ROI Painter Panel and Tool Settings
The ROI Painter tools, which can be used for manual segmentation tasks and for editing regions of interest and multi-ROIs, are available on the ROI Painter panel, shown below.
ROI Painter panel
A. Brush B. Brush tools C. Point & Click tools D. Smart Grid and Snap tools E. Path tool F. Region tools
Brush… Indicates the color mode and lets you set the diameter of the brush for the Brush, Point & Click, Smart Grid, and Snap tools (see ROI Painter Tool Settings).
Brush tools… You use the available Brush tools — Full, Adaptive Gaussian, and Local Otsu — to paint selections on 2D views (see Painting with the Brush Tools).
Point & Click tools… You use the Point & Click tool to grow regions of interest based on the standard deviation of intensity values within the selected dataset and their connectivity (see Painting with the Point & Click Tools).
Smart Grid and Snap tools… You use the Smart Grid tool to fill boundary mask regions defined by an overlaid grid on 2D views (see Painting with the Smart Grid Tool), while you use the Snap tool by simply dragging on a feature of interest (see Painting with the Snap Tool). The contour line that snaps to the gradient that defines the edges of the region will be filled automatically when you release the mouse.
Path tool… You use the Path tool to create regions of interest that consist of single lines set at a specific diameter (see Painting with the Path Tool).
Region tools… You use the Region tools to label pixels within regular and irregular shaped regions on 2D views (see Painting with the Region Tools).
ROI Painter Tool Settings
The behavior of an ROI Painter tool is determined by its selected mode and settings.
| Description | |
|---|---|
| Brush |
Indicates the current color mode and lets you set the diameter of the brush for the Brush, Point & Click, Smart Grid, and Snap tools.
Color modes… Two color modes — 'Single-color mode' and 'Two-color mode' — are available for labeling regions of interest and multi-ROIs (see Painting in Single and Two-Color Modes). Brush size… You can set the diameter of the brush for the Brush, Point & Click, Smart Grid, and Snap tools by entering a number of pixels or diameter. You can also use the scroll wheel on your mouse to increase or decrease the brush size. Click the Reset |
| Add |
You add labeled voxels to an ROI or multi-ROI in 'Add mode'.
|
| Remove |
You remove labeled voxels from an ROI or multi-ROI in 'Remove mode'.
Note In cases in which a background is set for a multi-ROI, labeled voxels that are removed will be added automatically to the background class (see Setting a Class as the Background). |
button to reset the diameter of the brush back to its default setting.Options for Working in 2D Views
You can choose to work on single or multiple slices, as well as define a domain of intensity values, whenever you work in 2D views.
| Description | |
|---|---|
| Single slice | In 'Single slice' mode, you can add and remove on the current slice only. |
| Multiple slices |
In 'Multi-slice' mode, you can add and remove on multiple slices that extend through the volume according to the selected brush size.
Note Applicable to the Brush, Point & Click, and Path tools. |
| Define range | You can select the Define range option on the ROI Tools panel to define a domain of intensity on 2D views, which is highlighted in red by default. Any voxel with a value outside the defined range will not be selectable with any of the ROI Painter tools when painting (see Defining Intensity Ranges). |
Options for Working in 3D Views
You can choose which object you work whenever you work in 3D views.
| Description | |
|---|---|
| Object drop-down menu | Lets you select the object — a dataset or region of interest — that you want to work on when you use the ROI Painter tools in 3D views.
Image… Lets you work on all visible voxels of the selected image data. You can adjust window leveling to help isolate the features that you need to label (see Window Leveling). Region of interest… Lets you work on the labeled voxels of the selected region of interest. In this case, you will only be able to use the Brush tools in Remove mode. |
Painting in Single and Two-Color Modes
Two color modes — 'Single-color mode' and 'Two-color mode' — are available for labeling regions of interest and multi-ROIs. These modes, shown below, appear whenever you select one or more ROIs or multi-ROI classes.
Brush modes
Single-color mode… In this mode, which appears whenever one ROI or one multi-ROI class is selected, you can use the Brush tools to label any voxel by holding down Left Ctrl (or your configured 'Add with key'). Holding down Left Shift (or your configured 'Remove with key') lets you remove voxels from the selected ROI or multi-ROI classes. You should note that in the case of painting multi-ROIs, this is a change from previous versions. Previously, voxels were only removed from the selected class when painting in Single-color mode. In version 2024.1 and later, voxels will be removed from all classes.
Two-color mode… In this mode, which appears whenever multiple ROIs or multi-ROI classes are selected, only the labeled voxels belonging to the selected ROIs (in Exclusive mode*) or to the selected classes of a multi-ROI will be affected when painting. Holding down Left Ctrl (or your configured 'Add with key') will relabel voxels from 'B' and the shown intermediary colors to 'A'. Holding down Left Shift (or your configured 'Remove with key') will relabel voxels from 'A' and the shown intermediary colors to 'B'. The identification of selected ROIs and selected multi-ROI classes as A, B, and C is shown below.
Selected ROIs and multi-ROI classes
Two-color mode can be particularly useful whenever the results of an automated segmentation may need manual editing to assign labeled voxels from one or more multi-ROI classes to another class or from one ROI to another. As shown below, only the labeled voxels highlighted in yellow are re-assigned to those highlighted in blue when painting in Two-color mode.
