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Quickstart guide

Aim

To use RTNeuron to visualize your first Sonata data.

../_images/soma_cropped.png

Running RTNeuron

  1. Download the RTNeuron AppImage and save it in your preferred location. In this tutorial we will assume this is your Downloads directory, that is ~/Downloads.

    Attention

    RTNeuron is only supported on Ubuntu 16.04 and higher. It does not run on macOS or Windows, even if using a Ubuntu virtual machine.

  2. To make the AppImage executable, you can use the user interface or the command line.

    To use the user interface:

    1. Navigate to the directory where you saved the AppImage, right click the file and select Properties

    2. Change to the Permissions tab.

    3. Make the file executable by selecting Allow executing file as program or setting the Execute dropdown to Anyone. Close the properties dialog.

    4. Right click in the directory where you saved the file and select Open in terminal.

    To use the command line:

    1. Open a terminal and navigate to the directory where you saved the AppImage:

      cd ~/Downloads
      
    2. Make the AppImage executable by running the following command:

      chmod +x rtneuron_x86_64.AppImage
      
  3. Run the AppImage by entering:

    ./rtneuron_x86_64.AppImage
    
  4. The interactive Python shell will start. To view a circuit, run the command:

    start_app()
    

    This will start the RTNeuron Circuit Viewer user interface.

Loading Sonata data

  1. To visualize your Sonata data, click Browse and select your circuit_config.json or simulation_config.json file.

    Example data

    If you do not currently have any Sonata data but would like to try RTNeuron, you can download the Sonata source which contains example data. Save the download as (or rename it to) sonata.tar.gz.

    You must extract the data by running the following command from the terminal in the directory you downloaded it to:

    tar -xzf sonata.tar.gz
    

    You can now access the examples folder, which contains the 300_cells example Sonata data.

    ../_images/soma.png
  2. To exit RTNeuron, close the user interface window. To exit the interactive Python shell either: close the terminal, or enter the following command:

    exit
    

Congratulations

You can now use RTNeuron to visualize your Sonata data!