Pop-up menus are available for single and multiple selections that provide options for exporting, importing, and further processing regions of interest.
The following items are available when you select a single region of interest in the Data Properties and Settings panel.
Opens the Dataset Properties panel (see Dataset Properties). The basic and advanced properties related to an ROI can be viewed and modified here.
The following options are available to modify and transform regions of interest.
Opens the Dataset Cropper panel. In this panel you can crop an ROI (see Cropping Datasets).
Automatically crops the region of interest to the bounding box that encapsulates the labeled voxels of the ROI.
Opens the Dataset Sampler panel. In this panel you can modify spacing by upsampling or downsampling (see Sampling Datasets).
Copies the intersected values of the selected region of interest into the geometry, or shape, of another object and creates a new region of interest (see Resampling Geometries). This can be necessary if you need to extract statistics from an ROI, such as the minimum, maximum, or mean values of corresponding image data (see Statistical Properties), or intend to create a training set that includes the ROI.
Opens the Dataset Inverter panel. In this panel you can invert the labeled voxels within a region of interest (see Inverting Datasets).
Automatically applies transformations, such as translations, rotations, and scaling, that were applied to a reference object to the selected region of interest.
You should note that only objects that were previously transformed will be available as a reference in the Choose an Object dialog, shown below.
The following options are available for aligning regions of interest with the current scene views.
Automatically rotates the selected ROI so that the selected axis is aligned to the Z-axis of the world coordinate system.
Lets you automatically align the axis of inertia of the selected region of interest with the axis of inertia of another ROI.
Automatically aligns the centroid of the selected region of interest with the centroid of another object. Applicable objects include volumetric image data, regions of interest, multi-ROIs, and meshes. Reference objects can be selected in the Choose the Object to Align With dialog, shown below.
The centroid of a region of interest is calculated from the bounding box that encapsulates the labeled voxels of the ROI. It is not calculated from its geometry.
Automatically aligns the center of mass of the selected region of interest in the current 2D scene views. You should note that the center of mass is calculated from the labeled voxels within the bounding box of the ROI.
Lets you automatically reduce each connected component in a region of interest to a single-voxel wide skeleton, as shown below.
Original ROI (green) and skeletonized ROI (red)
For best results, any inner holes in the region of interest must be filled (see Filling Inner Areas).
The following options are available for refining regions of interest.
The Process Islands options — Remove and Isolate by voxel count or rank — let you refine threshold segmentation results or to isolate objects of a certain size (see Processing Islands).
Lets you minimize beam hardening effects.
Lets you close pores and inner holes that are smaller than a selected threshold distance, which is selectable in the Threshold dialog, shown below. The output of this process is a new region of interest.
Threshold dialog
As an example, closing the holes in an initial bone segmentation, including cortical pores and vascular canal inlets, is the first step in the bone analysis workflow for accurately quantifying morphometric indices (see Filling a Bone Segmentation for a more information about this feature).
In the example below, a small cortical pore and vascular canal inlet were closed on a threshold segmentation.
Automatically removes objects, which can be defined as groups of labeled voxels that are connected, within the current region of interest that intersect with a selected ROI or multi-ROI.
In the example below, the objects in the ROI with the orange circles that were touching the blue ROI were removed.

Touching objects are removed automatically from the selected ROI.
Creates a new region of interest that contains only labeled voxels with an original neighbor count greater than or equal to a selected threshold. Thresholds are selectable in the Neighbor Count dialog, shown below.
This option is often used in the topological analysis of skeletons.
The following option are available for creating multi-ROI from a region of interest or for creating and starting the analysis of generated multi-ROI.
Automatically creates a new connectivity multi-ROI, in which each group of connected voxels is labeled as a distinct object. In the 6-connected scheme, the propagation of connected components is done by strictly using the 6 faces adjacent to the current seed and will result in the maximum number of labeled objects.
Automatically creates a new connectivity multi-ROI, in which each group of connected voxels is labeled as a distinct object. In the 26-connected scheme, the propagation of connected components is done in all directions using the 6 faces, 12 edges, and 8 corners adjacent to the current seed and will result in the fewest number of labeled objects.
Creates a new connectivity multi-ROI and opens the Object Analysis dialog, in which you can further analyze the multi-ROI. See Analyzing Connected Components for information about analyzing the connected components in a multi-ROI.
Creates a multi-ROI, in which the labeled voxels of the selected ROI are assigned to a class. In this case, a multi-ROI created from a single ROI will contain one class (see Creating Multi-ROIs from Regions of Interest).
