Mechanical Properties of Biological Cells
Effects of Cellular Morphology on Elastic Modulus Measurements with Atomic Force Microscopy.
Chua X.Y., Lopez-Ayon, G.M., Magdesian, M.H., Sangji, M. H., Rigby, M. & Grutter, P. (2016)
Manuscript submitted to Biophysical Journal (2016)
Listed here are the Matlab codes that were written at our lab to obtain the data shown in this manuscript.
Provided are downloadable links to the respective Matlab files.
1. Visualisation of force-distance (FD) curves
These are the codes that were used to visualise the force-distance curves. Force-distance curves are plotted as figures and saved into Matlab fig and png type files.
a. FD_view_txt
This code supports .txt type data files, eg. Data files from the Bioscope II AFM (Veeco, Plainview, NY).
b. FD_view_ibw.m ; read_wave.m
This code supports .ibw type data files, eg. Data files from the MFP-3D-BIO AFM (Asylum Research, Santa Barbara, CA). In order to read the .ibw files, a read_wave.m code (written by Jason Bemis, University of Pittsburgh) is used.
2. Extracting the elastic modulus
These Matlab codes allow users to extract the elastic modulus of a sample from FD curves obtained using the Atomic Force Microscope.
This code supports .txt type data files, eg. Data files from the Bioscope II AFM (Veeco, Plainview, NY).
b. ElasticModulus_ibw.m ; read_wave.m
This code supports .ibw type data files, eg. Data files from the MFP-3D-BIO AFM (Asylum Research, Santa Barbara, CA). In order to read the .ibw files, a read_wave.m code (written by Jason Bemis, University of Pittsburgh) is used.
Along with the Elastic Modulus codes, there are three contact mechanics models that one can use depending on the geometries of the tip and the sample. These models were referenced from Puttock & Thwaite 1969, namely:
This refers to Case 1: Two spheres in contact with one another.
Eg, When indenting the cell body of a glioma cell (which has a parabolic topography) with a spherical beaded cantilever.
This refers to Case 2: A sphere in contact with a plane.
Eg, When indenting the periphery of a cardiomyocyte (which is relatively flat) with a spherical beaded cantilever.
This refers to Case 11: A sphere in contact with a cylinder.
Eg, When indenting an axon (which is cylindrical in nature) with a spherical beaded cantilever.
Questions can be directed to: Xue Ying Chua (xue.chua@mail.mcgill.ca)