Aivia Software
Neuron display
Neuron object groups are special types of 3D object groups composed of three object subsets: somas, dendrites and spines. A few ways methods of generating neuron object groups are the following:
Applying the 3D Neuron Analysis - FL recipe
Manually tracing with the Neuron Composer
This page covers display options that are specific to 3D neurons. General information on displaying object sets can be found in the Object Settings page.
Interface
An example of how neuron object groups appear in the Object Set Settings panel is shown below.
Rendering modes
You can specify the rendering mode in 3D View for each object set (somas, dendrites, and spines) in a neuron object group using the icons in the View column of the Object Set Settings table. Clicking on an icon in the View column brings up a list of three (3) rendering-mode options:
Rendering Mode | Icon | Description |
|---|---|---|
Solid Surface | | Renders meshes as solid, closed surfaces |
Wireframe | | Renders meshes as sets of connected line segments |
Points | | Renders meshes as point clouds |
Once a new rendering mode is selected, the displayed object sets are refreshed 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 (3) rendering-mode displays is shown below (click on an image to enlarge it).
| | |
Solid Surface | Wireframe | Points |
|
Rendering-mode options |
Trace render modes for dendrites
There are three (3) display modes for rendering representations of traced dendrites. Dendrite display modes are selected from the Trace Render Mode dropdown menu. The three (3) trace render modes are summarized below.
Trace Render Mode | Icon | Description |
|---|---|---|
Sphere (default) | | Renders a sphere for each point along the dendrite; the radius of each sphere is determined by the width of the dendrite trace |
Surface | | Renders the dendrite as a surface with thickness determined by the width of the dendrite trace |
Line | | 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 are refreshed automatically to reflect the new selection.
A comparison between the three (3) trace-render-mode displays is shown below (click on an image to enlarge it).
| | |
Sphere | Surface | Line |
Transparency
The percent transparency of each object set is indicated in the Alpha column of the Object Set Settings table. Click on the percentage in the Alpha column to show a slider that can be used to adjust the transparency of the object set.
Coloring options
There are seven (7) available coloring modes for neuron objects. The coloring modes can be selected from the menu that opens when the icon in the Color column of the object group/set is clicked. Descriptions of the coloring modes are summarized below.
Coloring Mode | Icon | Description | Example (click to enlarge) |
|---|---|---|---|
Solid Color | | Applies the same color to all objects | |
Color By Label | | Applies different colors to each object according to the object labels | |
Color By Object Type | | Applies the same color to all objects that are of the same object type | |
Color By Name | | Applies different colors to each object according to the object names | |
Color By Measurement | | Applies different colors to each object based on values for a user-specified measurement | |
Color By Class | | Applies different colors to each object based on object classifications | |
Color By Cell | | Applies different colors to each neuron, keeping all its components (soma, dendrites, and spines) the same color | |
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.
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.
Image credits
Meg Davies, National Institute of Health, Bethesda MD
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