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 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)
With the 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.
(
) indicates an option that can be toggled on or off.
(
) indicates a sub-menu.
| View | |
|---|---|
| Lighting () | Turn on or off lighting. Affects all rendering. |
| Anti-Aliasing () | Turn or on or off anti-aliasing (line smoothing). |
| Solid Background () | Turn on or off rendering a background color gradient. |
| Axes () | Turn on or off rendering of the axes. |
| Grid () | Turn on or off rendering of a 3D grid around the dataset. |
| Shape Complexity () | A sub-menu for setting the complexity (number of triangles) of rendered shapes. |
| Bounding Box () | A sub-menu for turning on or off rendering of bounding boxes for the dataset, region of interest, etc... |
| Center On () | A sub-menu for selecting the 3D rotation center. |
| Octree () | A sub-menu for controlling the rendering of the octree built during spine detection. |
| Reset XY (Axial) | Reset the 3D view to the default forward (XY) orientation. |
| Reset ZY (Side) | Reset the 3D view to the default side (ZY) orientation. |
| Reset XZ (Side) | Reset the 3D view to the default bottom (XZ) orientation. |
| Mode () | A sub-menu for setting the current mode (tool). |
| Volume Rendering | |
|---|---|
| Threshold... | Change the global threshold applied to the volume rendered dataset. |
| Opacity... | Change the opacity applied to the volume rendered dataset. |
| Show () | Toggle display of the splats. |
| Use Palette () | Turn on or off the coloring of splats using the current palette. |
| Surface Only () | Toggle whether only object surface splats are generated. |
| Use Point Pre-Rendering () | Render voxels as points during user interaction. |
| Regenerate | Executes the splat building procedure. A progress window will appear to allow cancellation. |
TIP: After running an image processing routine you can regenerate the splats (since the image data has presumably changed) by selecting . 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 from the menu of the 3D window brings up the following dialog box for adjusting the value of the threshold.
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 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.
Opacity
You can manually control the opacity of the volume rendering by selecting from the menu of the 3D window. This brings up the following dialog box for adjusting the value of the opacity.
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.