ROI Tools
The options on the ROI Tools panel let you create new regions of interest and multi-ROIs, define intensity ranges, apply operations to modify regions of interest and datasets, and export ROIs and multi-ROIs to meshes. Advanced operations, such as determining porosity and analyzing objects, are available in the context menu for selected ROIs and multi-ROIs (see ROI Pop-Up Menu and Multi-ROI Pop-Up Menu).
ROI Tools panel
A. Basic B. Import C. Range D. Morphological operations E. Operations F. Dataset operations G. Export
Basic
The Basic tools available in the ROI Tools panel let you create new regions of interest and multi-ROIs, clear and invert labeled voxels, as well as undo the last manipulation that was performed.
Basic
Creating New Regions of Interest
Before you use a manual segmentation tool, you must first create an empty region of interest. Shapes for the new object can either be taken from the dataset you intend to segment, or from another dataset, region of interest, or multi-ROI. You can create a new region of interest whenever you need to partition an image into additional segments.
How to Create a New Region of Interest
- Click the New button in the Basic box.
The New Region of Interest dialog appears.
- Enter a name and choose a highlight color for the new region of interest in the New Region of Interest dialog.
- Select a geometry in the Geometry drop-down list.
The geometry of the region of interest can be chosen from any available dataset, region of interest, or multi-ROI.
- Click OK.
The new ROI is added to the Data Properties and Settings panel (see ROI Properties and Settings).
Creating New Multi-ROIs
Before you use a manual segmentation tool, you must first create an empty multi-ROI. Shapes for the new object can either be taken from the dataset you intend to segment, or from another dataset, region of interest, or multi-ROI. You can also choose the number of classes for the new multi-ROI.
How to Create a Multi-ROI
- Click the New button in the Basic box.
The New Region of Interest dialog appears.
- Enter a name for the new multi-ROI in the New Region of Interest dialog.
- Select a geometry in the Geometry drop-down list.
The geometry of the multi-ROI can be chosen from any available dataset, region of interest, or multi-ROI.
- Check the Create as Multi-ROI option and then choose the required number of classes.
- Click OK.
The new multi-ROI is added to the Data Properties and Settings panel (see ROI Properties and SettingsMulti-ROI Properties and Settings).
Clearing Regions of Interest
Clearing means that every labeled voxel within the selected region of interest or multi-ROI will be unlabeled.
- Click the Clear button to clear the selected region of interest or multi-ROI.
Inverting Regions of Interest
Inverting means that every voxel that is not labeled in the selected region of interest will be labeled, while every voxel that was previously labeled will be unlabeled.
- Click the Invert button to invert the selected region of interest.
Undoing Operations
- Click the Undo button to undo the last manipulation that was performed.
You should note that some segmentation operations cannot be reversed by clicking Undo.
Import Tools
The options in the Import box allow you to import ROIs, as well as to load ROI templates.
Import tools
How to Import a Region of Interest
- Click the From File button.
- Navigate to and select the required region of interest in the Load from File dialog.
Note Regions of interest are saved in the ORSObject file format (*.ORSObject).
- Click Open.
The imported ROI is added to the Data Properties and Settings panel.
Range Options
The options in the Range box allow you to define an intensity domain on a dataset and then create a new region of interest in which all voxels within the selected range are labeled. You can also add or remove a range from a selected ROI. Intensity domains are also applicable to other tools, such as the ROI Painter tools, morphological operators, and clipped regions. In this context, any voxel with a value outside the range will not be selectable.
Range
Morphological Operations
The morphological operations of Dilate, Erode, Open, Close, and Smooth can be applied to refine regions of interest and the selected class of a multi-ROI.
Morphological operations
Operations
The options in the Operations box let you fill the inner areas of a selected region of interest, add or remove clipped regions, as well as interpolate 2D regions to create a 3D region of interest.
Operations
Filling Inner Areas
After creating a region of interest with a range of data, you may notice that pixels within inner areas of the ROI were not included in the segmentation. To correct this omission, you can fill internal, enclosed portions of a selected region of interest.
| Description | |
|---|---|
| 3D | Fills all internal, enclosed portions of the selected region of interest in all axes. |
| 2D (X) | Fills all internal, enclosed portions of the selected region of interest along the X-axis. |
| 2D (Y) | Fills all internal, enclosed portions of the selected region of interest along the Y-axis. |
| 2D (Z) | Fills all internal, enclosed portions of the selected region of interest along the Z-axis. |
How to Fill Inner Areas
- Select the required region of interest in the Data Properties and Settings panel.
- Choose a fill operation in the Fill inner areas box.
- Click the Apply button.
Adding and Removing Clipped Regions
Subvolumes defined by a clipped region on can be added to or removed from a segmentation.
How to Add or Remove Clipped Regions
- Select the required region of interest in the Data Properties and Settings panel.
- Click the Clip
button in the lower section of the panel. This option is available in the Clip box. - Adjust the Clip box on the 2D or 3D views of the dataset, as required (see Clipping).
- Do one of the following:
- Click the Add button to add the clipped region to the selected region of interest.
- Click the Remove button to remove the clipped region from the selected region of interest.
Interpolating Regions of Interest
This option for regions of interest lets you interpolate 2D regions through volumetric image data to create a 3D region of interest. You can choose the direction of the interpolation. For best results, the feature you select for interpolation should be regularly shaped, such as a cylinder or sphere.
In the following example, a series of 2D regions were defined on a number of slices in the XY oriented view (left) and then interpolated in the Z axis. The results of the interpolation is shown in an XZ oriented view (right).
Interpolated region of interest
How to Interpolate Regions of Interest
- Define a series of 2D regions on the feature of interest that you need to segment.
- Select the direction of interpolation in the drop-down menu.
- Click the Apply Button.
The 2D portions of the region of interest are interpolated through the image stack.
Dataset Operations
The options in the Dataset operations box let you overwrite dataset values, split a region of interest at the Otsu threshold, and export a copy of the selected dataset intersecting the ROI (see Applying Image Operations).
Dataset operations
