Creating ROIs - ekatrukha/BigTrace GitHub Wiki

Before creating ROIs it is useful to be familiar with Display and navigation options.
In the beginning, we advise to activate tracing icon Panel Tracing.

In general, all types of ROIs in BigTrace are made by creating a set of points in 3D (3D vertices).
Depending on the ROI types:

  1. button point single point (sphere);
  2. button polyline polyline (points, connected by straight or spline segments);
  3. button semi-auto semi-auto curve trace (points, connected by curved traces);
  4. button one-click one-click curve trace (points, connected by curved traces);
  5. button crossection cross-section plane (a plane fitted to a set of points).

So the process of any ROI creation is a process of addition/deletion of 3D points.

Point addition happens by clicking on the canvas displaying the dataset (shortcut F, see below). In this case, the plugin finds a maximum intensity voxel in the direction of the click, creates a 3D point/vertex with its coordinates, assigns it to the selected ROI type, and updates the displayed ROI shape.

The addition/deletion of ROI points is managed by the following shortcuts/buttons. They all are arranged close to each other on the keyboard (like arrow keys or WASD combination in computer games), so it should be convenient to keep left-hand fingers on them.

  • shortcut F adds a new point to the ROI selected in the ROI Manager list. If no ROI is selected, it creates a new ROI with one point. If you want to make a new ROI, first use deselect shortcut (see below).
  • shortcut G removes/deletes the last point added to ROI.
  • shortcut H deselects ROI (or stops tracing).
  • shortcut Y reverses the order of points (first becomes last and vice versa). Basically, for polyline/trace ROIs it makes another end of a curve active, so new points will be added from that end. The current final added point has a square around it.
  • shortcut E selects the ROI closest to the clicked point.

In the case of multicolor images, the point location (maximum intensity voxel) will be determined only by the source (channel) selected in the "Active" drop-down list of Panel Tracing.

In the timelapse dataset, each ROI is assigned to a specific time point.

Double-click on the ROI name in the ROI Manager list brings the viewer's focus on it.

Newly added/created ROI will be automatically assigned to a group, currently selected in the Groups drop-down menu of the Panel Tracing.

Here is a short demo showing interface usage:

BigTrace_roi_interface_0 2 0

This covers the basic features of ROIs creation/editing.
For more information about ROIs features,
please read about ROIs Groups, Panel Tracing, Semi-auto tracing, One-click tracing.