Cell Adhesion and Migration Analysis Toolbox

This zip file contains code, data and documentation associated with the Cell Adhesion and Migration Analysis Toolbox. This Toolbox provides data analysis and organization tools for cell adhesion and migration data. To this end, this Toolbox provides a set of analysis features that can be combined to gain a coherent and comprehensive picture of the cell adhesion and migration systems. Some of the provided features may also be used in isolation to address alternate questions (i.e. complex processes other than cell adhesion/migration). The code is tailored to handle microscopy-derived multi-scale, multivariate time series data that can be image based or constitute extracted quantitative feature datasets from cell adhesion and migration experiments. This document describes the features listed in the table of contents and how the Cell adhesion and migration analysis Toolbox allows their implementation

Fibronectin_Modulation_Dataset

The associated .csv files constitute quantitative datasets underpinning the manuscript "Heterogeneity in mesenchymal motility reflects adaptive switching between two distinct migration modes", by Shafqat-Abbasi et al. Three datasets are presented with equivalent structures, reflecting data derived from multiscale, high resolution imaging of randomly migrating H1299-PL cells. These datasets focus on comparison of cells: attached on different concentrations of fibronectin (extracellular-matrix ligand, Fibronectin_Modulation_Dataset); following inhibition of Rho-associated kinase (ROCK, Y27632 inhibitor) or a control treatment (DMSO, ROCK_Modulation_Dataset); or following siRNA-mediated depletion of talin 1 protein levels compared to control siRNA treatment (Talin_Modulation_Dataset). Accordingly, each data set is divided into two conditions (denoted “1” or “2”), between which feature values are quantitatively compared throughout the manuscript. In each case, the values 1 and 2 in the “condition” column refer to: Fibronectin_Modulation_Dataset: 1 = 2.5 µg/ml FN (2580 observations), 2 = 10 µg/ml FN (7000 observations); ROCK_Modulation_Dataset: 1 = DMSO (2666 observations), 2 = 6 µM ROCK Inh (985 observations); Talin_Modulation_Dataset: 1 = Control siRNA (3154 observations), 2 = talin 1 siRNA (6263 observations). Column structure within the files is as follows. The first 6 columns are indexing columns, wherein the: experimental condition is defined (1 vs 2, as above); experimental date is define; individual cell identities are defined; the mesenchymal cell migration mode is defined (0 = undetermined, e.g. dead cells or cells in contact; 1 = Discontinuous migration mode; 2 = Continuous migration mode); cell centre of area (row), and; cell centre of area (column) are defined. The following 60 columns define quantitative features extracted based on image analyses. These include 5 Behavioral features and 55 Organizational features, as defined in Figure 3 – figure supplement 1