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Viewing in 2D

The main window of NeuronStudio allows you to look at the data as a front, side or bottom orthogonal projection. By default NeuronStudio displays the front view of the data when a dataset is first opened. You can change the viewing direction by selecting the desired direction from the View menu or by clicking on the viewing direction buttons of the tools panel:

  • Use Forward View or View >> Forward (XY) to set the viewing direction to front.
  • Use Side View or View >> Side (ZY) to set the viewing direction to side.
  • Use Top View or View >> Top (XZ) to set the viewing direction to top.

Translating

To reposition the data inside the main window, switch to translate mode by selecting the move tool Move Tool from the tools panel of the main window. You may also select Edit >> Mode >> Translate from the menu. While in translation mode you can move the view by clicking and dragging anywhere in the image. You may zoom in and out with the scroll wheel as well. If the menu item View >> Center & Limit Image is checked then translation beyond the boundaries of the image is not permitted.

TIP: Pressing the T key will switch to the translate mode as well.

The magnet tool Magnet Tool can also be used almost exactly as described above to translate the display. With this tool active, simply drag and click anywhere within the display where a vertex of the model is NOT present. You must NOT click on any vertices since this will cause those vertices to become selected and translated, instead of the display.

TIP: Pressing the G key will switch to the magnet mode as well.

Projections

By default the program uses a maximum intensity projection but you may choose a different type specified in the Run >> Projections sub-menu. Currently the program can create maximum, minimum, and sum projections. See below for some examples of different projections for a typical confocal dataset.

Maximum Intensity Projection Sum Intenstiy Projection Minimum Intensity Projection
Maximum Intensity Projection Sum Intensity Projection Minimum Intensity Projection for the inverted dataset.

Palette

You may also choose to apply a color map to the projections (and volume rendering) for enhanced visibility, or to visualize certain aspects of the dataset. Select View >> Palette from the main menu to see a list of the available palettes. Some examples are shown below.

Standard Palette Inverted Palette Topographic Palette Intensity Mask Palette
Standard Palette. Inverted Palette Topographic Palette Intensity Mask Palette

Temporary Display

A few features are provided for temporarily showing or hiding the model and spines. Select View >> Flash Model to hide the model and spines for a short period. The F4 key is a shortcut for this feature. Select View >> Flash Hidden to temporarily display all hidden model vertices and spines. The F3 key is also provided as a shortcut.

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Send questions or comments to: alfredo.rodriguez@mssm.edu