Classes and Scalar Information

The Classes and scalar information box, shown below, indicates the name of each class in the multi-ROI, the number of labeled voxels, and the color assigned to each class. If available, you can also view scalar information related to each class. You can show or hide any class by toggling the visibility control, as well as set a class as the background. In addition, a Pick tool is available for visually selecting a class in a view.

Classes and scalar information

Labels

The following items and options are available in the Classes and scalar information group box for a selected multi-ROI:

Classes and scalar information

 

Description

Visible

Lets you show or hide the colored highlight applied to the labeled voxels within a class.

Color

Is the color of the highlight that is applied to the labeled voxels within a class.

Note The opacity of the highlight is adjustable with the sliders in the 2D opacity and 3D opacity boxes..
Opacity

Lets you adjust the opacity of each labeled class independently. Click the Opacity icon in the classes list to open the Opacity slider, as shown below. You can then adjust opacity from 0 to 100 percent with the slider.

Note Whenever you change the opacity of a class, the global opacity settings selected in the Opacity and color box will not be applied. However, you can right-click a class with an individually set opacity and then choose Use Global Opacity in the pop-up menu to reinstate the global opacity settings.

Name

Is the name assigned to a class.

Count

Is the total number of labeled voxels in a class.

Label

Indicates the label number assigned to each class or the selected scalar information (see Scalar Information).

Pick

Lets you visually select a multi-ROI class or multiple classes by picking in a 2D or 3D view.

  • Hold down Left Shift and then click to select a multi-ROI class in a view with the Pick tool.

  • Hold down Left Ctrl and then click to select multiple multi-ROI classes in a view with the Pick tool.

Add

Lets you add one or more classes to the multi-ROI as follows:

Add Class… Automatically adds a new class to the multi-ROI.

Add Multiple Classes… Lets you choose the number of classes to add to the multi-ROI.

Remove

Deletes the selected class.

Merge

Merges the selected classes.

Note The class name and color of the merged class are whose associated with the class you selected first and that is identified as 'A'.

Background class

If enabled, labeled voxels that are removed from any class, as well as unlabeled voxels that are painted, will be added automatically to the set background class (see Setting a Class as the Background).

Labeled voxels count

Indicates the number of labeled voxels in the selected class.
Scalar information Measurements that were computed for the selected multi-ROI, imported from a file, or copied from another object, are available in the Scalar information group box (see Scalar Information).

Measurements that were previously computed for the selected multi-ROI, imported from a file, or copied from another object, are available in the Scalar information group box, as shown below. Measurements are available in the drop-down menu.

Scalar information box

Scalar information settings and options
 

 

 Description

Measurement

 

Indicates the current measurement that is selected and mapped in the views of the multi-ROI. Scalar information for a multi-ROI can be generated with the Scalar Generator (see Generating Scalar Values) or computed in the Object Analysis dialog (see Analyzing Connected Components).

Min… Indicates the minimum value of the currently selected measurement.

Max… Indicates the maximum value of the currently selected measurement.

You should note that the Label measurement refers to the identifier assigned to each labeled component in the multi-ROI and that the maximum value may not be equal to the label count. For example, if you have merged, split, or deleted objects. The label count is always the total number of labeled components in the multi-ROI.
Histogram

Lets you plot the distribution of a selected measurement and extract basic statistics, such as the minimum, maximum, mean, and standard deviation value of the selected measurement.
Export

Lets you export selected scalar values to a comma-separated values file (*.csv extension).

Import

Lets you import scalar values from a comma-separated values file (*.csv extension).

In addition the operations available for labeling and editing classes (see Labeling Multi-ROIs), a number of additional options are available in the Classes and Scalar Information pop-up menu for automatically labeling voxels, importing and extracting regions of interest, as well as merging and deleting classes.

Classes and Scalar Information pop-up menu

The pop-up menu items available for single and multiple selections are described below.

Classes and Scalar Information pop-up menu

 

Description

Assign a Color to Each Class from a LUT

Lets you automatically assign colors to each class from a selected LUT.

Look at Center of Mass

Automatically aligns the center of mass of the labeled voxels of the selected class(es) in the center of the current 2D scene views.

Note The center of mass is calculated from the bounding box of the labeled voxels within the selected class(es).

Label All Voxels as Class*

Automatically labels all voxels in the multi-ROI as the selected class.

Note In this case, all voxels previously labeled as other classes will be removed.

Add All Unlabeled Voxels to Class*

Automatically adds all unlabeled voxels to the selected class.

Clear Class(es)

Removes all labeled voxels from the selected class or classes.

Delete Class(es)

Deletes the selected class or classes.

Merge Classes**

Available for multiple selection only, merges the selected classes.

Note The class name and color that are retained are whose associated with the first selected class.
Swap Classes*** Swaps the Label index of the selected classes.
Separate Connected Components
(6-connected) or (26-connected)

Lets you separate the connected components within a selected class or classes based on 6-connected or 26-connected connectivity.

In image processing, connectivity is the way in which voxels in 3-dimensional images relate to their neighbors and are labeled as separate components. You should note that a set of voxels in an image that are connected to each other is often called a connected component.

6‐connected… Propagation is done by strictly using the 6 faces adjacent to the current seed and will result in the maximum number of connected components.

