The Neuron Composer lets you create new or edit existing neuron objects (generated using the 3D Neuron Analysis recipe) in 3D View manually. The Neuron Composer provides tools for editing dendrite segments, add soma (cell bodies) and spines. When you are finished with editing, the Neuron Composer automatically updates the neuron measurements as well as the display of the edited neurons.
Interface
The Neuron Composer is one of eight tools found in the 3D Tools tab in the Analysis Panel. Go to 3D View to show the 3D Tools tab. Click on the 3D Tools tab and click on the Neuron Composer icon 
to launch the tool. The Neuron Composer is composed of three (3) main sections, highlighted in the GUI diagram on the right:
- Toolbar lets you select the editing tool (or "Edit Mode")
- Tool options provide options that are relevant to the selected tool for fine-tuning the editing tool; this section is only shown when you have selected a tool in the Toolbar
- General operations provides options to specify the output location of the edited objects as well as the options to undo or redo an operation
When you first, launch the Neuron Composer, the display settings will be updated to show image channels and render neuron objects as wireframes and colored by object label.
On this page:
Toolbar
The toolbar contains the editing tools for the Neuron Composer. When you select a tool, you will enter a specific edit mode that lets you edit a certain part of the neuron object (i.e. soma, dendrite, or spines).
Description and function for each tool are summarized in the table below:
| Name | Icon | Hot key | Description |
|---|---|---|---|
| Predict Dendrite |
| E | Toggles the predict dendrite mode for algorithm-assisted dendrite tracing |
| Draw Dendrite |
| D | Toggles the neuron pencil tool for WYSIWYG dendrite tracing in the 3D volume |
| Connect neurons |
| C | Toggles the dendrite point connection mode for joining dendritic segments |
| Delete dendrite points |
| F | Toggles the delete dendrite point tool that removes highlighted dendritic points |
| Add spine |
| S | Toggles the one-click spine creation tool |
| Add soma |
| A | Toggles the mesh spot creator tool for one-click soma creation |
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| Neuron Composer GUI |
Tool options
When you select an editing tool from the Toolbar, the Tool Options section will be displayed if there are options available for the given tool. The options available are as follows:
| Tool | GUI display | Description |
|---|---|---|
Draw Dendrite Predict dendrite |
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| Add spine |
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| Add soma |
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| Predict dendrite |
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General operations
The general operations section provide basic operations that applies to each edit modes within the Neuron Composer. Depending on the edit mode selected, some options may be shown or hidden. The available options in this section are summarized below.
| Option | Icon | Edit Modes | Description |
|---|---|---|---|
| Add to object set |
| All except Connect dendrite and Delete dendrite points | Specify the object set to output the edited objects to |
| Undo |
| All | Undo the last editing operation |
| Redo |  | All | Redo the most recent editing operation |
| Create soma |  | Add Soma | Create new soma object to the specified object set based on the detected area in the preview |
| Shortcut / hot key | Edit Modes | Action |
|---|---|---|
Shift + A | Add Soma | Confirms soma creation |
Ctrl + Left Click | Predict Dendrite | Terminate a potential path by holding control and clicking on the path |
H | Predict Dendrite | Hide the current segment trace while the key is held |
Using neuron composer
To launch the Neuron Composer tool, click on the 3D Tools tab above the Analysis Panel in Aivia and select the Neuron Composer tool from the 3D Tools toolbar. This will open the Neuron Composer interface.
Trace new dendrites
The Draw Dendrite tool lets you draw new dendrites directly on the 3D volume. Click on the Draw Dendrite tool icon 
or press the D key on your keyboard to enter this mode. The cursor display will change to a pencil with the tip of the pencil (lower left corner) as the tracing position.
Before tracing a dendrite, make sure the channel displaying the dendrite is visible. Depending on the intensity of the dendrite and the density of objects in the volume, you may need to adjust the lookup table or add a clipping plane in the Display Settings to isolate the desired dendrite. The Draw Dendrite tool uses ray tracing to find the closest opaque (i.e. non-background) signal directly in the line of sight of the displayed volume. To trace, hold down the left mouse button while dragging the mouse cursor along the dendrite.
Each point the Draw Dendrite Tool finds along the dendrite is shown as a gray sphere in the volume. As you trace along the dendrite, additional gray spheres (dendrite points) will be added to the trace. To finalize the trace, release the left mouse button. Aivia will connect the detected dendrite points to form a single dendritic segment - it will also attempt to clean-up the trace by removing any points that overlap the constructed trace.
The video on the right shows an example of using the Draw Dendrite tool to trace dendrites.
Adjust dendrite radius
You can adjust the dendrite radius by moving the slider or entering a new value into the textbox. Increasing the dendrite radius will result in thicker dendrite traces as well as increasing the search radius for finding dendrite points. This option is useful for tracing dendrites with discontinuous signals. The radius parameter is relative to your computer display and not to the physical width of the dendrite in the image.
Enhance trace
This option will override the dendrite radius by aligning the drawn segment to the center of the dendrite and adjusting the radius locally at each dendrite point detected based on intensity in the volume. For best results, make sure the contrast between the dendrite segment and the background is as high as possible.
Predictive modes
This tool lets you highlight predicted dendritic segments on the 3D volume. Click on the Predict Dendrite tool icon 
or press the E key on your keyboard to enter this mode.
In the case your data set has soma and you want to include them in the analysis, we suggest you first detect the soma of interest and then use the Predict Dendrite tool. See Create Soma section below for details on how to do this. The detected area is shown as an overlay in silver over the image.
