I started working on motility in around 2014. This package represents a framework for the analysis of how agents move through 3D space. The package's functionality has been expanded and updated over the years that I have been working on it.
A sample graph (there are loads more): for this Levy flight, translational and turn speeds are inversely correlated.
The framework is written in Python3, employing object-oriented design.
Each agent is tracked through space and time, and the path that it follows is captured as a Track object.
Tracks comprise Positions that capture location and some other summary statistics.
Usually many agents are observed simultaneously, and these are collected into a Profile of Tracks.
build.py contains a variety of methods for commencing an analysis.
The most typical analysis I have performed is to capture agent spatio-temporal position data as a CSV file.
Example files can be found in the sample_data directory, alongside example analyses.
Examples of how to use the package are found in the tests directory.
There is facility to contrasting several profiles (e.g. different experiments or populations of cells).
See the contrast_profiles.py module for details.
This repository is relatively new, because the first iteration of the model was released as a ZIP file with the corresponding 2016 PLOS Computational Biology paper. Since that time, this model (and theme of work) has contributed to the following papers.
Hywood, J. D., Rice, G., Pageon, S. V, Read, M. N., & Biro, M. (2021). Detection and characterisation of chemotaxis without cell tracking. Journal of the Royal Society Interface, 18, 20200879.
Galeano Niño, J. L., Pageon, S. V, Tay, S. S., Colakoglu, F., Kempe, D., Hywood, J., … Biro, M. (2020). Cytotoxic T cells swarm by homotypic chemokine signalling. ELife, 9, 1–40. https://doi.org/10.7554/elife.56554
Moran, I., Nguyen, A., Khoo, W. H., Butt, D., Bourne, K., Young, C., … Phan, T. G. (2018). Memory B cells are reactivated in subcapsular proliferative foci of lymph nodes. Nature Communications, 9(1), 3372. https://doi.org/10.1038/s41467-018-05772-7
Read, M. N., Bailey, J., Timmis, J., & Chtanova, T. (2016). Leukocyte Motility Models Assessed through Simulation and Multi-objective Optimization-Based Model Selection. PLOS Computational Biology, 12(9), e1005082. https://doi.org/10.1371/journl.pcbi.1005082
Hywood, J. D., Read, M. N., & Rice, G. (2016). Statistical analysis of spatially homogeneous dynamic agent-based processes using functional time series analysis. Spatial Statistics, 17, 199–219. https://doi.org/10.1016/j.spasta.2016.06.002
Code is made available under the GNU General Public License version 3.
If you have any questions about this code, or how to apply it to your own data, please get in contact.
motility_analysis was written by Mark N. Read <mark.norman.read@gmail.com>_.