Multi-ROI Pop-Up Menu

Opens the Image Properties panel, in which the basic and advanced properties related to a multi-ROI can be viewed and modified (see Image Properties).

The following options are available to modify and transform multi-ROIs.

Crop… Opens the Dataset Cropper panel. In this panel you can crop a multi-ROI (see Cropping Datasets). You should note that after cropping a multi-ROI, it is usually best to remove empty labels (see Refine). It may also be necessary to re-analyze the multi-ROI after cropping.

Padding… Lets you add padding to a multi-ROI. You can choose a value for the padded area voxels, as well as set padding to the plus and/or minus side of each axis in the Dataset Padding panel (see Dataset Padding).

Crop to Bounding Box… Automatically crops the region of interest to the bounding box that encapsulates the labeled voxels of the multi-ROI.

Sample… Opens the Dataset Sampler panel, in which you can modify spacing by upsampling or downsampling (see Sampling Datasets).

Resample Geometry… Copies the intersected values of the selected multi-ROI into the geometry, or shape, of another object to create a new multi-ROI (see Resampling Geometries). This can be necessary if you intend to create a training set that includes the multi-ROI. After resampling a multi-ROI, it is usually best to remove empty labels (see Refine). It may also be necessary to re-analyze the multi-ROI.

Invert… Opens the Dataset Inverter panel. In this panel you can invert the X, Y, and Z axes of the multi-ROI, as well as apply an axis transformation (see Inverting Datasets).

Apply Transformation From… Applies transformations, such as translations, rotations, and scaling, that were applied to a reference object to the selected data (see Applying Transformations from Other Objects).

The following options are available to align multi-ROIs with the current scene views.

With Current View… Automatically rotates the selected multi-ROI so that the selected axis is aligned to the Z-axis of the world coordinate system.

Centroid With… Automatically aligns the centroid of the selected multi-ROI with the centroid of another object. Applicable objects include volumetric image data, regions of interest, other multi-ROIs, and meshes. Reference objects can be selected in the Choose the Object to Align With dialog.

The following options are available for refining multi-ROIs.

Remove Objects That Touch Another ROI or Multi-ROI… Automatically removes objects, which can be defined as groups of labeled voxels, within a selected multi-ROI that intersect with an ROI or other multi-ROI (see Removing Objects That Touch Another ROI or Multi-ROI).

Remove Empty Labels… Removes all labels that do not contain any data. This can occur after resampling the shape of a multi-ROI or after objects have been removed in the Object Analysis panel.

Provides options for separating the connected components in a multi-ROI and analyzing multi-ROIs.

New Multi-ROI (6-Connected)… Creates a new multi-ROI, in which connectivity is determined strictly using the 6 faces adjacent to the current seed.

New Multi-ROI (26-Connected)… Creates a new multi-ROI, in which connectivity is determined using the 6 faces, 12 edges, and 8 corners adjacent to the current seed.

Analysis… Opens the Object Analysis dialog, in which you can further analyze the multi-ROI (see Analyzing Connected Components).

Creates a new multi-ROI in which all voxels are labeled.

Provides options for generating convex hulls from multi-ROIs. You should note that some of the following options may not be available if the selected multi-ROI contains an excessive number of labeled objects.

As a Multi-ROI, Each Label Being Filled… Generates a series of convex hulls, as filled objects, for each connected component contained in the selected multi-ROI (see Generating Convex Hulls).

As a Multi-ROI, Each Label as an Outer Shell ROI… Generates a series of convex hulls, as outlined objects, for each connected component contained in the selected multi-ROI (see Generating Convex Hulls).

As a Mesh for Each Multi-ROI Label… Generates a series of convex hulls, as outlined objects, for each connected component contained in the selected multi-ROI (see Generating Convex Hulls).

Lets you compute a Watershed segmentation, in which the labeled objects in the selected multi-ROI will be used as the seed points and the expanded components will then be overwritten into the initial multi-ROI (see Computing Watersheds).

Lets you compute a Watershed segmentation, in which the labeled objects in the selected multi-ROI will be used as the seed points and the expanded components will then be overwritten into the initial multi-ROI (see Computing Watersheds 2D).

The following options are available for creating new box shapes from multi-ROIs.

Current Bounding Box… Automatically creates a box that corresponds to the dimensions of the labeled voxels in the selected multi-ROI.

Current Box… Automatically creates a box that corresponds to the dimensions of labeled and unlabeled voxels in the selected multi-ROI.

Current Clip Box… Automatically creates a box that corresponds to the dimensions of the clip box applied to the selected multi-ROI.

Lets you create a new multi-ROI with isotropic spacing that is aligned to the selected viewing angle of the current 2D view (see Deriving New Volumes from the Current View).

Lets you create a new multi-ROI with isotropic spacing that is aligned to the selected viewing angle of the current 2D view (see Deriving New Volumes from the Current View).

The following options are available for exporting multi-ROIs.

Export as ORSObject… Exports the multi-ROI in the ORS Object (*.ORSObject extension) file format (see Exporting Objects).

Export Measurements Table… Lets you export data in the multi-labeled ROI in the comma-separated values (*.csv extension) file format.

To CZI… Exports the selected items in the CZI file format (*.czi extension).

