Trace vessels (user-guided) panel (3D)

• Corrects for lack of precision with mouse clicks.
• Enables closing a loop while tracing.
• Lets you resume tracing from an ending by clicking the ending.

A new color is used every time you start a new vessel.

Each point you click that falls outside the field of view is re-centered automatically.

Displays vessels that are already traced as lines (instead of showing thickness).

The three tracing methods are based on algorithms that work by tracing along the vessels one point at a time, and by producing three measurements at each point: (X,Y,Z) coordinate, thickness, estimated position of the next point.

Directional Kernels

With this method, four directional kernels are matched to the image data. For a given point within the vessel, 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.

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 vessel. These clusters are then used to position the nodes that define the centerline of the vessel.

For details on the algorithm, see Three-Dimensional Neuron Tracing by Voxel Scooping (Rodriguez, Ehlenberger, Hof, & Wearne, 2009).

By default, ends a vessel with a single right-click. If you uncheck this option, you'll see a right-menu when you right-click, providing you with additional options.