ROI Properties and Settings

List of ROIs

All regions of interest that are available are listed in the top section of the Data Properties and Settings panel.

Click the Regions of Interest icon at the top of the Data Properties and Settings panel to see the available ROIs (see Filters for information about filtering the listed items).
Click the Eye icon on the left side of a listed item to show or hide the region of interest in the 2D views of the current scene.
Click the 3D icon to show or hide the ROI in the 3D view of the current scene.
Click the color box to change the highlight color applied to the region of interest. You should note that the color box indicates the currently selected color, as well as the color with the selected opacity applied.
See Object List for more information about changing the visibility of an ROI, as well as renaming and copying ROIs.
Select a region of interest to view basic information about the ROI and its statistical properties (see Basic Properties and Statistical Properties) and access settings to modify its appearance in 2D and 3D views (see 2D Settings, Opacity and Color, and Clip). Right-click a region of interest to apply operations, access analysis functions, or to export the ROI (see ROI Pop-Up Menu).

See Object List for more information about changing the visibility of ROIs, as well as renaming and copying ROIs.

You can toggle the visibility and opacity of selected objects in 2D views with the available keyboard shortcuts (see Visibility and Opacity Toggles).

Basic Properties

The information available for a selected region of interest includes its geometry, size, and volume.

Basic properties
	Description
Width	Indicates the total number of pixels along the X-axis and its physical dimension*.
Height	Indicates the total number of pixels along the Y-axis and its physical dimension*.
Depth	Indicates the total number of pixels along the Z-axis and its physical dimension*.
Time steps	Indicates the size of the time (T) dimension.
Total voxels	Indicates the total number of voxels in the region of interest. Calculated as widthheightdepth*time steps.
Volume	Indicates the total volume occupied by the region of interest. Calculated as voxels*pixel size cubed.

* Calculated as pixels*spacing.

Statistical Properties

The information available for a selected region of interest includes the volume of all labeled voxels within the ROI, as well as the percentage of that volume within the shape that defines the geometry of the ROI. Other statistics include the minimum, maximum, and mean values of the labeled voxels that correspond to a selected dataset. You can also compare the volume of a selected region of interest with another ROI.

Statistical properties

ROI statistical properties
	Description
Labeled voxels	Indicates the total number of voxels that are labeled within the ROI.
Volume (labeled voxels)	Is the volume of all labeled voxels in the selected region of interest. Percentage volume… Is the comparative percentage of the volume of labeled voxels (all values that fall within the histogram) and the total number of voxels within the selected region of interest. The total number of voxels is calculated from the shape of the region of interest, and includes both labeled and unlabeled voxels.
Auto refresh	If selected, the number of labeled voxels and the volume of labeled voxels will be updated automatically whenever changes are made to the ROI. Refresh… Lets you manually update the number of labeled voxels and the volume of labeled voxels.
Surface (interpolated) Surface (Lorensen 1987)	Is the surface area of the labeled voxels in the selected region of interest, calculated with two methods. Surface (interpolated)… In this case, measurements of surface area are computed voxel-wise, i.e. the area of the exposed faces of voxels is summed. This method may perform poorly when evaluating curved and irregular discrete objects. Measurements provided by Surface (Lorensen 1987) may be more accurate. Surface (Lorenson 1987)… In this case, measurements of surface area are computed using the marching cubes algorithm, as described in William E. Lorensen, Harvey E. Cline, Marching Cubes: A High Resolution 3D Surface Construction Algorithm. ACM SIGGRAPH Computer Graphics, 21(4), July 1987, pp 163-169 (DOI:https://doi.org/10.1145/37402.37422). Click the Compute Surface button to compute the surface of the ROI.
Feret diameters*	Provides measurements of the size of the selected region of interest in an arbitrary direction. Min Feret diameter… Indicates the shortest distance between any two points along the boundary of the labeled voxels at an arbitrary angle, also known as minimum caliper diameter. Max Feret diameter… Indicates the longest distance between any two points along the boundary of the labeled voxels at an arbitrary angle, also known as maximum caliper diameter. Mean Feret diameter… Indicates the mean value of the Feret diameters over a sufficient number of orientations. In Dragonfly, measurements for the mean Feret diameter are taken every 5 degrees. Click the Compute Feret Diameter button to compute the Feret diameters of the selected region of interest.
Dataset	Allows you to extract statistics for the selected dataset. Values are calculated for the labeled voxels within the ROI that correspond with the image data. Min… Indicates the minimum intensity value and is expressed in the native units of the dataset. Max… Indicates the maximum intensity value and is expressed in the native units of the dataset. Mean… Indicates the mean value and is expressed in the native units of the dataset. Click the Refresh button to compute or update the dataset statistics. If Auto refresh is selected, information will be updated automatically whenever the selected region of interest is altered.
Comparative volume	Allows you to compare the volume of a selected ROI with the current region of interest. Click the Refresh button to compute or update the volume statistics. If Auto refresh is selected, information will be updated automatically whenever the selected region of interest is altered.
	Click the Copy to Clipboard button to copy the ROI statistical properties to your clipboard, which can then be pasted into another application.