Opens the Measurement Inspection panel, in which you can plot statistical properties on a histogram and highlight selections in 2D and 3D views (see Evaluating Multi-ROIs with the Measurement Inspector).

Lets you create a Points Set that marks the centroid of each labeled object in the multi-ROI.

Provides a shortcut for selecting macros that can be executed for a single multi-ROI. You should note that the sub-menu will only contain shortcuts to macros for which the selection matches the first step requirements.

Opens the Scalar Generator dialog, in which you can add measurements and other values to the discrete objects within a multi-ROI (see Generating Scalar Values for Multi-ROIs).

Lets you assign a new unit to the scalar values in a multi-ROI (see Assigning Units to Scalar Values).

Lets you delete selected scalar values from a multi-ROI (see Deleting Scalar Values from Multi-ROIs).

Lets you export the scalar values contained in a selected multi-ROI to a comma-separated values (*.csv extension) file (see Exporting Scalar Values from Multi-ROIs).

Lets you import scalar values contained in a selected comma-separated values (*.CSV extension) file (see Importing Scalar Values from CSV Files to Multi-ROIs).

Lets you copy selected scalar values contained from a multi-ROI to another multi-ROI (see Copying Scalar Values From Multi-ROIs).

Opens the User Data dialog, in which you can view detailed object descriptions, as well as add fields to further describe the selected multi-ROI (see Managing User Data).

Lets you graph the inter-relationship between connected components (see Creating Graphs from Connectivity).

Lets you create images from the scalar values computed for a multi-ROI. You can then select the scalars from which you want to create your new images in the Select Scalars dialog.

Adds a new class to the multi-ROI in which all unlabeled voxels are labeled.

Creates a dataset in which each object in the multi-ROI is assigned a different value. If the multi-ROI contains 1,000 objects, then the resulting dataset will have 1,000 values with each value corresponding to a distinct object.

Creates an ROI that consolidates all distinct (labeled) objects in the multi-ROI into a new region of interest.

Lets you generate a series of warped multi-ROIs with the same number of classes.

Extracts a new region of interest from each connected component in the selected multi-ROI.

For example, if there are 100 connected components in the selected multi-ROI, then selecting the Extract ROIs item will result in 100 new regions of interest — one for each connected component — being added to the Data Properties and Settings panel .

Lets you grow labels to their Feret box within the local lower or upper Otsu of a selected dataset.

Lets you add padding to a multi-ROI. In this case, you can choose the padding for the X, Y, and Z axes, as well as a value for the added voxels, in the series of dialogs that appear.

Creates a new multi-ROI with one labeled connected component from a multi-ROI that contains a number of labels that were merged. For example, through a Boolean operation.

Lets you create a new multi-ROI in which objects with the same label that are not connected are split. For example, when you create a greylevel multi-ROI from a dataset (see New Greylevel Multi-ROI).

In the following example, the original multi-ROI with six labeled objects extracted from the data values of dataset is on the left. After splitting the non-connected labels of the greylevel multi-ROI, there are 165 labeled objects, as shown on the right.

Results of splitting non-connected labels

Transforms a multi-ROI by applying a Watershed segmentation using the labeled objects in the multi-ROI as the seed points and a selected dataset as the landscape image (see Watershed Transforms).

Lets you update the spatial scale of the selected multi-ROI to obtain the correct values for measurements (see Spatial Scale Calibration).

Lets you extract macros that can be played to understand the history of an object or to create new objects from complex scenarios that make use of multiple tools (see Extracting Object Histories).

The following options are available to modify and transform multi-ROIs.

Resample Geometries… Copies the intersected values of the selected multi-ROIs into the geometry, or shape, of another object to create a new multi-ROI (see Resampling Geometries). This can be necessary if you intend to create a training set that includes the multi-ROIs.

The following options are available to align multi-ROIs with the current scene views.

With Current View… Automatically rotates the selected multi-ROI so that the selected axis is aligned to the Z-axis of the world coordinate system.

Automatically computes the interfacial surface, which is defined as the boundary between two phases, for the selected multi-ROIs. You should note that computations are performed in 3D with interpolated surfaces, not with pixel-wise methods.

The following options are available for generating 3D models for multi-ROIs.

Generate Interfacial Mesh… Generates a normal, sampled, or cubic mesh that describes the interfacial surface, which is defined as the boundary between two phases, for the selected multi-ROIs.

The following options are available for exporting multi-ROIs.

Export as Multiple ORSObjects… Exports the selected items in the ORS Object (*.ORSObject extension) file format to a selected folder as multiple files (see Exporting Objects).

Export as ORSObject… Exports the multi-ROI in the ORS Object (*.ORSObject extension) file format (see Exporting Objects).

Export Measurements Table… Lets you export data in the multi-labeled ROI in the comma-separated values (*.csv extension) file format.

To CZI… Exports the selected items in the CZI (*.czi extension) file format.

Provides a shortcut for selecting macros that can be executed for multi-selected multi-ROIs. You should note that the sub-menu will only contain shortcuts to macros for which the selection matches the first step requirements.

Lets you compare an automated or manual segmentation with a ground truth and objectively evaluate the results with a number of metrics (see Evaluating Segmentations).

Lets you update the spatial scale of the selected multi-ROIs to obtain the correct values for measurements (see Spatial Scale Calibration).