Data and software code for "Endothelial cells stably infected with recombinant Kaposi’s sarcoma-associated herpesvirus display distinct viscoelastic and morphological properties"
Data and code supporting work presented in article.
File: 01_preprocessing_macro.ijm
Description: A simplified macro outlining time-lapse image pre-processing prior to mitochondria-tracking analysis in TrackMate (Image J). Preprocessed files are saved in .tif format.
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File: 02_compute_logplot_msd.py
Description: Python code to import csv track files, compute i-msd and e-msd (using trackpy), and plot 2 sets of data at a time (e.g. HuARLRT2 vs HuALRT2-rKSHV) of e-msd and bulk msd on the same logarithmic axis, and save plot in high resolution of 300 dpi.
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File: 03_particle_tracking_data.xlsx
Description: e-msd and powerlaw exponent data of all 4 cell lines used in the study, i.e. HuARLT2, HuARLT2-rKSHV, LEC, & LEC-rKSHV over 37.6s. MSDs are fitted between 0 and 2 s of lag time.
Contents:
- sheet 1 (data_description)
- sheet 2 (MSD for Hu and HuKS)
- sheet 3 (MSD for LEC and LECKS)
- sheet 4 (MSD powerlaw exponents)
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File: 04_fit_powerlaw_plot.py
Description: Function to compute the MSD powerlaw exponent for each eMSD between 0-2s, keeping only good fits (R^2>0.7), and plot in log axes. Two sets of data can be plotted at a time, and plot saved in high resolution of 300 dpi.
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File: 05_cell_morphology_data.xlsx
Description: Cell morpholopgy data of the aspect ratio (AR), roundness (R) and Circularity (C)computed using the PHANTAST plugin and FIJI.
Contents:
- sheet 1 (data_description)
- sheet 2 (Aspect ratio measurements for all 4 cell lines)
- sheet 3 (Roundness values for all 4 cell lines)
- sheet 4 (Circularity values for all 4 cells lines)
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File: 06_compute_morpho_diff.py
Description: Function to compute relative differences of cell morphology parameters aspect ratio, circularity, and roundness, and plot the data.
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Funding
National Research Foundation of South Africa (grant number IFR14011761118 to TF)
South African Medical Research Council (grant number SIR328148 to TF)
The World Academy of Sciences and the National Research Foundation of South Africa (TWAS-NRF Doctoral Fellowship SFH180603339513 & MND210817632453 to MMS)
University of Cape Town (JW Jagger Centenary Gift Scholarship to MMS)
Carnegie Corporation of New York to the University of Cape Town (DEAL Postdoctoral Fellowship to MMS)
A world-class micro-imaging platform for biomedical and infectious diseases research in southern Africa (revised version of proposal WT104942MA, 2014).
Wellcome Trust
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