Creates a multi-ROI, in which the labeled voxels of the selected ROI are assigned to a class and any unlabeled voxels are assigned to an additional class named 'Complement'. In this case, a multi-ROI created from an ROI will contain two classes (see Creating Multi-ROIs from Regions of Interest).
Automatically creates a multi-ROI in which the segments contained within the selected region of interest are labeled as separate connected components. You should note that segments are determined by first skeletonizing the region of interest, applying a watershed, and then expanding the ROI and assigning a label to each branch.
The computed multi-ROI will appear as a new item in the Data Properties and Settings panel (see Graphing Multi-ROIs).
The following options are available for creating distance maps and to map the volume thickness of a region of interest.
Creates a distance map from the selected ROI (see Creating Distance Maps).
Creates a signed distance map from the selected ROI (see Creating Distance Maps).
Creates a geodesic distance map in which the shortest path from a seed point that joins all points inside a region of interest are mapped. You should note that LUTs can be applied to geodesic distance maps, which can be examined in 2D and 3D views and are computed using the Fast Marching method.
Geodesic distance map of a pore network
You will to select a seed point in the Choose a Seed ROI dialog when you create a geodesic distance map.
Automatically computes local thickness for each point in the selected region of interest. You should note that computations are based on the sphere-fitting method and that local thickness is defined as the diameter of the largest sphere which fulfills two conditions:
The following options are available from generating convex hulls from a region of interest.
Generates a convex hull as a filled region of interest for the selected ROI (see Generating Convex Hulls).
Generates a convex hull as an outlined region of interest for the selected ROI (see Generating Convex Hulls).
Generates a convex hull as a mesh for the selected ROI (see Generating Convex Hulls).
The following options are available for computing the degree of anisotropy within a region of interest.
Lets you compute the degree of anisotropy for the selected region of interest using the mean intercept length (MIL) method (see Computing Anisotropy).
Lets you compute the degree of anisotropy for the selected region of interest using the star volume distribution (SVD) method (see Computing Anisotropy).
Automatically identifies region of interest segments as connected and non-connected porosity (see Connected Porosity).
The following options are available to generate 3D models from a region of interest.
Generates a contour mesh that describes the surface of a region of interest bound to a threshold (see Generating Contour Meshes from ROIs).
Automatically creates a graph in which the segments contained within the skeletonized region of interest are assigned to edges and vertices. The scalar values of Euclidean Length are computed automatically for each edge (see Graphing Regions of Interest).
Automatically creates a graph in which the segments contained within the skeletonized region of interest are assigned to edges and vertices. The scalar values of Euclidean Length, Segment Index, Segment Euclidean Length, Segment Length, and Segment Tortuosity are computed automatically (see Graphing Regions of Interest).
Dense graph
The following options are available for creating new box shapes.
Current Bounding Box… Automatically creates a box that corresponds to the dimensions of the labeled voxels in the selected region of interest.
Current Box… Automatically creates a box that corresponds to the dimensions of the labeled and unlabeled voxels in the selected region of interest.
Current Clip Box… Automatically creates a box that corresponds to the dimensions of the clip box currently applied to the selected region of interest.
In all cases, you can choose to create a box with a specific spacing or granularity in the Create a Box from ROI dialog. For example, in cases in which you will use the box to compute scalar and vector fields.
Create a Box from ROI
Saves the selected region of interest as a template (see ROI Templates).
Allows you to save reformations, such as oblique and double-obliques, that were applied with the Walk tool and other methods. The result is a new region of interest formatted in the current space (see Creating Oblique Views).
The following options are available for exporting regions of interest and the properties of an ROI.
Exports the selected ROI in the ORS Object file format (*.ORSObject extension). ORS files are proprietary binary formatted files in which data is written sequentially and XML (Extensible Markup Language) is appended after the binary data (see Exporting Objects).
Exports the basic and statistical properties of the selected ROI in the comma-separated values (*.csv extension) file format. The basic properties of an ROI include its name, unit used, width, height, depth, time index, total voxel count, and volume. The exported statistical properties of an ROI include the tagged voxel count, volume of the labeled voxels, percentage volume, as well as the min, max, mean, and standard deviation of labeled voxels that intersect with all available datasets that share the same shape as the selected ROI.
Exports the basic and statistical properties of the selected ROI in the GDT1 file format. The basic properties of an ROI include its name, unit used, width, height, depth, time index, total voxel count, and volume. The exported statistical properties of an ROI include the tagged voxel count, volume of the labeled voxels, percentage volume, as well as the min, max, mean, and standard deviation of labeled voxels that intersect with all available datasets that share the same shape as the selected ROI.
