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Viewing in 3D

In addition to the 2D display window, NeuronStudio also gives you the ability to visualize your data in 3D. Once you load a dataset select View >> 3D Viewer... from the main menu. This window allows you visualize the image data, the traced model, and the spines that you have detected. (see image below)

NeuronStudio 3D Viewer

With the move tool Move Tool selected use the mouse to click and drag over the window. This causes the data to rotate around its center. Holding down the Ctrl key while dragging translates the view. Holding down Shift key while dragging up and down zooms in or out.

TIP: With the move tool selected, you may change the interaction mode by right-clicking on the 3D display window and selecting from the context menu as shown in the image. Note that using the Ctrl or Shift keys always over-rides the current mode.

Note that this window contains a top-level menu. The View menu is used to control various rendering options and to change the mouse tool mode. The Volume Rendering menu is used to control and regenerate the rendering of splats, which are volume rendering elements.

(c) indicates an option that can be toggled on or off. (s) indicates a sub-menu.

TIP: After running an image processing routine you can regenerate the splats (since the image data has presumably changed) by selecting Volume Rendering >> Regenerate. We allow you to explicitly choose this, rather than running it automatically, since generation of the splats can be a lengthy operation.

In addition to the rendering of the dataset and model, the current seed and/or region of interest is also drawn for easier visualization.

Global Threshold

A threshold is applied to the volume rendered dataset to limit the amount of data that is visualized. This threshold is global since it is used for the whole dataset, regardless of local variations in intensity. Selecting Volume Rendering >> Threshold... from the menu of the 3D window brings up the following dialog box for adjusting the value of the threshold.

The 3D Volume Rendering Threshold Dialog

The threshold value can be set anywhere within the range of 0 to 255. Although this is the range of intensity values for an 8-bit greyscale dataset, the value will be scaled to the appropriate bit depth of the current dataset, for example 12 or 16 bit greyscale. If the Regenerate Volume Rendering checkbox is selected, the volume rendering will be automatically regenerated if the OK button is pressed. The volume rendering can be regenerated at any time by selecting Volume Rendering >> Regenerate from the menu of the 3D window. Press Cancel or close the dialog to abort changing the value. Press the Default button to reset the threshold to a default value of 20.


You can manually control the opacity of the volume rendering by selecting Volume Rendering >> Opacity... from the menu of the 3D window. This brings up the following dialog box for adjusting the value of the opacity.

The 3D Volume Rendering Opacity Dialog

If Automatic by Intensity is checked then each volume rendered element will have an opacity value set by the intensity of the voxel at that position. A voxel with an intensity of 255 (in 8-bit datasets) will therefore be fully opaque while a voxel with an intensity of 0 will be fully transparent.

If Automatic by Intensity is unchecked, a slider control is enabled for adjusting the opacity. The opacity you select will be applied globally to all volume rendered elements. The 3D display is updated dynamically as the slider is dragged.

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