26‐connected… Propagation is done in all directions, using the 6 faces, 12 edges, and 8 corners adjacent to the current seed. This will result in the fewest number of connected

components.

Note In either case, each separated component will be assigned to a new class.
Process Islands

In cases in which you need to refine threshold segmentation results or need to isolate objects of a certain size, you can now remove small objects from a selected class, as well as isolate larger objects. These operations can be based on voxel counts or by rank. The options for processing islands within a selected class are shown in the screen capture below and are described in the following text. Options for processing Islands Right-click a class in the Classes and scalar information box and then choose Process Islands in the pop-up menu. You can then choose to remove or keep objects as described below.

Remove by Voxel Count (6‐connected or 26‐connected)… Removes all objects, as determined by the 6-connected or 26-connected method, that have a voxel count lower than a selected threshold. Voxel counts can be selected in the Minimal Voxel Count dialog.

Keep by Voxel Count (6‐connected or 26‐connected)… Keeps all objects, as determined by the 6-connected or 26-connected method, that have a voxel count higher than a selected threshold. Voxel counts can be selected in the Maximal Voxel Count dialog.

Remove by Largest (6‐connected or 26‐connected)… Removes a selected number of the largest connected components, as determined by the 6-connected or 26-connected method and as ranked by voxel count. The number of components to remove can be selected in the Remove Biggest Count dialog.

Keep by Largest (6‐connected or 26‐connected)… Keeps a selected number of the largest connected components, as determined by the 6-connected or 26-connected method and as ranked by voxel count. The number of components to retain can be selected in the Isolate Biggest Count dialog.

Note Components with an identical voxel count are considered as unique objects when they are ranked.

Extract Class as an ROI
Extract Each Class as an ROI

Creates a new region of interest that contains the labeled voxels of the selected class or creates new regions of interest that contain the labeled voxels of the selected classes.
Import ROI*

Lets you modify the labeled voxels within the selected class as follows:

Add to class… Adds the labeled voxels of the selected region of interest to the class.

Overwrite class… Replaces the labeled and unlabeled voxels of the class with the labels of the selected region of interest.

Remove from class… Removes the labeled voxels of the selected region of interest that intersect with the labeled voxels of the class.

Intersect with class… Keeps only the labeled voxels of the selected region of interest that intersect with the labeled voxels of the class.
Export Class(es) as a Thickness Mesh

Lets you export a selected class as color-coded thickness mesh that shows referential values of the local thickness between boundary points. Thickness is calculated as the diameter of a hypothetical sphere that fits within each boundary point.

Do the following if you need to apply smoothing prior to exporting the mesh:

  • Choose a smoothing method — Laplacian Smoothing or Hamming Windowed Smoothing — in the Export as Thickness Mesh dialog.

    Note You can adjust additional properties for Hamming Windowed Smoothing in the Advanced Parameters dialog. Click the Advanced Properties button to open the dialog.

  • Choose the number of iterations required.

When processing is complete, the exported thickness mesh will appear on the Data Properties and Settings panel. Thickness meshes can be examined in 2D and 3D views.
Export Class(es) as a Sampled Thickness Mesh

Lets you export a selected class as sampled color-coded thickness mesh that shows referential values of the local thickness between boundary points. In this case, you can select the required sampling values for the X, Y, and Z axes in the Export as Sampled Thickness Mesh dialog.

Do the following if you need to apply smoothing prior to exporting the mesh:

  • Choose a smoothing method — Laplacian Smoothing or Hamming Windowed Smoothing — in the Export as Thickness Mesh dialog.

    Note You can adjust additional properties for Hamming Windowed Smoothing in the Advanced Parameters dialog. Click the Advanced Properties button to open the dialog.

  • Choose the number of iterations required.

When processing is complete, the exported thickness mesh will appear on the Data Properties and Settings panel. Thickness is calculated as the diameter of a hypothetical sphere that fits within each boundary point. Thickness meshes can be examined in 2D and 3D views.
Export Class(es) Histogram(s) to CSV

Lets you export histograms of labeled data in the comma-separated values (*.csv extension) file format. In this case, the data associated with each label will appear in a separate row and the number of pixels in each bin will appear in the columns.

You can then choose the image to extract the values for the histograms in the Choose an Image to Create Histograms dialog, shown below.

Note You can select up to a maximum of 1000 labels for exporting label histograms to CSV.
Label All Voxels in Shape as Class*

Lets you label all of the voxels in a shape, as follows:

  • Create the required 3D shape, such as a box (see Adding and Editing Shapes).

  • Resize and/or reposition the shape so that it only includes the voxels that you want to label.

  • Right-click the class that you want to edit and then choose Label All Voxels in Shape as Class in the pop-up menu.

  • Choose the required shape in the Choose a Shape dialog and then click OK.
Remove Shape from Class

Lets you clear all labeled voxels within a shape, as follows:

  • Create the required 3D shape, such as a box (see Adding and Editing Shapes).

  • Resize and/or reposition the shape so that it only includes the voxels you want to remove.

  • Right-click the class that you want to edit and then choose Remove Shape from Class in the pop-up menu.

  • Choose the required shape in the Choose a Shape dialog and then click OK.

* Available for single selections only.
** Available for multiple selections only.
*** Available for two selections only.