilan Davis at the Department of Biochemistry, University of Oxford and in collaboration with the Micron Advanced Imaging Facility.
UPDATE: ParticleStats2.0 is currently being developed by Russell Hamilton (Dept Genetics, University of Cambridge) in collaboration with Anne Ferguson-Smith with new features for comparing tracking data, cell migration and behavioural assays
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.
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.
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ParticleStats::Kymographs:
Analysis of the dynamics of separating kinetochores as displayed in kymographs
New for ParticleStats2.0::ParticleStats::TrackAlign
Analysis and comparison of tracking data
New for ParticleStats2.0::ParticleStats::Behavioural
Analysis of the dynamics of zebrafish movement in behavioural tracking experiments
ParticleStats::Cell:
Analysis of migrating cells
Planned for ParticleStats3.0
ParticleStats Publication (please cite if using ParticleStats in your work):
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]
Kay 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]
