D RAGONFLY R ELEASE N OTESV ERSION 3.5

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Title
Dragonfly Release Notes
Release date2018.03.29
Reference number TM021-A-03

Object Research Systems (ORS) Inc. • 760 Saint‐Paul West, Suite 101 • Montreal (QC) H3C 1M4 • www.theobjects.com

Release Notes
Version 3.5
This document describes the new features, product enhancements, and otherimprovements implemented in the Dragonfly and Dragonfly Pro 3.5 software release.
You should read these release notes carefully before you install this new version.

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New Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5

Active Contour . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Overlay Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Shapes Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Shape Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Create a Structured Grid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Extract a Structured Grid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Modifying Regions of Interest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
New Features for Meshes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Mesh Decimator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Mesh Registration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Deviation Maps. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Map Scalar Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Copy Scalar Values. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Delete Scalar Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Sampling Rates for Generating Thickness Meshes . . . . . . . . . . . . . . . . 17
Export Meshes in VTK File Format . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
New Options for Regions of Interest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Interpolate ROI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Generate Contour Mesh. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
New Binary Image from ROI. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Invert . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Align Axis of Inertia . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Look at Center of Mass . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Visual Effects for Regions of Interest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
New Options for Multi‐ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Copy Scalar Values. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Delete Scalar Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Orthographic Projection Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Scale Bar for Orthographic Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Scene View Orientation Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

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4Auto Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
2D View Text Annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Advanced Options and New Filters for Image Processing . . . . . . . . . . . . . . 25
Advanced Options. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
New Filters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Default Output for Arithmetic Operations . . . . . . . . . . . . . . . . . . . . . . . 26
Modified Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
New Options for Image Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
New Dataset from Marked Slices . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Normalize Histogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Overwrite Dataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
New Options for Selected Objects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Align Centroids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Apply Transformations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Support for CZI Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Product Enhancements and Other Changes. . . . . . . . . . . . . . . . . . . . . .28

Updates for Aligning Image Slices. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Registration Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Selection Box Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Visual Effects for Clipped Regions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Measurement Inspector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
3D Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Scene’s Views Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Shadow Opacity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Auto Focus. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Points Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Auto Generate Caption . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Data Export . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Path Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Configurable Control Points for Annotation Tools . . . . . . . . . . . . . . . . . . . . 35
Additional Support for Time‐Enabled Data . . . . . . . . . . . . . . . . . . . . . . . . . 36
T Size for Importing Raw Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Navigation Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Export Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Visual Plane Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Support for 4K Displays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Developer Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Preferences Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .40
System Requirements Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .40

Extending Dragonfly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Getting Help. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Request a New Feature. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Dragonfly Release Notes

TM021-A-03

Menu Item Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .38

Release Notes Version 3.5
New Features

New Features

The 3.5 software release for Dragonfly and Dragonfly Pro provides the following newfeatures. For information about product enhancements and other changes, such as new
registration methods and other improvements for aligning slices in an image stack,visual effects for clipped regions, optimized lighting controls, and support for timeenabled data, see Product Enhancements and Other Changes on page 28.

Active Contour
You can use the new Active Contour tools to quickly and efficiently complete
segmentation tasks by adding a series of paths to the 2D views of volumetric image
data and then generating a mesh that fully describes the surface of the targeted featureof interest.
In the example below, a surface mesh was generated from the marked paths added tothe contour of the femoral head, neck, and top of the thigh bone. Marked paths areshown in orange, while the generated surface mash appears in blue.

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Surface mesh generated with the Active Contour tools

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56 Release Notes Version 3.5
New Features

Choose Tools > Active Contour on the menu bar to open the Active Contour panel,shown below.

Active Contour tab

The Active Contour panel includes tools to create a group of paths, draw paths in
Freehand or Snap mode, edit paths, and iterate selected paths.
You can generate a surface mesh that describes the segmentation target after therequired number of paths have been added to a group. Generated meshes are added
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automatically to the Data Properties and Settings panel.

