Neuron objects is a special type object groups are special types of 3D objects object groups composed of three partsobject subsets: somasomas, dendrite dendrites and spine. They can be generated via several waysspines. A few ways methods of generating neuron object groups are the following:
- Applying one of the 3D recipesNeuron Analysis - FL recipe
- Manually tracing one in with the Neuron EditorComposer
This page covers display options that are specific to 3D neurons. General information on displaying object sets can be found in the Object Set Settings page.
Interface
Object groups that are of the An example of how neuron object type will groups appear in the Object group display as Set Settings panel is shown below:.
| Panel | ||||||
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On this page:
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Rendering modes
You can specify the rendering mode in 3D View for each component of the neuron object group set (somasomas, dendrites, dendrite and spines) in 3D view separately by clicking on the icon associated with the selected a neuron object group using the icons in the View column of the Object Set Settings table. Clicking on the icon will bring an icon in the View column brings up a list of render mode options that are available for the selected item. There are three optionsthree (3) rendering-mode options:
| Rendering Mode | Icon | Description |
|---|---|---|
| Solid surfaceSurface |
| Sets mesh rendering to solid surface modeRenders meshes as solid, closed surfaces |
| Wireframe |
| Sets mesh rendering to wireframe modeRenders meshes as sets of connected line segments |
| Points |
| Sets mesh rendering to point cloud mode |
| Renders meshes as point clouds |
Once a new rendering mode is selected, the displayed object sets will refresh are refreshed automatically to reflect the new selection.
| Info |
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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 (3) rendering-mode displays
areis shown below (click on
thean image to enlarge it)
:.
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| Solid |
| Surface | Wireframe | Points |
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| Render Rendering-mode options |
Trace render modes
For the dendrite sets, therefor dendrites
There are three (3) different display options modes for rendering a representation representations 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 Dendrite display modes are selected from the Trace Render Mode dropdown menu. The three dendrite (3) trace render modes are summarized below:.
| Dendrite Trace Render Mode | Icon | Description |
|---|---|---|
| Sphere (default) |  | Sets dendrite rendering to sphere mode, with each sphere representing a Renders a sphere for each 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 Renders the dendrite as a surface with thickness determined by the width of the dendrite trace |
| Line |
| Sets dendrite rendering to line mode, Renders the dendrite as a line; the width of the dendrite trace does not impact the appearance of the dendrite in this mode |
Once a new trace render mode is selected, the displayed object sets
will refreshare refreshed automatically to reflect the new selection.
A comparison between the three
dendrite(3) trace-render-mode displays
areis shown below (click on
thean image to enlarge it)
:.
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| Sphere | Surface | Line |
Coloring options
There are six seven (67) available coloring modes for 3D surfacesneuron objects. The coloring options modes can be specified by clicking on selected from the menu that opens when the icon in the Color column in of the object group display section. Description /set is clicked. Descriptions of the coloring modes are summarized below:.
| Coloring Mode | Icon | Description | Example (Click click to enlarge) |
|---|---|---|---|
| Solid colorColor |
| Applies the same color to all objects |
|
| Color by labelBy Label |
| Applies different colors to each object according to its the object labellabels |
|
| Color by object typeBy Object Type |
| Applies the same color to all objects that are of the same object type |
|
| Color by nameBy Name |
| Applies different colors to each object according to the object namenames |
|
| Color by measurementBy Measurement |
| Applies different colors to each object based on values on for a user-specified measurement |
|
| Color by classBy Class |
| Applies different colors to each object based on its classificationon object classifications |
|
| Color by cellBy Cell |
| Applies different colors to each neuron object, keeping all its components (soma, dendrites, and spines) the same color |
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Export options
Like other types of object sets, neuron object sets can be exported as 8-bit binary masks, 16-bit labelled masks, and 32-bit labelled masks via the Export Objects to a Mask icons 
in the object set rows of the Object Set Settings table. Additionally, neuron object groups can be exported to an Aivia-specific format as well as to 16-bit labelled masks, where voxels have intensities that correspond to the neuron cells that contain them, via the Export Objects to a Mask icon in the object group rows.
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Neurons can be exported to other formats, such as SWC and HOC, via File > Export > Neuron Objects. See the Export Neuron page for more information. |
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