Tracing trees with the automatic mode(3D)

There are two ways to implement automatic tracing:

• For a tracing using the defaults, click the Trace button.
• For a more accurate or faster tracing, adjust the settings first, then click the Trace button. The settings give you the opportunity to review seed placement, which is used to initiate the automatic tracing.

To continue incomplete automatic tracings, you can use the user-guided tracing mode.

Tracing after adjusting the settings

1. Click the Tree button to display the Trace Trees panel and select Automatic.
2. Select a tracing method.
   Directional Kernels

   With this method, four directional kernels are matched to the image data. For a given point within the dendrite/axon, the algorithm identifies the best positions and orientations for the top, bottom, left, and right kernels surrounding the point. The positions and orientations results are combined to estimate the next point to trace. Points are estimated until a set of stopping criteria is met.

   The same algorithm was used in AutoNeuron. For details on the algorithm, see Rapid automated three-dimensional tracing of neurons from confocal image stacks (Al-Kofahi, Lasek, Szarowski, Pace, Nagy, Turner, and Roysam, 2002).

   Rayburst Crawl

   The detection is implemented from a branch centerline to its outer edges (manuscript in preparation).

   Voxel Scooping

   This algorithm generates clusters of voxels iteratively along the dendrite/axon. These clusters are then used to position the nodes that define the centerline of the dendrite/axon.

   The same algorithm is used in NeuronStudio (developed by the Mount Sinai School of Medicine). For details on the algorithm, see Three-Dimensional Neuron Tracing by Voxel Scooping (Rodriguez, Ehlenberger, Hof, & Wearne, 2009).

3. Click the Show settings button.
4. In the Display Seeds tab, click the Display Seeds button.
   • Optional: To change the seed color, use the color picker next to the Hide Seeds button.
   • To adjust the number of seeds, use the slider and the density buttons.
5. Click the Refine Seeds tab.
   1. Click the validate Seeds button. the program applies an algorithm to evaluate seed placement.
   2. Optional: To decrease the number of unwanted seeds, increase the Refine filter value .
   3. Optional: Add or remove seeds manually.
   Adding seeds
   • To add a seed, click in the image.
   • To change the color of manually added seeds, use the color picker.
   Removing seeds
   1. Select the Remove radio button.
   2. Hover the mouse over a branch to see the circular cursor.
   3. Hold down CTRL and scroll the mouse wheel to resize the cursor.
   4. Click in the image to remove seeds within the cursor radius OR hold down CTRL and drag to remove contiguous seeds.
6. Click the Trace tab to modify the tracing settings.
   Settings

   • Sensitivity: Use the slider or type a value to adjust sampling density.
   • Gap tolerance: Use the slider to change the maximum acceptable distance between two segments to make a connection.
   • Remove traces shorter than: Enter a value to ignore objects that may be mistaken for traces in a noisy image.
   • Connect branch segments: Check to have the program connect branches according to the Branch Connections Criteria defined in the Advanced Settings (see details in Trace Trees (automatic) panel (3D)).
7. Click the Trace button to start tracing.
8. If you decide to change the tracing method, click the Clear Tracing button first, then click Trace again.

 

Also see Tracing trees with the user-guided mode(3D)