Dragonfly Release Notes

Release Notes Version 3.5
New Features

Overlay Panel
Image and text overlays can now be added to 2D and 3D scene views to illustratefindings with text, graphs, screen captures, and other information. For example, you
can display a corporate or institutional logo as an image overlay over an animatedsequence and annotate key frames with titles and captions that describe importanttransitions.
3D view with image and text overlays

The overlays available on the Overlays panel, shown below, can be included in animatedsequences and screen captures and can be saved with a session or in the .ORSObject
file format.
Overlays panel

The following overlay options are available in Dragonfly 3.5.
Options for overlays

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Description
Image

Adds a selected image to the current scene view, such as a company or
institutional logo, graph, or image captured from Dragonfly. Images can beresized and positioned as required, and opacity is adjustable.

Text

Adds a text overlay to the current scene view. The text color, font face, size,
and alignment are selectable in the Overlay Editor and opacity is adjustable.
Text overlays can be resized and positioned as required.

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8 Release Notes Version 3.5
New Features

The options for editing overlays are available in the Overlay Editor, shown below.
Text Overlay Editor

Shapes Panel
This Dragonfly release features a new Shapes panel. Shapes are fully editablegeometrical forms that can be added to a scene to enhance 3D visualizations of selected
objects. The visual effects for shapes — boxes, capsules, cylinders, planes, and spheres— include clipping, edge contrast, fill, look-up table functions, and window leveling.
These effects can be applied to volumetric image data, regions of interest, multi-ROIs,
and meshes.
In the example below, multiple shapes with different effects — clip, edge contrast, anda look-up table — were applied to volumetric image data.

The visual effects that you create with the shapes available on the Shapes panel can be
included in animated sequences and in screen captures.
Shapes panel

Dragonfly Release Notes

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Shapes and visual effects

Release Notes Version 3.5
New Features

The different geometrical forms available in the Shapes panel — Box, Capsule, Cylinder,
Plane, and Sphere — are described in the table below.
Types of shapes
Description
Box

Creates a basic box-shaped object, or cuboid, that has six flat sides. All of its faces are rectangles and allof its angles are right angles.

You can resize and rotate the box, as well as change its position within a 2D or 3D view with the control
points.
CapsuleCreates a three-dimensional geometric shape consisting of a cylinder with two hemispherical caps oneach end.

You can increase or decrease the height and radius of the capsule, rotate it, as well as change its position
within a 2D or 3D view with the control points.

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CylinderCreates an object with two identical flat ends that are circular and one curved side. The cylinder has thesame cross-section from one end to the other.

You can increase or decrease the height and radius of the cylinder, rotate it, as well as change its position
within a 2D or 3D view with the control points.

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New Features

Description
Plane

Creates a flat, two-dimensional surface.

You can rotate the plane, as well as translate it with the handle.
SphereCreates a 3D object shaped like a ball, in which every point on its surface is the same distance from thecenter.

You can resize a sphere, as well as change its position within a 2D or 3D view.

Each shape that is created or imported appears on a separate line in the top section of
the Data Properties and Settings panel, as shown below. The bottom section contains alist of all available objects — volumetric image data, regions of interest, multi-ROIs, andmeshes — to which shape effects can be applied. You should note that it is possible toapply shape effects to multiple objects and to apply multiple effects simultaneously.

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Shape properties and settings

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Release Notes Version 3.5
New Features

The visual effects described below can be applied to data that corresponds either to theinside or outside of the selected shape.
Visual effects for shapes
ExampleDescription

Clip

If checked, the data of the selected visuals that corresponds to the insideor outside of the shape will be clipped.

Edge Contrast*

If selected, the intensity values of selected image data that correspond to
the inside or outside of the shape will be modulated with the values of
their gradient modulus to produce an image in which edges areemphasized and other features are semi-transparent.
The degree of contrast can be adjusted with the Contrast slider, as
shown below.

Fill**

If selected, voxels contained within the inside or outside of the shape will
be filled with a solid color.

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To select a fill color, click the color swatch and then choose a color in the
Color dialog.

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12 Release Notes Version 3.5
New Features

ExampleLookup Table andAbsolute LUT*

Description
If selected, a lookup table function (LUT) or an absolute LUT will beapplied to the image data of selected visual(s) that corresponds to theinside or outside of the shape. LUTs determine how regions within
specific arrays of intensity are highlighted and how color is applied.
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.
Window Leveling*

If selected, new window level values can be applied to the image data of
selected visual(s) that corresponds to the inside or outside of the shape.
The width of the window, as well as its center value, can be selected with
the Width and Center sliders, as shown below.

