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Getting SuperSegger

  1. Check Software Requirements

    In order to use SuperSegger you need to have the MATLAB software with the following toolboxes: Image Processing Toolbox, Neural Network (Deep Learning) Toolbox, Statistics and Machine Learning Toolbox, Global Optimization Toolbox, Parallel Computing Toolbox (not necessary).

  2. Download SuperSegger

    NEW!   SuperSegger has been updated to work with the improved segmentation algorithm, Omnipose.
    The modified version, SuperSegger-Omnipose, and further installation instructions can be found here.

    There are two options for downloading the code:

    • Simple option: zipped archive

      1. Navigate to SuperSegger GitHub or SuperSegger-Omnipose Github.
      2. Click the green button on the right 'Clone or Download' and then select 'Download Zip'.

    • Advanced option: git clone

      The benefit of cloning from git instead of downloading the zip file is that you can easily obtain the new version of the code if there are improvements or bug fixes later on. In order to clone the git repository:

      1. Open a terminal window
      2. Create/Navigate to the directory where you would like the code to reside
      3. Run the following command in terminal : git clone https://github.com/wiggins-lab/SuperSegger.git or git clone https://github.com/tlo-bot/supersegger-omnipose.git
      4. Every time you want to update the software, navigate to the SuperSegger directory and run the following command in terminal : git pull

  3. Set the MATLAB Path

    In order for MATLAB to be able to find the different pieces of the code the SuperSegger folder needs to be in your path.

    1. In the Home tab, in the Environment section, click Set Path. The Set Path dialog box appears.
    2. Click Add with subfolders and add the SuperSegger folder.
    3. Click Save.

  4. Optional: Read tutorials and dowload sample files
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