ROI Properties and Settings

Each region of interest that is created or imported appears on a separate line in the top section of the Data Properties and Settings panel. You can control the visibility of a region of interest within a scene with the icons available in the top section of the panel, extract information about the selected region of interest, as well as access opacity settings and tools in the lower section. A pop-up is also available that provides access to additional tools for processing regions of interest (see ROI Pop-Up Menu).

ROI properties and settings

ROI Properties and Settings panel

A. List of ROIs B. Basic properties C. Statistical properties D. Tools E. 2D settings F. 2D opacity G. 3D opacity H. Clip

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 currently selected scene. Click the 3D icon to show or hide the ROI in a 3D view. 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 Opacity, 3D Opacity, 2D Settings, and Clip).
  • Right-click a region of interest to apply operations, access analysis functions, or to export the ROI (see ROI Pop-Up Menu).
The arrangement of objects in the Data Properties and Settings list determines the order of visibility in a view. Objects at the top of the list, such as regions of interest, are displayed over like objects that are lower down (see Object List for more information).
You can toggle the visibility and opacity of selected objects in 2D views with the available keyboard shortcuts (see Visibility and Opacity Toggles).

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 width*height*depth*time steps.
Volume (total voxels) Indicates the total volume occupied by the region of interest. Calculated as voxels*pixel size cubed.

* Calculated as pixels*spacing.

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

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.

Surface (interpolated)

Is the surface area of the labeled voxels in the selected region of interest, calculated with the Fast Marching method.

Click the Compute Surface button to compute the interpolated surface.

Feret diameters*

Provides measures 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.

The option to create histograms of regions of interest are available in the Tools box (see Plotting Histograms).

Tools options

Tools box

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

If the Show only contour item is checked, the highlight applied to the selected ROI will only appear along the contour of the region of interest.

Use the Highlight slider, shown below, to adjust the opacity of the colored highlight applied to labeled voxels in 2D views.

2D opacity settings

2D opacity

The Highlight and Labeled data sliders in the 3D opacity box, shown below, 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.

3D opacity settings

3D opacity

You can change the highlight applied to a region of interest, 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.

3D opacity and Global volume opacity

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 opacity. The appearance of a region of interest, or multiple ROIs, can also be adjusted in the Opacity Settings dialog (see Opacity Settings).
3D opacity settings
  Description

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).

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

Clip box

Additional options let you apply visual effects to clipped regions (see Visual Effects for Clipped Regions). 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).

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 region of interest.

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.

Visual effects and properties
  Example Description

Original ROI

Included for reference purposes. This is the original appearance of the region of interest, with a highlight applied.

 

Look-up tables

If selected, a look-up table (LUT), cyclical, or an absolute look-up table function will be applied to image data that corresponds to the region of interest. LUT functions determine how regions within specific arrays of intensity are highlighted and how color is applied (see Using the LUT Editor).

Look-up tables can be selected in the drop-down menu, as shown below.

Note If you choose an absolute LUT, color mapping will be applied independently of window leveling. This means that the colors mapped to specific values will be retained whenever leveling values are changed. For regular LUT functions, colors will be remapped to the range of values defined by the window width.

Clip

If selected, all data that corresponds to the region of interest will be clipped.

Window Leveling

If selected, new window level values can be applied to image data that corresponds to the region of interest.

The width of the window, as well as its center value, can be selected with the Width and Center sliders, as shown below.

In some cases, you may find it advantageous to apply multiple effects to a visual or visuals. For example, edge contrast, window leveling, and a look-up table. You should note that when rendering a visual, Dragonfly will apply the selected effects in the order in which they appear in the Effects panel. If required, you can reorder selected effects with the Up and Down buttons on the right side of the panel, as shown below. Reordering effects will have an impact on the final look of the visual by either subtly or dramatically changing its appearance.

Reordering effects

You may need to adjust an effect property after reordering selected effects.