* Applicable to selected image data and image data corresponding to selected regions of interest and multi-ROIs.
** For selected image data, all voxels within the bounding box will be considered. For selected regions of interest and multi-ROIs, only labeledvoxels will be considered. For selected meshes, only voxels that correspond to the surface of the mesh will be considered.

In some cases, you may find it advantageous to apply multiple effects to selectedvisuals. For example, edge contrast, window leveling, and a look-up table. You shouldnote that Dragonfly applies selected effects in the order in which they appear in the
Effects panel. Reordering effects will have an impact on the final look of the visual by
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either subtly or dramatically changing its appearance.

Dragonfly Release Notes

Release Notes Version 3.5
New Features

You can reorder selected effects with the Up and Down buttons on the right side of thepanel, as shown below.
Reordering effects

Shape Options
A number of options — Create Structured Grid, Extract a Structured Grid, and Add/
Remove from a Region of interest — are available in the pop-up menu for shapes.

Create a Structured Grid

Creates a dataset (structured grid) from the subvolume defined by the box shape. The
dataset type created can be a channel, region of interest, or multi-ROI, and the input
data and geometry can be selected in the appropriate dialog — Create a Channel,
Create an ROI, or Create a Multi-ROI.
Create a Channel dialog

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Extract a Structured Grid

Extracts a dataset (structured grid) from the subvolume defined by the box shape andthe intersecting data values of a selected object.

Modifying Regions of Interest

The following options are available for modifying regions of interest with the shapes
available on the Shapes panel.

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14 Release Notes Version 3.5
New Features

Add to ROI… Adds all voxels contained in the subvolume defined by the current shape toa selected region of interest. You should note that only intersecting voxels will be added
to the region of interest.

Remove from ROI… Removes all intersecting voxels of the subvolume defined by theshape from the selected region of interest.

New Features for Meshes
A number of new options are available in Dragonfly 3.5 for working with meshes. You
can reduce the number of vertices, edges, and triangles in a mesh, register meshes to areference, manage scalar information, and select sampling rates for generating
thickness meshes from regions of interest. These new features are described in thefollowing topics.

Mesh Decimator

This Dragonfly release provides a Mesh Decimator, for cases in which you need toreduce the number of vertices, edges, and triangles in a mesh. Surface simplification is
one way to enable real-time, interactive visualization of large, complex meshes.
The example below illustrates a progressive mesh decimation.
Decimated meshes

Original mesh

Original mesh decimated by 50%

Original mesh decimated by 75%

Dragonfly’s new Mesh Decimator lets you choose a decimation method and a reduction
target. The overall shape, volume, and boundaries of the original mesh will bepreserved as much as possible during the simplification process.
Right-click the required mesh in the Data Properties and Settings panel and then choose

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Mesh Decimator in the pop-up menu to open the Mesh Decimator panel.

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Release Notes Version 3.5
New Features

Mesh Decimator panel

The following parameters are available for decimating meshes.
Parameters available for the Mesh Decimator
Description
Mesh

Indicates the currently selected mesh, to which the decimation will be applied. If required, you can selectanother mesh in the drop-down menu.

MethodTwo methods are available in Dragonfly to reduce the number of vertices, edges, and triangles in a mesh
— Pro decimation and Quadric decimation. These methods work by the iterative elimination ofcomponents identified through local geometric optimality criteria. You should note that both methods willattempt to preserve the overall shape, volume, and boundaries of the original mesh as much as possible.

Target decimator

Lets you set the target reduction as a percentage ([0,1]) of components to be removed. For example, if themesh contains 100 triangles and a Target Reduction of 0.90 is set, there will be approximately 10
triangles, a 90% reduction, after the decimation.
NOTE If the cost of removing a component is too high, then it will not be removed and the selected target
reduction may not be reached.

Create new mesh

Lets you choose an output target — at the input so that the original mesh is transformed, or at the output
so that a new mesh is created and the original remains unmodified.
NOTE Whenever possible, you should try to retain the original mesh so that you can compare the originaland reduced versions.