* The Feret diameter, or Feret's diameter, is a measure of an object’s size in an arbitrary direction. This measurement, which can be defined as the distance between the two parallel planes restricting the object perpendicular to that direction, is also sometimes called the caliper diameter as it can refer to the measurement of object size with a caliper. This measure is often used in the analysis of particle sizes in microscopy, where the minimum Feret diameter can be used as the equivalent diameter in a sieve analysis.

Tools

You can use the Histogram tool that is available in the Tools box to visualize and analyze the distribution of intensity values of image data that corresponds to the labeled voxels of a region of interest (see Analyzing Histograms of Regions of Interest).

Tools

Tools box

2D Settings

The options in the 2D settings box, shown below, let you change the appearance of ROIs in the 2D views of the current scene.

2D settings

Show only contour… If checked, the highlight applied to the selected ROI will only appear as a contour. You can adjust the thickness of the contour with the Contour thickness slider.

Opacity and Color

The Opacity and color settings let you adjust the opacity of the highlight applied to the selected region of interest and apply a LUT in 2D and 3D views, as well as fine-tune some lighting settings in 3D views.

Settings for 3D Views

The Diffuse, Specular, Highlight, and Labeled data sliders in the Opacity and color box control how regions of interest appear in 3D views. You can also control the opacity of unlabeled voxels with the Global volume opacity slider on the Scene's Views Properties panel, as well as apply a LUT to the ROI.

Opacity and color settings for 3D views

3D opacity

For example, you can extract regions of interest so that only the ROIs are visible, or you can subtract regions of interest so that everything except the regions of interest is visible.

Extracted and subtracted region of interest

ROI highlighted in clipped rendering (left), ROI extracted by increasing the Highlight and Labeled data opacity and decreasing the Global volume opacity of unlabeled data (middle), ROI subtracted by setting the Highlight and Labeled data opacity to 0 and Global volume opacity to 100%.

You must make sure that the selected region of interest is visible in both the scene (Eye icon) and in the 3D view (3D icon) to control its appearance. The appearance of a region of interest, or multiple ROIs, can also be adjusted in the Opacity Settings dialog (see Opacity Settings).

Opacity and color settings for 3D views
	Description
Use LUT	If checked, the colors of the applied LUT will be mapped to the underlying dataset values. ROI with solid color highlight (left) and with LUT applied (right) Note You can select the required LUT by clicking the region of interest's color box in the Data Properties and Settings object list. LUTs will then be available in the LUT dialog.
Diffuse	Lets you vary the strength of diffuse light reflected from the surfaces of the region of interest and is a characteristic of light absorbed by surfaces. Increasing this property with the Diffuse slider will result in surfaces being more defined.
Specular	Lets you vary the strength of specular reflections originating from the surfaces of the region of interest and is a characteristic of light reflected from shiny surfaces. Increasing this property with the Specular slider will result in increased reflections.
Highlight	Adjusts the opacity of the colored highlight applied to the selected region of interest. At a value of 100%, the highlight will be fully opaque. At a value of 0%, the highlight will be transparent.
Labeled data	Adjusts the opacity of all image data that is visible in the view and that corresponds to the labeled voxels in the region of interest. At a value of 100%, labeled data will be fully opaque. At a value of 0%, labeled data will be transparent. Note Controls for adjusting the opacity of unlabeled data (Global volume opacity) is available on the Scene's Views Properties panel, as shown below, and in the Opacity Settings dialog (see Opacity Settings).

Clip

The tools in the Clip box, shown below, let you clip interactively along orthogonal planes of the selected region of interest in 3D views (see Clipping).

Clip box

You can also add and remove clipped regions from regions of interest (see Adding and Removing Clipped Regions), as well as use the Clip tool to crop a region of interest (see Cropping Datasets).

Visual Effects for Clipped Regions

The options in the Visual effects box, shown below, let you apply a selected visual effect or a combination of visual effects to the 3D view of a clipped region of interest (see also Visual Effects for Clipped Regions).

Visual effects

Visual effects box

The properties of the visual effects that can be applied to a region of interest are described in the following table.

3D effects
	Example	Description
Reference		Clip box and region of interest without any 3D effect applied.
Clip ROI		If selected, all data that corresponds to the region of interest will be clipped.
Opacity		If selected, the opacity of the data of that corresponds to the region of interest can be modified with the Opacity slider as shown below.
Window Leveling		If selected, new window level values can be applied to map color ramps (LUTs) to physical values (intensity) so the color map is physically representative of the image data. In this case, the highlight applied to the ROI will be removed automatically. The width of the window, its center value, and gamma value can be modified with the sliders, as shown below.