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

See Tracing trees with the user-guided mode(3D) and the tutorial (PDF) for step-by-step instructions

 

Tracing options

  • 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.

Automatically selects a different color every time you start tracing a new tree.

Automatically re-centers image/data at location of last click.

Displays trees that are already traced as lines.

 

User-guided tracing options

 

Method

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

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.

To trace an entire image, the algorithm computes seed points determined via a grid search of points located inside a dendrite/axon. From each seed point, the algorithm traces segments of dendrites/axons. It then merges the segments to form complete neuronal trees.

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).

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

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).

 

Place ending using right-click

By default, ends a tree 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.