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Advanced settings for automatic tracing (3D)

See Trace Trees (automatic) panel (3D)

 

Seed detection

Use the slider to adjust the sampling density.

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

 

Tracing

List of pre-selected values for specific image types. Use them as a starting point.

Check this box to enable detectors that are Z-aligned. These detectors are in addition to two default detectors that can move left, right, up, and down.

For best results, we recommend to enable this option for most images, but to keep it off for brightfield.

In addition to using detectors, it is possible to fit and model super-ellipsoids at each tracing point.

  • This usually gives better XYZ location and diameter estimations, and requires relatively wide vessels (in pixels).
  • The number of iterations represents the accuracy-vs-time in fitting the super-ellipsoid.
  • More accurate fittings with higher number of iterations will typically take more time.

The four (top bottom left and right) detectors have a variable size (in pixels). The longer the detector, the better it responds to gaps, although it might miss curved segments.

Adjust the range to optimize the tradeoff between gap detection and curved segments detection.

The detector moves in 3D, and rotation and shifting values constrain the movement.

Maximum 3D turning angle when moving along the vessels.

Movement inward or outward from the vessel centerline when moving along. For example, if Shifting is set to 3 pixels and the right detector detects an edge 5 pixels away from the centerline, search for the next point will be implemented between +/- 3 pixels away from the centerline, i.e., between 2 and 8 pixels away from the centerline. Shifting accommodates the variation in vessel thickness along the process length.

 

Branch connections

Largest gap

This value determines the largest distance that the software will "jump" to make a connection.

 

Max deviation angle

This is the maximum angle considered by the program when connecting branches. The maximum value is 180°.

Min ratio of diameters

When two branches are considered for connection based on their respective location in (X, Y, Z) space, the program compares the branch diameters of the end point of each branch. If the ratio of the diameters is greater than the specified value, the software connects the two branches and recolors according to the branch that is closest to the soma (if the soma is traced).

  • Use the slider or type a value to set the minimum ratio.

Example:

The software compares Branch A and Branch B.

  • Branch A's diameter at end point (DA) > Branch B's diameter at end point (DB).
  • The default ratio is 50%.

The software connects A and B if DB>= (DA/2)