qCMA: a desktop application for Quantitative Collective cell Migration Analysis

Amit Zeisel, Assif Yitzhaky, Cindy Kӧrner, Mattia Lauriola, Hadas Cohen, Wolfgang J. Kӧstler, Yosef Yarden, Stefan Wiemann and Eytan Domany

Support:
Additional information regarding the GUI and the image processing can be found in the supplementary information file.
Correspondence regarding technical issues should be addressed to Assif Yitzhaky .

Example datsets:

Fluorescent images: W23_flour_example.zip

Phase-contrast images: EGF1h_16_example.zip

qCMA Installation (v1.3):

Source code:

qCMA - Download MATLAB Source Code (the main function is gui_qcma.m)

Merge well - Merge Well software (optional): Download MATLAB Source Code (the main function is generic_merge_well_gui.m))

Standalone software:

Windows:

1. If MATLAB 7.11 (2010b) is NOT installed on your computer, you will have to download and install MCRInstaller.exe (Matlab Component Runtime).

2. Download gui_qcma.exe to some folder and launch.

(Merge Well software (optional): Download generic_merge_well_gui.exe to some folder and launch).

Linux:

1. Download and extract gui_qcma and run_gui_qcma.sh to some single folder.

Verify that those files are executable:

chmod +x gui_qcma
chmod +x  run_gui_qcma.sh

2.      If MATLAB 7.12 (2011a) is NOT installed on your computer:

A. Download and install MCRInstaller.bin (Matlab Component Runtime), by typing:

chmod +x MCRInstaller.bin
./MCRInstaller.bin

B. From the folder in step (1) execute the following at the command prompt:

./run_gui_qcma.sh <mcr_directory>

<mcr_directory> is the directory where MCR is installed. For example, if you have your MCR installed in

/mathworks/home/application/R2010a/v715, run the shell script as:

./run_gui_qcma.sh /mathworks/home/application/R2010a/v715

3.      If MATLAB 7.12 (2011a) is installed on your computer:

From the folder in step (1) execute the following at the command prompt:

./run_gui_qcma.sh <matlabroot>

<matlabroot> is the directory where MATLAB 7.12 is installed on the machine (you can use the matlabroot command in order to find out). For example, if your MATLAB is installed in /mathworks/devel/application/matlab

Run the shell script as:

./run_gui_qcma.sh /mathworks/devel/application/matlab

Mac:

1. Download and extract gui_qcma_mac.zip to some folder.

2. If MATLAB 7.13 (2011b) is NOT installed on your computer:

A. Download and install MCRInstaller.zip (Matlab Component Runtime).

B. From the folder in step (1) execute the following at the command prompt:

./run_gui_qcma.sh <mcr_directory>

<mcr_directory> is the directory where MCR is installed. For example, if you have your MCR installed in

/mathworks/home/application/R2010a/v715, run the shell script as:

./run_gui_qcma.sh /mathworks/home/application/R2010a/v715

3. If MATLAB 7.13 (2011b) is installed on your computer:

From the folder in step (1) execute the following at the command prompt:

./run_gui_qcma.sh <matlabroot>

<matlabroot> is the directory where MATLAB 7.13 is installed on the machine (you can use the matlabroot command in order to find out). For example, if your MATLAB is installed in /mathworks/devel/application/matlab

Run the shell script as:

./run_gui_qcma.sh /mathworks/devel/application/matlab