Region of Interest

Regions of interest (ROIs) are areas of an image, which can be used as input into subsequent data analysis. ROIs can be defined manually, as explained in this page, or automatically through processing such as clustering.

Feature List

Overview

The ROI panel can be found on the right on the main interface (number 1 in the image below).

Data Visualisation Interface

  1. Region of interest list
  2. Save region of interest list
  3. Load region of interest list
  4. View statistics on ROI
  5. Add/edit/delete ROIs

Generate ROI

To create an ROI manually, the Edit button on the main interface in the ROI panel must be clicked. This then opens the ROI List Editor, shown below, displaying the ion image which was previously active in the main interface.

Edit a region of interest

To create a new ROI, first click the + button, and then in the new window, select an ROI name and colour and then click OK. This then adds the new ROI to the list (bottom left in the interface). The highlighted ROI is then displayed on top of the image, and any selected tool (defined below) can then be applied directly to the image by clicking and/or dragging.

Pencil
Assign individual pixels to the ROI.
Line
Assign all pixels which fall along a line drawn by the user to the ROI.
Rectangle
Assign all pixels which fall within a rectangle drawn by the user to the ROI.
Ellipse
Assign all pixels which fall within an ellipse drawn by the user.
Poly
Define an arbitrary shaped region of interest.
Eraser
Toggle button. When active, use any shape to define an area to remove from the current region of interest. When deactivated, areas are added to the ROI.
Threshold
Assign all pixels based on thresholds applied (see Threshold for more details).
Move
Allows dragging of the ROI to a new location.

Threshold

When selecting the Threshold button, the following window will be shown, with the fields automatically poplated with the minimim and maximum intensity of the displayed ion image.

Threshold options

Calculate statistics

Once one or more regions of interest have been defined, it is possible to investigate the differences between these regions further.

Export ROIs

Selecting the ‘save’ button in the ROI panel will bring up a dialog box for selecting an output location for the .rois file.