One click tracing - ekatrukha/BigTrace GitHub Wiki

BigTrace has a one-click tracing mode that tries to find a curve based on one initial point.
In this mode, selecting a point on the canvas with the F shortcut initiates a tracing process first in one, and then the other direction:

Until the tracing is finished, the ROI manager is locked, but dataset navigation and zoom in/out shortcuts (D and C) are still available. A small box is displayed around the active end to highlight the process.

As a result, it adds a new LineTrace3D ROI, that can be further edited/refined using Semi-auto-tracing mode.
Alternatively, when the ROI is selected, using shortcut R it is possible to add straight segments at the end of the curve (no tracing is performed). Or delete end segments using shortcut G.
If LineTrace3D ROI is edited and selected, at any moment one can continue tracing from one end using the same shortcut F.

For now, this is a new "proof-of-concept" feature, we are aware that sometimes it gets confused at the intersections. But it is a work in progress, so further improvements are expected.

Settings

To show the parameters dialog, double-click on the icon.

Tracing

Settings at this tab define parameters for both Semi auto tracing and One-click tracing modes.

Curve thickness along axes parameters specify the approximate thickness of curves of interest in each dimension (in pixels!). A good estimate for these values can be made by plotting the intensity profile perpendicular to a curve in each dimension and fitting it with the Gaussian function. SD of this Gaussian is the value that is needed.
Basically, it is an SD of Gaussian Derivative convolution filters for each dimension used to calculate the Hessian matrix.
Alternatively, one can look at the rendered TraceBox volume, if the curves are too dotty, these values can be increased.

Trace only cropped volume checkbox decides, in case of crop applied to a dataset, whether the tracing will continue outside the cropped volume.

One click trace

Intermediate vertex placement (px, >=3) How often intermediate points (vertices) will be placed in LineTrace3D during auto-tracing. Smaller values make tracing a bit slower, but they make further ROI editing easier.

Constrain directionality (0-1) instructs the auto-trace algorithm on how "straight" you expect the curve to be. Higher values correspond to the more straight curves, while lower values allow more bent, flexible curves. In more detail: it is a minimum of a cosine of the angle between the curve calculated direction in two neighboring voxels.