Semi auto tracing

Semi-auto tracing mode traces curves between a sequence of user-selected points.

In this mode, when new point/ROI is started (with F), plugin switches to "TraceBox" mode, i.e. it zooms-in to the clicked point and shows a TraceBox around this point. TraceBox is a special sub-volume of original data.

The image shown inside TraceBox is not the voxel original data, but rather "curve saliency", kind of "tubeness". For more details: it is made by calculating Hessian matrix of subvolume and for each voxel summing up two largest negative eigenvalues (if two largest eigenvalues are not negative, it is assumed to be zero).

One can keep adding new points inside current location of the TraceBox using F shortcut. In this mode plugin will try to find most optimal path through the volume connecting last points.

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 and press F, 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 Roi Manager Settings.

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

Depending on the size of TraceBox and computer's performance it can take some time for TraceBox to appear, check the progress bar at the bottom of BigTrace panel.