Full auto tracing - UU-cellbiology/BigTrace GitHub Wiki

Full auto tracing mode tries to "trace everything" automatically.
How does it work?
First, it makes an "already traced" volume mask, marking volumes of existing ROIs
as "no enter zone". If there are no ROIs, mask is created empty.
It identifies a pixel with the maximum intensity in the current volume (excluding mask) and initiates One-click tracing.
Once it is finished, it updates the "already traced" volume mask with the volume of the created ROI.
Then it looks for the next maximum intensity value in the masked volume,
and runs One-click tracing again (accounting for the mask), and this cycle goes on.

The tracing stops if the intensity of newly found maxima is below Min intensity trace start parameter.
Or if the stop (interrupt) icon is pressed.
The curve traces that contain fewer points than Min # points in curve are added to the mask,
but deleted from the ROI manager.

Since it runs One-click tracing, it depends on its settings, as well as on General tracing parameters.

In the case of timelapse data, it is possible to limit the number of analyzed frames.

This is a recently added feature, so it is a bit experimental.
You may need to play with parameters to get useful results.

The memory size of the volumetric trace mask is proportional to the dataset volume (per timepoint),
so this mode could be very slow and memory-consuming when applied to large datasets.

Here is an example running on the data kindly provided by Aafke Gros aafkegros.