Camera Modes
This option allows you to follow a predicted dendrite segment (in sections) in Follow mode or the entire dendrite in Pan-Only mode.
Connect dendrites
You can connect any points on an existing dendrite to any points on a different dendrite or a soma using the Connect Neurons tool. Click on the Connect Neurons icon 
or press the C key on your keyboard to activate the edit mode. There are three (3) types of connections:
| Connections | Effect |
|---|---|
| End point-to-end point | Extend existing dendrite |
| End point-to-intermediate point | Create dendrite branch at intermediate point |
| End point-to-soma | Create root at end point and create new dendrite |
|
| Extend a dendrite segment |
Connect dendrites
To connect two dendrites, mouse the cursor over an existing dendrite point and hold down the left mouse button. The point will be highlighted in red. Move your cursor while holding down the left mouse button to a dendrite point on another dendrite. If the connection is valid, the initial point will be highlighted in blue and the connection point will be in green.
Release the mouse button and the dendrite branches will be connected automatically. The dendrite segments will update automatically to reflect the new connections.
Connect to soma
Move your cursor to the dendrite end point closest to the soma and hold down the left mouse button. When you drag the cursor towards the soma, the Neuron Composer will recognize the connection and highlight the soma with a large green sphere. Release the mouse button to connect. The root point will be shown as a translucent shell over the dendrite end point.
Limitations
There are several restrictions in place to prevent invalid connections. A red sphere at the connection point will indicate that the selected connection point is invalid. The following table summarizes the restrictions and solutions to resolve the issue:
| Restriction | Solution |
|---|---|
| Joining segments from two neuron objects is not allowed | Separate the segment from the incorrect neuron with Delete Dendrite Point prior to connecting the segments |
| Joining segments belonging to the same neuron object (i.e. loops) is not allowed | Separate the segment from the incorrect dendrite with Delete Dendrite Point prior to connecting the segments |
| Joining Dendrite end point to the same Soma is not allowed | Separate the segment from the incorrect segment from the incorrect dendrite with Delete Dendrite Point prior to connecting the end point to the soma |
| Joining more than two (2) segments to a single dendrite point is not allowed | Connect the segments at adjacent dendrite points - each point can have a maximum of two branches |
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| Creating a branch point |
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| Connecting a dendrite end point to a soma |
Delete dendrite point
You can delete individual points on a dendrite using the Delete Dendrite Points tool. Click on the Delete Dendrite Points tool icon 
or press the F key on your keyboard to activate this mode. Your cursor will change to a scissor while you are in this mode.
When you hover the cursor over a dendrite segment, the dendrite point to be removed will be highlighted in red. Press the left mouse button to delete the highlighted dendrite point.
Delete dendrite segments
To delete a dendrite segment, it is recommended that you use the Delete Dendrite Points tool to isolate the segment first. Once the segment is separated, exit the Neuron Composer and change the object selection mode to Single Item from the Zoom Bar. Click on the segment you wish to delete to select and press the Delete key on your keyboard to remove.
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| Delete dendrite point |
Create spines
Dendritic spines are protrusions on dendrites that interact with nearby neurons at the synapse. In the Neuron Composer, you can add spines to a dendrite using the Add Spines tool. To activate, click on the Add Spines tool icon 
or press the S key on your keyboard.
To add a spine, click on the spine heads on the image near an existing dendrite. A purple sphere will highlight the location where you clicked (as determined by ray tracing) and the Neuron Composer will automatically detect the size of the spine head and attaches the spine head to the nearest dendrite segment with a spine neck.
You can adjust the search distance for spine detection in the tool using the Spine Search Range options slider or textbox. The tool will look for the nearest dendrite segment within the specified search range. The value corresponds to the distance in voxels from the specified spine head location to the center of the traced segment.
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| Add new dendritic spine |
Create soma
You can add soma, or neuron cell bodies, to the image using the Add Soma tool in the Neuron Composer. To activate the tool, click on the Add Soma tool icon or press the A key on your keyboard.
When you select the Add soma tool, the cursor will change to a pencil icon. Click anywhere on the image where a soma is located and a preview is generated at the location where you clicked. The detected area is shown as an overlay in silver over the image. If you are satisfied with the detection, you can click the Create soma button in the General Operations section or press Shift + A on your keyboard to create the soma.
The created soma is a single, continuous surface that surrounds the clicked location. Surfaces that are separate from the continuous surface will not be used for creating the soma.
Adjust soma detection
You can change how far the detected soma extends from the clicked location by changing the Search Range slider or textbox. The live surface preview will automatically update as you modify the search range parameter. You can click anywhere on the image again to update the search location.
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| Preview surface from Add Soma tool |
Undo or redo an operation
You can undo an operation by clicking on the Undo icon 
in the General Operations section or press Ctrl + Z on your keyboard. To redo an operation, press the Redo icon or Ctrl + Y on your keyboard. The order of undo / redo operation is determined by the last operation or the most recent operation completed respectively, regardless of the edit mode used.
Specify object set output
You can specify the object set to output the edits to using the Add to dropdown menu. If a neuron object set exists, the Neuron Composer will automatically select the object set as the default output set.
To output the edited objects to a new object set, click on the dropdown menu and select the <Create object group> option.
To output the edited objects to a different object set, click on the dropdown menu and select the desired output object group option.
Note: You can only output Neuron Composer output to a neuron object group.