Creating Mask ROIs

Mask ROIs can be used in a number of different contexts — such as for training and applying deep models, computing Watersheds, and processing image data for an in-depth analysis. When applied, masks limit computations to a subset of the original data, which can help reduce processing times and increase accuracy.

You can create mask ROIs directly in the Create Mask panel (see Creating Mask ROIs in the Create Mask Panel) or you can create mask ROIs from shapes (see Creating Mask ROIs from Shapes). The resulting mask ROI is a new region of interest with the same shape as the selected image data and that is fully labeled within the selected range and increment.

Right-click the required image data in the Data Properties and Settings panel and then choose Create Mask in the pop-up menu to open the Create Mask panel, shown below.

Create Mask dialog

How to Create a Mask ROI in the Create Mask Panel
  1. Right-click the required image data in the Data Properties and Settings panel and then choose Create Mask in the pop-up menu.
  2. Choose the extent of the mask in the Start and End edit boxes for the X, Y and Z axes.

    This will determine the area of the ROI that is fully labeled.

  3. Choose an increment for labeling, as required.

    Note At a setting of '1', all slices within the selected range will be labeled. At a setting of '2', every second slice will be labeled, at a setting of '3', every third slice will be labeled, and so on.

  4. Click Create Mask.

    A new region of interest, with the same shape as the selected image data and that is fully labeled only within the selected area, is added to the Data Properties and Settings panel.

  5. Save the ROI, if required (see Exporting Objects).

Two options are available for creating mask ROIs from shapes — you can remove all labeled voxels from a selected region of interest that are outside of a shape (see Creating Mask ROIs by Removing Labeled Voxels from an ROI), or you can add labeled voxels to a selected ROI that are inside a shape (see Creating Mask ROIs by Adding Labeled Voxels to an ROI).

In this case, you will be removing all of the labeled voxels from a selected region of interest that are outside of a shape, such as a box, cylinder, or sphere.

Original ROI and shape (on left) and Mask ROI (on right)

How to Create a Mask ROI by Removing Labeled Voxels from an ROI
  1. Choose the required 3D shape, such as a box, cylinder, or sphere, on the Shapes panel (see Adding and Editing Shapes).

    The shape is added to the Data Properties and Settings panel and appears in the workspace.

  2. Resize and/or reposition the 3D shape so that it only includes the area of the region of interest that you want to define as the mask, as shown below.

  3. Right-click the shape in the Data Properties and Settings panel and then choose Mask ROI in the pop-up menu.
  4. Choose the region of interest that you want to mask in the Choose an ROI dialog.

  5. Click OK.

    All labeled voxels that are outside of the shape are removed from the selected ROI.

  6. Save the changes you made to the ROI, if required (see Exporting Objects).

In this case, you will be adding labeled voxels to a selected region of interest that are within a shape, such as a box, cylinder, or sphere.

Defined shape (on left) and after creating a mask ROI (on right)

Mask ROI

How to Create  Mask ROI by Adding Labeled Voxels to an ROI
  1. Create a new region of interest that has the same geometry as the dataset you need to mask, as follows:
    • Select the dataset you need to mask in Data Properties and Settings dialog.
    • Click the New button in the Basic box on the ROI Tools panel (see Creating New Regions of Interest).
    • Select a name and geometry for the ROI in the New Region of Interest dialog and then click OK.

      The new ROI, which does not contain any labeled voxels, is added to the Data Properties and Settings panel.

  2. Click the shape that best corresponds to the mask you want to create, such as a box, cylinder, or sphere, on the Shapes panel (see Adding and Editing Shapes).

    The shape is added to the Data Properties and Settings panel and appears in the workspace.

  3. Resize and/or reposition the selected shape so that it only includes the area that you want to define as the ROI mask.

  4. Right-click the shape in the Data Properties and Settings and then choose Add to ROI in the pop-up menu.
  5. Choose the region of interest you created previously in the Choose an ROI dialog.

  6. Click OK.

    All voxels that are inside the shape are labeled.

  7. Save the changes you made to the ROI, if required (see Exporting Objects).