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Semi auto tracing

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Eugene Katrukha edited this page Apr 14, 2023 · 12 revisions

BigTrace has a semi-auto tracing mode semi-auto tracing mode icon that allows you to trace curves between a sequence of user-selected 3D points.
When you start tracing a new point/ROI (with the F shortcut), the plugin switches to "TraceBox" mode. This zooms-in to the clicked point and shows a TraceBox around this point.

The TraceBox is a special sub-volume of the original data, and the image shown inside it is a type of "tubeness" called "curve saliency." This is made by calculating the Hessian matrix of the subvolume and summing up the two largest negative eigenvalues for each voxel.

start tracing

In semi-auto tracing mode, you can keep adding new points inside the current location of the TraceBox using the F shortcut. The plugin will try to find the most optimal path through the volume connecting the last added point.

In this mode:

  • the last added (tip) point of the trace can be removed using G shortcut.
  • Advance TraceBox forward happens with T shortcut. It moves TraceBox so it is positioned around the last added point.
  • Reverse active tracing point of current curve with Y shortcut. The other end (tip) of the trace becomes active.
  • Straight line connection/segment (not tracing) can be added with R shortcut.
  • Finish/deseclect current tracing with H shortcut. *
  • Start new trace in the TraceBox mode with V shortcut.

Since algorithm connecting points sometimes gives weird results, especially trying to jump over gaps in lines, in some areas straight line R connection works better.

If you want to edit/continue an existing trace, select it in the list first (or at the canvas using E) and press F. The plugin will calculate and show TraceBox around the last added point.

TraceBox brightness/contrast/LUT color can be adjusted as with other sources (shortcut S), it is always the last source in the list.

TraceBox parameters (size, advance degree, Hessian smoothing factors, etc) can be adjusted in Panel Tracing settings.

Zoom in/out shortcuts (D and C) are still working in this trace mode.

Please note that depending on the size of the TraceBox and your computer's performance, it may take some time for the TraceBox to appear. You can check the progress bar at the bottom of the BigTrace panel for updates on this.

Developed in Cell Biology group of Utrecht University.
Check out Updates history. The plugin and this wiki are under constant development.
E-mail for any questions, feedback, errors or suggestion or tag @ekatrukha at image.sc forum.

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