DOI: 10.5061/dryad.8pj52vk
title: Data from: Using a continuum model to decipher the mechanics of embryonic tissue spreading from time-lapse image sequences: an approximate Bayesian computation approach

description: Advanced imaging techniques generate large datasets that are capable of
 describing the structure and kinematics of tissue spreading in embryonic
 development, wound healing, and the progression of many diseases.
 Information in these datasets can be integrated with mathematical models
 to infer important biomechanical properties of the system. Standard
 computational tools for estimating relevant parameters rely on methods
 such as gradient descent and typically identify a single set of optimal
 parameters for a single experiment. These methods offer little information
 on the robustness of the fit and are ill-suited for statistical tests of
 different experimental groups. To overcome this limitation and use large
 datasets in a rigorous experimental design, we sought an automated
 methodology that could integrate kinematic data with a mathematical model.
 Estimated model parameters are represented probability density
 distributions, which can be constructed by implementing the approximate
 Bayesian computation rejection algorithm. Here, we demonstrate this method
 with a 2D Eulerian continuum mechanical model of spreading embryonic
 tissue. The model is tightly integrated with quantitative image analysis
 of different sized embryonic tissue explants spreading on extracellular
 matrix (ECM). Tissue spreading is regulated by a small set of parameters
 including forces on the free edge, tissue stiffness, strength of cell-ECM
 adhesions, and active cell shape changes. From thousands of simulations of
 each experiment, we find statistically significant trends in key
 parameters that vary with initial size of the explant, e.g., cell-ECM
 adhesion forces are weaker and free edge forces are stronger for larger
 explants. Furthermore, we demonstrate that estimated parameters for one
 explant can be used to predict the behavior of other explants of similar
 size. The predictive methods described here can be used to guide further
 experiments to better understand how collective cell migration is
 regulated during development and dysregulated during the metastasis of
 cancer.
description: Processed_MATLAB_Data_2010This zip file contains the following files: - boundaries.mat (boundary positions) - densratios.mat (density ratio calculations) - 1.txt (initial boundary positions) - initial_mask.tif (initial segmentation) for each of 50 explants in the 2010 data setS5-Figure-2009-Fibronectin-Spreading-RateThis zip folder contains the image files for Xenopus animal cap explants spreading on different concentrations of fibronectin. Each imaging position has a folder that contains a data image sequence (last frame is the mircometer), the segmented image sequence for each position analyzed, and the area information. The main folder also includes scale information and an excel file that collects the data together.Processed_MATLAB_Data_2014This zip file contains the following files: - boundaries.mat (boundary positions) - densratios.mat (density ratio calculations) - 1.txt (initial boundary positions) - initial_mask.tif (initial segmentation) for each of 6 explants in the 2014 data setRaw_Image_Data_and_Processed_SegmentationThis zip file contains the following files: - raw time-lapse images - segmented images (denoted by "Seg" in the file name) for each of 56 explants, as well as 1mm scale bar imagesData_Strain_Boundary_2014_Pos3-4-6This zip file contains the following folders/files: - boundaries folder (individual text files with boundaries for each time point) - strains/epsx_crop.tif (Cauchy strain epsilon_xx) - strains/epsxy_crop.tif (Cauchy strain epsilon_xy = epsilon_yx) - strains/epsy_crop.tif (Cauchy strain epsilon_yy) for Pos3, Pos4, and Pos6 explants in the 2014 data setData_Strain_Boundary_2014_Pos7-8-9This zip file contains the following folders/files: - boundaries folder (individual text files with boundaries for each time point) - strains/epsx_crop.tif (Cauchy strain epsilon_xx) - strains/epsxy_crop.tif (Cauchy strain epsilon_xy = epsilon_yx) - strains/epsy_crop.tif (Cauchy strain epsilon_yy) for Pos7, Pos8, and Pos9 explants in the 2014 data setData_Strain_Boundary_2010_Pos0-4This zip file contains the following folders/files: - boundaries folder (individual text files with boundaries for each time point) - strains/epsx_crop.tif (Cauchy strain epsilon_xx) - strains/epsxy_crop.tif (Cauchy strain epsilon_xy = epsilon_yx) - strains/epsy_crop.tif (Cauchy strain epsilon_yy) for Pos0-Pos4 explants in the 2010 data setData_Strain_Boundary_2010_Pos5-9This zip file contains the following folders/files: - boundaries folder (individual text files with boundaries for each time point) - strains/epsx_crop.tif (Cauchy strain epsilon_xx) - strains/epsxy_crop.tif (Cauchy strain epsilon_xy = epsilon_yx) - strains/epsy_crop.tif (Cauchy strain epsilon_yy) for Pos5-Pos9 explants in the 2010 data setData_Strain_Boundary_2010_Pos10-14This zip file contains the following folders/files: - boundaries folder (individual text files with boundaries for each time point) - strains/epsx_crop.tif (Cauchy strain epsilon_xx) - strains/epsxy_crop.tif (Cauchy strain epsilon_xy = epsilon_yx) - strains/epsy_crop.tif (Cauchy strain epsilon_yy) for Pos10-Pos14 explants in the 2010 data setABC Method Parameter SetsThis zip file contains the 10,000 parameter sets obtained from the ABC Method for each of the 18 explants analyzed in the manuscript (in .mat file format).Tukey ComparisonsThis spreadsheet contains the statistical analysis for determining the Tukey Comparisons for the 4 parameters F/k, k/b, alpha, and rho_unstressed when comparing all 18 explants (results from 10,000 parameter sets).Linear Regression Hypothesis Test on ParametersThis spreadsheet contains the statistical analysis for the Linear Regression t-test for the 4 parameters F/k, k/b, alpha, and rho_unstressed when comparing all 18 explants (results from 10,000 parameter sets).Explant Naming ConventionThis spreadsheet contains information on the explant numbering system used in the paper and the naming system used in the data set, along with the initial area measurement.READMEREADME file for all of the data files in this package.Explant Average Area Change Over TimeThis spreadsheet contains measurements of the average area change over time for 59 explants.Raw_Image_Only_Data_2010This zip file contains raw time-lapse images of explants from the 2010 data set: Pos3 (contains one explant in the image), and Pos4-11 and Pos14 (contains multiple explants in the image). It also contains the raw time-lapse image and segmented image (denoted by "Seg" in the file name) for Pos7exp1.