The code contained in the cell-migration-spatialcoord-onelayer project was developed for work in numerically simulating the collective migration of cells and tissues in 2D using partial differential equations with a moving boundary. It is described in various papers including:
Tracy L. Stepien, Holley E. Lynch, Shirley X. Yancey, Laura Dempsey, and Lance A. Davidson, Using a continuum model to decipher the mechanics of embryonic tissue spreading from time-lapse image sequences: An approximate Bayesian computation approach, PLOS ONE, 14 (2019), e0218021, DOI: 10.1371/journal.pone.0218021.
and is based off of code developed for the work described in the following papers:
Julia C. Arciero, Qi Mi, Maria F. Branca, David J. Hackam, David Swigon, Continuum model of collective cell migration in wound healing and colony expansion, Biophysical Journal, 100 (2011), 535-543, DOI:10.1016/j.bpj.2010.11.083.
E. Javierre, C. Vuik, F.J. Vermolen, and A. Segal, A level set method for three dimensional vector Stefan problems: Dissolution of stoichiometric particles in multi-component alloys, J. Comput. Phys. 224 (2007), 222-240, DOI: 10.1016/j.jcp.2007.01.038
S. Chen, B. Merriman, S. Osher, and P. Smereka, A simple level set method for solving Stefan problems, J. Comp. Phys. 135 (1997), 8-29, DOI: 10.1006/jcph.1997.5721
S. Osher, and J.A. Sethian. Fronts propagating with curvature-dependent speed: algorithms based on Hamilton-Jacobi formulations. J. Comput. Phys. 79 (1988), 12-49, DOI: 10.1016/0021-9991(88)90002-2
Images: The raw experimental time-lapse images of Xenopus laevis embryonic tissue migration and their corresponding MATLAB-processed files can be downloaded from Dryad via the following DOI: 10.5061/dryad.8pj52vk
The MATLAB processed files should be placed in a root-level folder titled 'experimental_data' for all of the code to run.
Applications: The code in this package is developed for MATLAB. Furthermore, the following MATLAB packages were also used:
- emcee_mymod: My modification of the GWMCMC routine to obtain a posterior distribution of parameter estimates to match the simulations to experimental data
- forward_problem: Code to run the forward problem, in other words, to simuate tissue explant migration
- inverse_problem: Code to run parameter estimation
- mylib: Auxiliary files for the numerical method
- mylib_par: Auxiliary files for the numerical method where parfor loops are used
- post-processing-plot-making: Code to create figures and movies
- results: Contains MATLAB data files containing the posterior distribution parameter estimates and code for related figures, as well as code for statistical analysis
Copyright 2012-2019 Tracy Stepien. This is free software made available under the MIT License. For details see the LICENSE file.