Thresholding
The options in the Range box on the ROI Tools panel, shown below, allow you to define an intensity domain of dataset values and then apply the selected range as a threshold segmentation. In addition, you can add or remove a range from a selected ROI or from the selected class of a multi-ROI. Intensity domains are also applicable to other tools, such as the ROI Painter tools, and the morphological operators. In this context, any voxel that corresponds to a value outside the range will not be selectable or be affected by an applied operation.
Range
| Description | |
|---|---|
|
Define range |
Applies an intensity domain on the 2D views of the selected dataset, which is highlighted in a constant color. Note The highlight color can be selected in the Colors preferences (see Selecting the Colors Preferences). |
|
Lower Otsu* |
Automatically sets the range between 0 and the Otsu threshold. |
|
Upper Otsu* |
Automatically sets the range between the Otsu threshold and the maximum data value in the selected dataset. |
|
Dataset |
Lets you select the dataset on which you want to define the intensity domain, as shown below.
Note This option is available only when multiple datasets are visible in the current view. |
|
Show histogram |
Toggles the visibility of the histogram. |
|
Log Y |
If selected, the Y-axis will be plotted in log scale. |
|
Histogram |
Shows how data values are distributed within the selected dataset. The darkest parts will appear on the left side of the graph, the midtones will appear in the middle, and the brightest parts (highlights) on the right side. Note You can adjust the range with left or right Range sliders (window width), as well as drag from the middle of the selected range to translate the range values (window center). |
|
Selected range |
Indicates the minimum and maximum selected threshold values.
|
|
Plotted range/Data range |
Indicates the range of values plotted on the histogram, as well as the minimum and maximum values within the selected dataset.
|
|
Interpolation |
Lets you choose an interpolation method — Nearest, Linear, or Cubic — in cases in which you add to or remove labeled voxels from a selected region of interest that has a different geometry than the dataset on which the range is defined. |
|
Add |
Adds labeled voxels within the selected range to the current region of interest. |
|
Add to New |
Creates a new region of interest in which all voxels within the selected range will be labeled. |
|
Remove |
Removes labeled voxels within the selected range from the current region of interest. |
* In the Otsu thresholding technique, the optimal value that minimizes the weighted within class variances of two classes — foreground and background — is computed. You should note that minimizing the within class variance is the same as maximizing the between class variance.
Defining Intensity Ranges
Defined intensity ranges can be used to create a threshold segmentation, define the seeds for a Watershed computation, or to limit the application of the ROI Painter tools or morphological operators within a selected range.
How to Define an Intensity Range
- Select the image data on which you plan to define the intensity range in the Data Properties and Settings panel.
- Select the Define range option in the Range box on the ROI Tools panel.
The full range of data in the selected dataset is applied by default.
Note If multiple datasets are visible in the current scene, make sure that the dataset that will provide the required range is selected in the Dataset drop-down menu.
- Check the Show histogram option to plot a histogram of the intensity values, recommended.
You can scale the Y-axis in log scale by checking Log Y.
- Define the intensity range that best describes the feature(s) you need to segment or the range of data that you want to modify.
- Drag the left or right Range sliders to change the minimum or maximum values of the intensity range (window width).
- Drag from the middle of the selected range to translate the intensity range values (window center).
- Enter the required values in the Selected range edit boxes.
- Click the Lower Otsu button to set the range between 0 and the Otsu threshold or click the Upper Otsu button to set the range between the Otsu threshold and the maximum value in the selected dataset.
- Drag the left or right Range sliders to change the minimum or maximum values of the intensity range (window width).
- Verify the selected range on other image slices within the image stack, recommended.
Creating Threshold Segmentations
Creating a region of interest within a range of data can provide a good first step in the segmentation process. If required, you can refine the initial segmentation (see Refining Threshold Segmentations) or you can separate and classify objects within the region of interest (see Connected Components Analysis).
Threshold segmentation of a fracture
How to Create a Threshold Segmentation
- Define the intensity range that best describes the feature(s) you need to segment (see Defining Intensity Ranges).
- Click the Add to New button in the Range box to create a new region of interest.
All voxels within the specified range will be labeled in the new region of interest. Information about the new region of interest is displayed in the lower section of the Data Properties and Settings panel (see ROI Properties and Settings).
- Refine the initial segmentation, as required (see Refining Threshold Segmentations).
Refining Threshold Segmentations
An initial threshold segmentation may contain unwanted objects, such as mounting aids, stray pixels, and noise. In this case, you can apply the Process Islands options to remove unwanted objects (see Processing Islands). For example, you can isolate the largest object or objects in the region of interest by choosing Isolate (6-connected) nth First Biggest in the Process Islands sub-menu and then selecting the number of objects that you want to keep.
You can also edit threshold segmentation results by applying morphological operators such as Open, Close, and Smooth (see Applying Morphological Operations) or by filling inner areas (see Filling Inner Areas). You can also use the ROI Painter tools to manually edit a threshold segmentation (see ROI Painter Tools), as well as clean-up an initial segmentation in the Object Analysis dialog (see Analyzing Connected Components).
Adding and Removing Ranges from ROIs
If required, you can add or remove labeled voxels within a selected range to or from a region of interest.
How to Add or Remove a Selected Range from an ROI
- Define the required intensity range (see Defining Intensity Ranges).
- Do any of the following, as required:
- Select a region of interest in the Data Properties and Settings panel and then click the Add button.
All voxels within the selected range are labeled.
- Select a region of interest in the Data Properties and Settings panel and then click the Remove button.
All labeled voxels within the selected range are remove from the region of interest.
Information about the region of interest, which is displayed in the lower section of the Data Properties and Settings panel, is updated automatically (see ROI Properties and Settings).
- Select a region of interest in the Data Properties and Settings panel and then click the Add button.
