Code Repository for the thesis: Microsystems to study the mechanobiology of cell adhesion
Algorithms for Strain Array Characterization Matlab code
Custom MATLAB codes were written for a semi-automated user interface using impixel that allows the user to click-and-store the location of fiducial markers at each pressure designated by the strain array control system (see illustration below). This location information is stored as x and y vectors in a MAT file.
Pressure Control Unit Interface App Code
This code is installed and run in a personal computer to communicate with arduino microcontroller. The code includes functions to set PID gains and send a desired pressure waveform. The code is coded in C sharp (i.e., C++ ) code and can be installed as a standard Windows software, uninstalled in the Control Panel of Windows. Once the software is installed, one can find the program Valve Control Interface and Communication GUI in Start up> All programs. Through a computer, this code talks to an arduino board, which is already downlowed for the embeded code, which will be described in the section 7. The GUI enables the user to interact graphically and control the controller unit. Communication elements such as BAUD rate are easily accessible from the GUI. A graph in GUI shows the current pressure as it is received. Access to a PID controller parametes is allowed and the target pressure can be either constant or varying. The communication is done over a Serial port. Significant parts of this program are segments of open source code found over the internet called ZedGraph (http://sourceforge.net/projects/zedgraph/).
Microcontroller (Arduino) code for PID control
This is an Arduino code that communicates with a PC in order to control pressure through valves. The controller is a PID controller that is imported from a PID library. This program is meant to be used in conjunction with a GUI developed in Visual C#.
TFM analysis Matlab code
This code calculates the cell-cell and cell-ECM forces (i.e., Fy and Fx) from the traction force map data in text file format and the ROI of the cell-cell junction in the comma-separated value format (csv file).
Ratiometric FRET analysis Matlab code
All of the Matlab code has been tested under Matlab version R2013a with an image processing tool box. This Matlab code reads tiff image files of FRET, mTFP, and mYFP and calculate the ratio of FRET intensity / (FRET intensity + mTFP intensity)
FLIM-FRET analysis Matlab code
This Matlab code reads output from SPCImage and calculates the FRET efficiency. Time-domain FLIM experiments and FLIM data analysis were performed as described previously (1,2) using SPCImage software (Becker Hinkl) and Matlab (Mathworks). Fluorescence lifetime was determined by fitting a double-exponential decay model. FRET % is calculated by following equation: where τ is lifetime of mTFP1 of E-cadherin FRET sensor as a weighted-average lifetime from SPCImage software and τ donor is mTFP1 of E-cadherin FRET sensor as described previously (3).
|Type of resource
|May 10, 2009 - October 30, 2014
|Sim, Joo Yong
|Pruitt, Beth L.
|strain array code
|FRET analysis code
|TFM analysis code
|Mechanical Engineering Department School of Engineering
|Sim, Joo Yong. (2015). Microsystems to study the mechanobiology of cell adhesion. PhD Dissertation. Stanford University. Available at https://purl.stanford.edu/th550kv3016
|Simmons CS, et al. (2011) Integrated strain array for cellular mechanobiology studies. J Micromech Microeng 21(5):054016.
|Sim JY, et al. (2012) Uniaxial cell stretcher enables high resolution live cell imaging. 2012 IEEE 25th International Conference on Micro Electro Mechanical Systems (MEMS), pp 854–857.
|Grashoff C, et al. (2010) Measuring mechanical tension across vinculin reveals regulation of focal adhesion dynamics. Nature 466(7303):263–266.
|Day RN, Booker CF, Periasamy A (2008) Characterization of an improved donor fluorescent protein for Forster resonance energy transfer microscopy. J Biomed Opt 13(3):031203.
|Borghi N, et al. (2012) E-cadherin is under constitutive actomyosin-generated tension that is increased at cell–cell contacts upon externally applied stretch. Proc Natl Acad Sci 109(31):12568–12573.
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- This work is licensed under a Creative Commons Attribution 3.0 Unported license (CC BY).
- Preferred Citation
- Sim, Joo Yong and Pruitt, Beth L. (2014). Code Repository for the thesis: Microsystems to study the mechanobiology of cell adhesion. Stanford Digital Repository. Available at: http://purl.stanford.edu/qt411pj4511
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