Terms of use:

Explorer Tutorials

Tutorial 00: Adjusting sizes

Tutorial 01: Basic controls

Mouse controls:

  • Explained in Tutorial 00
    • Mouse wheel to zoom in or out, hold the “shift” key to fast zoom. hold the “ctr” key to inverse zooming direction

Keyboard controls:

  • Explained in Tutorial 00
    • “a” and “d” : previous or next slice
    • “w” and “s” : previous or next slice (fast)
    • “space” : switching focus between left and right hemisphere
  • Explained in Tutorial ?????
    • “q” and “e” : select an image for the top layer, or the layer beneath the top layer, respectively
    • “c” show the focus center
    • “1” : hide or show the background image
    • “2”,“3” : hide or show the image/annotation in the layer beneath the top layer (Background)
    • “4”,“5” : hide or show the image/annotation in the top layer (Overlay)
    • “6”,“7” : hide or show atlas information

Tutorial 02: Opening data and using the flatmap navigation


Voice has been generated using TTS (default parameters).


The Nora-StackApp is based on the Nora medical imaging platform. Therefore, you might find the First Steps tutorial useful, too.

Basic keyboard and mouse controls:

  • Keep the left mouse button pressed while moving the cursor to navigate withing slices
  • Keep the right mouse button pressed while moving the cursor to shift a section
  • Use the mouse wheel to switch slices
  • Use the mouse wheel while keeping the control key pressed to zoom

You can also use the quick navigation menu as shown below:


Download a copy from the RIKEN CBS data portal. Select the NORA-StackApp folder as shown in the image below.

To download the StackApp, click on the symbol in the upper right corner. It will open the download window (you might need to allow pop-up windows for the repository site). Below a screenshot of the download window:

Please download the version for your OS (linux,mac or win). We have tested it on Ubuntu Linux, Windows 11 and an M1 Mac. Below a screenshot that illustrates how to run it from a Mac. Windows and Linux work in a similar way. You won't need to install the app, just unzip the folder. In the example below, we used the Desktop as destination. In a sub-folder of the unzipped folder, you will find the “Noraview” application (on Windows Noraview.exe). Starting it should bring up the main interface as shown below:

The work-spaces menu provides several pre-defined work-spaces for marmosets.

Download Tracer Data

When you download the Nora-StackApp, you already have the atlases and the template images that are used for the work-spaces. But you might want to download tracer data image stacks and additional atlases from the RIKEN CBS data repository:

  1. Anterograde tracer data: “Volumetric_anterograde_tracer_data”
  2. Retrograde tracer from the Marmoset Brain Connectivity Project
  3. Atlases: Use the Nora-optimized versions under “STPT_reference_image_space” → “Nora-StackApp_versions”

Marmoset Workspaces

The Nora-StackApp shows multiple 3D image stacks in a grid of views. Each view can show a section of an image. A view shows one main image (e.g. a background image) and can have multiple “overlays”. An overlay can be another image, such as a tracer signal, or an atlas. The example below shows the default marmoset workspace with two views, each showing a different slicing. It also shows the atlas tool.

You can increase or decrease the number of views. Having more views can be helpful to show two different images side-by-side. Reducing the number of views gives a view more space on the screen.

The image below shows the default workspace, that shows our average template as background image. We have selected a nifti file with an anterograde tracer signal from our hard disk, and use the drag-and-drop feature of Nora to drop it into the first view as a new overlay. We then took the hand button of the tracer overlay and dropped it into the second view as well.

Open the BMCA-Explorer, and use the brain-symbol shown below, and drag and drop it into the explorer to set the current Explorer position to the same position as in Nora.

The video below shows a demonstration, including interaction the with BMCA-Explorer:

tools/explorer.txt · Last modified: 2023/07/03 04:23 by marhenrikoset