Supplemental materials for: Live time-lapse dataset of in vitro wound healing.
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The main directory contain multi-page .tif and .lsm files, each containing the
raw differential interference contrast (DIC) images of a single wound healing
experiment. Each such experiment has a corresponding directory that holds the data
needed for analysis:
. images directory holds the raw DIC images separated to single .tif files.
. MF directory holds the local velocity data, represented by two matrices (named dxs and dys) that contain the velocity component calculated for x- and y- coordinates correspondingly for each image pixel. The velocity is given in uM per Hour, and was calculated for patches of size 15uM x 15uM.
. ROI directory holds the segmentation data, namely for each image pixel a labeling as cellular or background pixel.
. experimentParams.mat is a file holding experimental parameters such as pixel
size in microns and time per frame.
A script named speedKymograph.m creates a kymograph per experiment that
displays the spatiotemporal dynamics of cell speed as function of time and distance
from the monolayer edge. The script accepts as input the main directory name, goes
over the .tif/.lsm data (each file holds raw data of a single time-lapse experiment) and
uses the intermediately processed data in the corresponding directories to generate the
kymograph. One copy of the kymograph is placed in the experimental directory and
the other in a directory named speedKymographs at the main directory. Two files are
generated in each of the two directories: a .mat file with the kymograph data and a
.bmp image for visualization. Please refer to the documentation in the script for
further information.
A file named metadata.mat contains a cell-array that links each time-lapse file to an
experimental condition (the field .experimentNames.), physical pixel size (in uM, the field 'picelSize'), time per frame (the field .timePerFrame.) and frame number when first contact occurred between cells from opposing borders of the wound.