Trace Trees (automatic) panel (3D)
See Tracing trees with the automatic mode(3D)
- For a tracing using the defaults, 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.
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 (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).
Settings
Display Seeds
Click the display seeds button to get a sense of how sensitivity and density are implemented.
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
The proram 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
Validate seeds button
The program 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.
Add seeds
To add a seed, click in the image.
To change the color of manually added seeds, use the color picker.
Remove seeds within circular cursor
- Select the Remove radio button.
- Hover the mouse over a branch to see the circular cursor.
- Hold down CTRL and scroll the mouse wheel to resize the cursor.
- Click in the image to remove seeds within the cursor radius OR hold down CTRL and drag to remove contiguous seeds.
Trace
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
Maximum distance between two segments to make a connection. If the distance is greater than the gap value, The program doesn't connect the segments.
Remove traces shorter than
Segments shorter than the value specified are not traced.
Connect branch segments
The program connects branches according to the Branch Connections Criteria set in the Advanced Settings.