Exports the selected region of interest to a series of image files (TIFF, JPEG, BMP, or PNG file formats), as raw data, or in the ORSObject file format (*.ORSObject), in which labeled voxels are assigned a value of 1 and all other voxels 0. The geometry of the exported files can be selected in the Choose a Target Dataset dialog, as shown below.
Exports ROIs in the CZI file format (*.czi extensioni), which is a proprietary file format used by ZEISS microscopes to save data.
Provides a shortcut for selecting macros that can be executed for a single ROI.
Opens the User Data dialog, in which you can view detailed object descriptions, as well as add fields to further describe the selected region of interest (see User Data).
Automatically computes the Euler characteristic number of the selected region of interest.
The following items are available when you select two or more regions of interest in the Data Properties and Settings panel.
The following options are available to modify and transform selected ROIs.
Copies the intersected values of the selected ROIs into the geometry (or shape) of another object to create new datasets. Might be necessary if you need to extract statistics from an ROI or multi-ROI, such as the minimum, maximum, or mean values of corresponding image data (see Statistical Properties), or intend to compute other measures that require consistent shapes.

The intersected values are copied into the new shape and the resulting objects appear in the Data Properties and Settings panel.
The following options are available to align selected ROIs.
Automatically rotates the selected ROIs so that the selected axis is aligned to the Z-axis of the world coordinate system.
Creates a new multi-ROI, in which the labeled voxels of each selected ROI is assigned to a class. For example, if you create a multi-ROI from five regions of interest, then the multi-ROI will contain five classes (see Creating Multi-ROIs from Regions of Interest).
Creates a new multi-ROI, in which the labeled voxels of each selected ROI is assigned to a class and all unlabeled, or 'complementary' voxels, are assigned to an additional class. For example, if you create a multi-ROI from five regions of interest, and some of the voxels in the regions of interest are not labeled, then the multi-ROI will contain six classes (see Creating Multi-ROIs from Regions of Interest).
The following options are available for creating distance maps from multiple regions of interest.
Create a Distance Map… Creates a distance map from the selected ROIs (see Creating Distance Maps).
Create a Signed Distance Map… Creates a signed distance map from the selected ROIs (see Creating Distance Maps).
Automatically computes the interfacial surface, which is defined as the boundary between two phases, for the selected regions of interest. You should note that computations are performed in 3D with interpolated surfaces, not with pixel-wise methods. You should also note that interfacial surfaces cannot be computed for overlapping ROIs, that is, ROIs that share labeled voxels.
The following options are available to generate 3D models from selected regions of interest.
Generates a normal, sampled, or cubic mesh that describes the interfacial surfaces, which can be defined as the point of contact between two phases, for the selected regions of interest. You should note that interfacial surfaces cannot be computed for overlapping ROIs, that is, ROIs that share labeled voxels.
Extracts a graph of the three-phase boundary shared between three selected regions of interest and computes the throat thickness (see Extracting Three-Phase Boundary Graphs).
Extracts a graph of the three-phase boundary shared between three selected regions of interest (see Extracting Three-Phase Boundary Graphs).
Saves the selected regions of interest as a template (see ROI Templates).
The following options are available for exporting multiple regions of interest.
Exports each selected region of interest in the ORS Object file format (*.ORSObject extension) to a separate file (see Exporting Objects).
Exports the selected regions of interest in the ORS Object File (*.ORSObject extension) to a single file (see Exporting Objects).
Exports the basic and statistical properties of the selected ROIs in the comma-separated values (*.csv extension) file format. The basic properties of an ROI include its name, unit used, width, height, depth, time index, total voxel count, and volume. The exported statistical properties of an ROI include the tagged voxel count, volume of the labeled voxels, percentage volume, as well as the min, max, mean, and standard deviation of labeled voxels that intersect with all available datasets that share the same shape as the selected ROI.
Exports the basic and statistical properties of the selected ROIs in the GDT1 file format. The basic properties of an ROI include its name, unit used, width, height, depth, time index, total voxel count, and volume. The exported statistical properties of an ROI include the tagged voxel count, volume of the labeled voxels, percentage volume, as well as the min, max, mean, and standard deviation of labeled voxels that intersect with all available datasets that share the same shape as the selected ROI.
Exports ROIs in the CZI (*.czi extensioni) file format, which is a proprietary file format used by ZEISS microscopes to save data.
Provides a shortcut for selecting macros that can be executed for the number of ROIs selected.
Lets you compute a Watershed segmentation, in which the labeled voxels in the selected regions of interest will be used as the seed points and the expanded ROIs will be overwritten into the initial ROIs (see Computing Watersheds).
Opens the Segmentation Comparator dialog, in which you can compare a region of interest with a ground truth of the same size and shape. For example, to objectively evaluate the prediction or performance of a segmentation model.