Trace Trees: Automatic mode (3D)

See Tracing trees in automatic mode (3D) for step-by-step instructions.

  • If you want to associate trees with a specific color channel, select a single channel using either the Channel panel on the left side of the 3D environment window or the Image Adjustment tool (on the Image and Workspace ribbons) in the main window (2D).
  • To trace using the default settings, click the Trace button.
  • For a more accurate or faster tracing, adjust the settings first (Show Settings), then click the Trace button.
  • To see the full panel, click Show Settings.

Detection Settings

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 is 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 software (developed by the Icahn School of Medicine at Mount Sinai). For details on the algorithm, see Three-Dimensional Neuron Tracing by Voxel Scooping (Rodriguez, Ehlenberger, Hof, & Wearne, 2009).

Show Settings

Display Seeds tab

Display/Hide Seeds

The Display/Hide Seeds button toggles between visible and invisible "seeds" that represent where Neurolucida 360 software would automatically trace trees. Clicking the display seeds button offers a preview of how the sensitivity and density settings affect results.

  • To change the seed color, use the color picker pull-down next to the Display/Hide Seeds button.

Sensitivity

Use the slider to adjust the sensitivity (%) to dim and low-contrast structures.

  • A value that is too high may result in seeds placed in the background where no branches exist.
  • A value that is too low may result in missing branches.

Density

Neurolucida 360 software applies an invisible grid to sample the image uniformly.

  • Coarse: Less grid lines and less sampling performed.
  • Medium: Optimizes density with speed, seed coverage, and final reconstruction accuracy.
  • Dense: More grid lines and more sampling performed. Dense sampling typically leads to longer processing times to produce more seeds and increase the tracing coverage. But accuracy may not improve as a result.

Refine Seeds tab

Validate seeds button

Click the Validate seeds button to enable refinement of seeds.

Neurolucida 360 software examines the possible seed-points' secondary characteristics to determine whether they are likely to belong to a branch.

Refine filter

The value indicates the quality of the match between seeds and branches. To change it, use the slider.

Edit seeds

  • Add seeds: When selected, clicking in the image adds a seed.

    • Change the color of seeds added using the color picker pull-down.
    • The Remove All Added button deletes seeds that were added manually.

  • Remove seeds within circular cursor: When selected, you can remove seeds.

    • Press and hold the CTRL key and scroll the mouse wheel to resize the cursor.
    • Click in the image to remove seeds within the cursor radius OR press and hold the CTRL key and drag to remove contiguous seeds

Trace tab

Sensitivity

Use the slider or type a value to adjust sensitivity to dim and low-contrast structures.

  • A higher value is more sensitive and can lead to tracings in the background where there is no neuronal structure.
  • A lower value can cause tracing to stop prematurely.

Gap tolerance

The relative gap that is tolerated between two potential tree segments to make a connection.

Remove traces shorter than __ µm

Segments shorter than the value specified are not traced.

Connect branch segments

Neurolucida 360 software connects branches according to the Branch Connections Criteria set in the Advanced Settings.

Advanced settings

See Advanced settings for automatic tracing (3D)