Neuron objects is a special type of 3D objects composed of three parts: soma, dendrite and spine. They can be generated via several ways:
- Applying one of the 3D recipes
- Manually tracing one in the Neuron Editor
This page covers display options that are specific to 3D neurons. General information on displaying object sets can be found in the Object group display page.
Interface
Object groups that are of the neuron object type will appear in the Object group display as shown below:
On this page:
Rendering modes
You can specify the rendering mode for each component of the neuron object group (soma, dendrite and spines) in 3D view separately by clicking on the icon associated with the selected object group in the View column. Clicking on the icon will bring up a list of render mode options that are available for the selected item. There are three options:
| Rendering Mode | Icon | Description |
|---|---|---|
| Solid surface | Sets mesh rendering to solid surface mode | |
| Wireframe | Sets mesh rendering to wireframe mode | |
| Points | Sets mesh rendering to point cloud mode |
Once selected, the displayed object sets will refresh automatically to reflect the new selection.
Depending on your hardware, the size of the image and the rendering mode chosen, it may take Aivia up to several minutes to fully render the display with the specified settings.
A comparison between the three rendering mode displays are shown below (click on the image to enlarge):
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| Solid surface | Wireframe | Points |
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| Render mode options |
Dendrite modes
For the dendrite sets, there are three (3) different display options for rendering a representation of the traced dendrites. To select a dendrite mode, click on the Expand 
icon next to the Dendrite set group in Display Settings to show the advanced options. Then select from the Dendrite mode dropdown menu.
The three dendrite modes are summarized below:
| Dendrite Mode | Icon | Description |
|---|---|---|
| Sphere (default) |  | Sets dendrite rendering to sphere mode, with each sphere representing a point along the dendrite; the radius of each sphere is determined by the width of the dendrite trace |
| Surface |  | Sets dendrite rendering to surface mode, with the thickness of the surface determined by the width of the dendrite trace |
| Line |
| Sets dendrite rendering to line mode, the width of the dendrite trace does not impact the appearance of the dendrite |
Once selected, the displayed object sets will refresh automatically to reflect the new selection.
A comparison between the three dendrite mode displays are shown below (click on the image to enlarge):
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| Sphere | Surface | Line |
Coloring options
There are six (6) available coloring modes for 3D surfaces. The coloring options can be specified by clicking on the icon in the Color column in the object group display section. Description of the coloring modes are summarized below:
| Coloring Mode | Icon | Description | Example (Click to enlarge) |
|---|---|---|---|
| Solid color |
| Applies the same color to all objects |
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| Color by label |
| Applies different colors to each object according to its object label |
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| Color by object type |
| Applies the same color to all objects that are of the same object type |
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| Color by name |
| Applies different colors to each object according to the object name |
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| Color by measurement |
| Applies different colors to each object based on values on a user-specified measurement |
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| Color by class |
| Applies different colors to each object based on its classification |
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| Color by cell |
| Applies different colors to each neuron object, keeping all its components (soma, dendrites and spines) the same color |
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