Welcome to the Post Analysis Homepage

This page contains MATLAB .m files that analyze data collected on microfabricated post array detectors (mPADs). These programs are free to download, but we ask that if you use them you site the following paper:

Lemmon CA, Sniadecki NJ, Alom Ruiz S, Tan JL, Romer LH, and Chen CS. “Shear force at the cell-matrix interface: enhanced analysis for microfabricated post array detectors”, Mechanics and Chemistry of Biosystems, 2005.

PostAnalysis 1.41

PostAnalysis 1.41 consists of a series of m-files that analyze images acquired from the microfabricated post array detector (mPAD) system. M-files are contained in a zip file, and are intended for use with Matlab version 6.5.1 and later.

Download PostAnalysis 1.41
(Right-click and choose “Save Target As”)

Installation:

After downloading the zip file, extract the m-files with WinZip. The folder containing the m-files must be added to the working path of Matlab. After starting Matlab, click on the ‘File’ menu tab and select ‘Set Path’. Then click on ‘Add with Subfolders’. Select the folder containing the m-files and click ‘ok’. Verify that the file name has been added and click ‘save’. Then click ‘ok’.

Running the Program:

PostAnalysis 1.41 must be run from the folder containing the images to be analyzed. First, switch the ‘Current Directory’ panel (on the left side of the Matlab screen in Matlab 6.5.1; at the top of the screen in Matlab 7) to the directory containing images to be analyzed. (Use the ‘…’ button to find the directory). In order for the program to run properly, the folder must contain three 12-bit TIF files with the suffix ‘Top.tif’, ‘Bottom.tif’, and ‘Actin.tif’ and the same prefix. You do not need to select these files; just verify that they are present in the current directory. After switching to the proper directory, type ‘analyze_posts_LT2’ (without the quotes) at the Matlab command prompt and press ‘enter’. A graphics window will open and will prompt for all needed inputs. Follow the instructions as directed. Some processes, such as rotation and cropping, can take 10-20 seconds to complete.

Troubleshooting/FAQ:

When I start the code, I receive an error saying that the variable ‘dir_names’ is unknown. The program cannot find the appropriate image files in the current directory. Verify that there are images with the appropriate suffixes in the current directory (see above).

Nothing seems to happen when I try to click on rotation points, drag the crop box, or select collapsed posts. You must click ‘ok’ on the textbox before the program will allow you to begin the operation.

I’ve selected collapsed posts, but can’t continue in the program. You must hit ‘enter’ with the crosshairs located over the image to continue.

I selected collapsed posts, but can’t tell which ones I’ve selected. Marked posts will not be labeled with yellow ’s until after you have hit ‘enter’ to continue (see above). You will have a chance to clear them and select again if you make mistakes.

I can’t get the fibronectin or vinculin analysis to run. At this point in time, modules for fibronectin and vinculin analysis have not been completed.

The program seems to have frozen. If you encounter a problem, you can use ‘ctrl-c’ to stop execution of the program.

Graphics Requirement: PostAnalysis 1.41 requires that screen resolution be set at least 1024 x 768 pixels.

Questions/Comments/Concerns:

Please contact Lew Romer (lromer@jhmi.edu),
Chris Chen (chrischen@seas.upenn.edu), or
Chris Lemmon (clemmon@vcu.edu) with questions or comments about the program and/or mPAD system.

Please direct technical questions related to the code functionality to Chris Lemmon (clemmon@vcu.edu).