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:

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.

On this page:

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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