qCMA: a desktop application for Quantitative Collective cell Migration Analysis

Amit Zeisel, Assif Yitzhaky, Cindy Kӧrner, Mattia Lauriola, Hadas Cohen, Wolfgang J. Kӧstler, YosefYarden, 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

 

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 +xgui_qcma
    chmod +x run_gui_qcma.sh
  2. If MATLAB 7.12 (2011a) is NOT installed on your computer:
    1. Download and install MCRInstaller.bin (Matlab Component Runtime), by typing:
      chmod +x MCRInstaller.bin
      ./MCRInstaller.bin
    2. 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:
    1. Download and install MCRInstaller.zip (Matlab Component Runtime).
    2. 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 thematlabroot 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