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 Panel).

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

Crop… Opens the Dataset Cropper panel, in which you can crop an object (see Cropping Datasets).

Padding… Opens the Dataset Padding panel, in which you can add padding to an object (see Dataset Padding).

Crop to Bounding Box… Automatically crops the object to the bounding box that encapsulates the labeled pixels of the object.

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

Resample Geometry… Lets you copy the intersected values of the selected object into the geometry, or shape, of another object (see Resampling Geometries). This can be necessary if you need to extract statistics, such as the minimum, maximum, or mean values of corresponding image data (see Statistical Properties), or intend to create a deep learning training set.

Invert… Opens the Dataset Inverter panel, in which you can apply an axis transformation to an ROI or multi-ROI, as well as invert the labeled voxels within an ROI (see Inverting Datasets).

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

The following options are available to align multi-ROIs.

With Current View… Automatically rotates the selected multi-ROI so that its orientation in the selected 2D view 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 images, 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 re-sampling the shape of a multi-ROI or after the labeled voxels in a class were removed.

The following options are available for separating the connected components in a multi-ROI. You can start a connected components analysis after computing measurements for the multi-ROI in which connected voxels are labeled (see Connected Components Analysis).

New Multi-ROI (6-Connected)… Automatically creates a new multi-ROI, in which each group of connected voxels is labeled as a distinct object. Propagation is done by strictly using the 6 faces adjacent to the current seed and will result in the minimum number of connected pixels (see 6-Connected and 26-Connected).

New Multi-ROI (26-Connected)… Automatically creates a new multi-ROI, in which each group of connected voxels is labeled as a distinct object. Propagation is done by strictly using the 6 faces, 12 edges, and 8 corners adjacent to the current seed and will result in the maximum number of connected pixels (see 6-Connected and 26-Connected).

Analysis… Opens the Object Analysis dialog, in which you can analyze multi-ROIs with computed scalar values (see Analyzing Objects).

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 labeled class contained in the selected multi-ROI (see Generating Convex Hulls from Multi-ROIs).

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

A Mesh for Each Multi-ROI Label… Generates a series of convex hulls, as outlined objects, for each labeled class contained in the selected multi-ROI (see Generating Convex Hulls from Multi-ROIs).

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). This option is available for Dragonfly 3D World ZEISS edition only. Contact Comet Technologies Canada Inc. for information about the availability of this version of Dragonfly.

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.

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 the 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 currently applied to the selected multi-ROI.

In all cases, you can choose to create a box with a specific spacing or granularity in the Create a Box From dialog.

Create a Box From dialog

Note Whenever you change the number of pixels on the local X, Y, or Z axes, the spacing values will be updated automatically to preserve the original shape of the box. You can also click the Advanced Properties button to open the Advanced Visual Box Properties dialog. You can modify an object's position in space and change its orientation in this dialog (see Advanced Dataset Properties).

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

Note In this case, the resulting multi-ROI may have anisotropic spacing.

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 from Current View).

The following options are available for exporting multi-ROIs.

As ORSObject… Exports the multi-ROI in the Dragonfly Object (*.ORSObject extension) file format (see Exporting Objects).

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

Selected Classes Histograms to Line-Based CSV… Exports histograms of the selected classes in the comma-separated values (*.csv extension) file format. You can choose the image from which values will be extracted in the Select an Image to Create Histograms dialog.

To CZI… Exports ROIs in the CZI file format (*.czi extension), which is a proprietary file format used by ZEISS microscopes to save data. This option is available for Dragonfly 3D World ZEISS edition only. Contact Comet Technologies Canada Inc. for information about the availability of this version of Dragonfly.

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

Lets you create a Points Set that marks the centroid of each labeled object in the multi-ROI (see Using the Points Tool).

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 Analyze and Classify Measurements dialog, in which you can import measurements from multi-ROIs and other objects for the cross-table analysis of feature vectors (see Analyzing and Classifying Measurements).

Opens the Compute Measurements dialog, in which you can add measurements and other values to the discrete objects within a multi-ROI (see Computing Measurements 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).

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).

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

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 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 gridded multi-ROI in the same shape as the selected multi-ROI (see Making Gridded Multi-ROIs).

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 3D tetrahedral meshes from the selected class or classes of the multi-ROI (see Generating 3D Tetrahedral Meshes).

Lets you create deformed or warped datasets. For example, to create additional data for deep model training.

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.

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.

With Current View… Automatically rotates the selected multi-ROIs so that their orientation in the selected 2D view is aligned to the Z-axis of the world coordinate system.

Automatically computes the interfacial surface that is common the selected multi-ROIs. You should note that interfacial surfaces cannot be computed for overlapping multi-ROIs, that is, multi-ROIs that share labeled voxels.

Note If more than two multi-ROIs are selected, the interfacial surface will be computed for the first multi-ROI selected (A) and the union of all other multi-ROIs selected (B + C + D...).

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 between the selected multi-ROIs, which is defined as the boundary between two phases.

Note If more than two multi-ROIs are selected, the interfacial mesh generated will be between the first multi-ROI selected (A) and the union of all other multi-ROIs selected (B + C + D...).

The following options are available for exporting multi-ROIs.

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

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

Export Measurements Table… Lets you export the scalar values in the selected multi-ROIs in the comma-separated values (*.csv extension) file format. In this case, multiple files will be exported, one for each selected multi-ROI.

To CZI… Exports ROIs in the CZI file format (*.czi extension), which is a proprietary file format used by ZEISS microscopes to save data. This option is available for Dragonfly 3D World ZEISS edition only. Contact Comet Technologies Canada Inc. for information about the availability of this version of Dragonfly.

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).