ROI Pop-Up Menu

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.

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.

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.

How to Remove Objects That Touch Another ROI or Multi-ROI

1. Right-click the region of interest you need to modify and then choose Refine Region of Interest > Remove Objects That Touch Another ROI or Multi-ROI in the pop-up menu.
2. Choose the ROI or multi-ROI that is touching parts of the region of interest that you are modifying in the Choose ROI or Multi-ROI dialog.

   

3. Click OK.

   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.

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 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 sphere encloses the point, but the point is not necessarily in the center of the sphere.
• The sphere is entirely bounding within the solid surfaces of the 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).

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).

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

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.

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.

• Choose the object with the required geometry in the Geometry drop-down menu.

  

• Click OK.

  The intersected values are copied into the new shape and the resulting objects appear in the Data Properties and Settings panel.

Automatically rotates the selected ROIs so that the selected axis is aligned to the Z-axis of the world coordinate system.

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).

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.