Trace Editor

The FARSIGHT 3-D Trace Editor

How to run it:

./trace_editor <input file>

Currently Trace Editor accepts the following file types as input:

• swc
• xml (RPI format)
• tks
• tif

Usage

The FARSIGHT 3-D trace editor has a two-fold purpose: (i) to correct errors in automatic tracing of tube like structures such as neurites and vessel centerlines; and (ii) to record the trail of user edits from which the performance of the automated tracing algorithm can be assessed. To achieve these purposes, the trace editor displays the grayscale image as a volume rendering, over which the traces (supplied in one of the accepted file formats) are overlaid. The traces can be viewed in the context of the original data from any angle and at any desired magnification.

Since the traces are represented as a sequence of points in 3-D space, they have a sense. Many automatic tracing algorithms produce a collection of trace fragments (segments) that don't have a consistent set of directions (sense). The trace editor is designed to cope with this challenge. It is also designed to allow "group editing". You can select multiple segments at once, and perform an edit operation over the selected set f segments.

Once the Trace Editor has successfully launched, you can point the computer mouse at a segment, and perform a right click operation on one or more trace segments to highlight them.

After you've selected some lines you can perform the following operations by pressing the key in parentheses.

• (l)ist: list information about the currently selected trace lines.

• (c)lear: deselect the currently highlighted lines.

• (d)elete: remove the selected trace lines from the displayed graph.

• (s)plit: Split each selected trace line into two parts, separating them at the point indicated by a sphere.

• (m)erge: attempt to merge traces based on selection. The MinEndPoints function determines the closest distances between trace endpoints, distances greater than the threshold are rejected. Conflicts between two lines attempting to connect to one endpoint are resolved by finding the closest endpoints.

• (f)lip: Flip the direction of the selected trace lines and update the rest of the tree consistently.