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Semi-Manual and Manual Tracing

In addition to automatic tracing and importing a model, new sections of the existing model can be created by both semi-manual and fully manual means.

Semi-Manual Tracing

The neurite tool Neurite Tool can be used to create new sections of the model.

Example:

Simply click and drag the cursor to define a direction. A line is drawn in the 2D display to help visualize this (see image below).

Manual Trace Example 1 Image 1

After the mouse button is released, NeuronStudio will begin to trace the segment. The image below shows how measurements are created along a dendrite. These are the same measurements that can be taken with the measurement tool (see also Taking Measurements).

Manual Trace Example 1 Image 2

The tracing will continue until another section of the model is encountered, or until an endpoint in the data is reached. The current region of interest (ROI) will also limit the progression of the tracing to it's boundaries.

The resulting section of the model depends on the quality and complexity of the data. The image below shows the model created by the previous trace. If possible, any created section will be joined to the existing model.

Manual Trace Example 1 Image 3

TIP: It may be necessary to activate multiple traces along the length of a dendrite.

Manual Tracing

You can also use the neurite tool Neurite Tool to trace a branch one node at a time. While in the neurite tool mode, click near the center of a branch in the 2D or 3D window to create a new node. NeuronStudio automatically determines the 3D position and diameter based on the data and creates the new node a that location. You may click in succession to form an entire path along a branch. Because this linking mechanism is based on the selection state of the previous node, you can avoid connectivity by hitting the 'Esc' key to deselect the last node or connect to another node by first selecting it (see Selection and Deselection for more details).

Example:

The image below shows a number of nodes being added along a branch in the 2D window.

Manual Trace Example 1 Image 1

The image below shows a number of nodes being added along a branch in the 3D window.

Manual Trace Example 1 Image 2

This method of creating a model is more precise, since you have full control over where each vertex will be placed, but requires more time and effort.

TIP: When targeting in the 3D window, make sure no other structures are in front of the desired branch.

Converting Samples to Dendritic Nodes

Since the neurite tool creates one or more measurements that are then automatically converted to a model, it follows that the measurement tool Measure Tool, which also creates measurements, can be used as well for this purpose.

Example:

The image below shows a number of measurements taken along a dendrite.

Manual Trace Example 2 Image 1

These can be converted into a section of the model by selecting Edit >> Convert Measurements from the main menu. The image below shows the result. As with the semi-manual tracing, the created section will possibly be joined to the existing model.

Manual Trace Example 2 Image 2

This method of creating a model is more precise, since you have full control over where each vertex will be placed, but requires more time and effort.

TIP: We recommend creating as much of the model by automatic and semi-manual means first.

Manual Splicing

Also presented here is an explanation of how a section of a model can be spliced into an existing one. As mentioned before, a manually traced or semi-manually traced section will attempt to connect with the current model. An example of a model with a gap is shown below.

Example:

You could simply select the two vertices at the end of the gap and create a connection between them. See also Editing the Model. An alternative strategy is to try to fill in the gap with a new section.

Manual Trace Example 3 Image 1

The next image shows a series of manual measurements taken within the gap. Note how the start and end measurements intersect vertices of the model.

Manual Trace Example 3 Image 2

Again select Edit >> Convert Measurements from the main menu to create the new section. In the image below you can see how the new section has been spliced into the previous model. You can attempt splicing in sections like this using the neurite tool as well.

Manual Trace Example 3 Image 3

TIP: The key point is that semi-manual or manual measurements that intersect vertices of the current model will create connections. This intersection must occur in 3D, so sometimes it may appear in 2D as though the measurement intersects, when in actuality it doesnt. See also Taking Measurements.

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Send questions or comments to: alfredo.rodriguez@mssm.edu