Mesh Registration

Dragonfly's new iterative closest point registration workflow can automatically register
meshes by applying the rotation and translation that best aligns the selected mesh witha reference. Right-click the required mesh in the Data Properties and Settings panel andthen choose Mesh Registration in the pop-up menu to open the Mesh Registration
panel, shown below.

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Mesh Registration panel

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16 Release Notes Version 3.5
New Features

Deviation Maps

For analysis and visualization purposes, you can compute and generate color-codedmeshes showing the deviation (distance) between the normals of two sets of meshes.
Referential values are color-mapped according to the applied look-up table (LUT) andthe type of distance map requested — signed or unsigned. Distance maps can be
examined in 3D and 2D views.
Deviation (distance) map measurements are added to the selected mesh and appear in
Scalar information box, as shown below.
Mesh scalar information

Map Scalar Values

This new option for Dragonfly 3.5, which is available in the Mesh pop-up menu, lets you
map selected measurements contained within a scalar mesh to another mesh or multiROI.
You can choose the scalar values you want to map to the selected mesh in the Choose ascalar value dialog, shown below.
Choose a scalar value dialog

NOTE Mapping for meshes to meshes is done with a closest face matching criteria, while
mapping for meshes to multi-ROIs is done through corresponding world coordinates.

Copy Scalar Values

This additional option for Dragonfly 3.5, which is available in the Mesh pop-up menu,
lets you copy selected measurements contained within a scalar mesh to another mesh.
You can choose the scalar values you want to copy to the selected mesh in the Choose ascalar value dialog, shown below.

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Choose a scalar value dialog

Dragonfly Release Notes

Release Notes Version 3.5
New Features

Delete Scalar Values

This new option for Dragonfly 3.5, which is available in the Mesh pop-up menu, lets you
delete selected measurements from scalar meshes.
You can choose the measurements you need to delete from a selected mesh in the
dialog shown below.
Choose a scalar value to delete dialog

Sampling Rates for Generating Thickness Meshes

For analysis and visualization purposes, Dragonfly can compute and generate colorcoded meshes that show the referential values of the local thickness between boundary
points. Thickness is calculated as the diameter of a hypothetical sphere that fits withineach boundary point.
As a new option for this software release, sampling rates for thickness meshes exported
from regions of interest are selectable.
Export options for thickness meshes

NOTE The use of simplified models is one way to enable real-time, interactive visualization oflarge, complex meshes.

Export Meshes in VTK File Format

This Dragonfly release provides the option to export meshes in the VTK file format.

New Options for Regions of Interest
A number of new options are available in Dragonfly 3.5 for working with regions ofinterest. You can interpolate 2D regions, align axes of inertia, generate contour meshes,and perform other functions. These new features are described in the following topics.

Interpolate ROI

The new Interpolate operation for regions of interest lets you interpolate 2D regions
through volumetric image data to create a 3D region of interest. You can choose theTM021-A-03

direction of the interpolation.
In the following example, a series of 2D regions were defined on a few slices in the XY
oriented view (on left) and then interpolated in the Z axis. The results of theinterpolation are shown on the right in an XZ oriented view.

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18 Release Notes Version 3.5
New Features

Interpolated region of interest

The Interpolate option for regions of interest, circled below, is available in the
Operations box on the ROI Tools panel.
Operations box

Generate Contour Mesh

In this Dragonfly release, you can generate contour meshes that describe the surface ofa region of interest in the Generate Contour Mesh panel.
In the following example, three contour meshes with different threshold values weregenerated from a region of interest created on the femoral head and neck of a thighbone.

The settings for generating contour meshes are available in the Generate Contour Meshpanel. Right-click the required region of interest in the Data Properties and Settings
panel and then choose Generate Contour Mesh to access the panel.

Dragonfly Release Notes

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Contour meshes (maximum threshold in white, mid in orange, minimum in blue)

Release Notes Version 3.5
New Features

Generate Contour Mesh panel

New Binary Image from ROI

Automatically creates a new dataset(s) in which the labeled voxels in the selected
region(s) of interest are assigned a value of 1 and unlabeled voxels are assigned avalue of 0.

InvertYou can now invert the voxels in a region of interest, or multi-ROI, and change theorder of axes in which they are read.
The settings for inverting regions of interest are available in the Dataset Inverter panel,shown below. Right-click the required region of interest in the Data Properties andSettings panel and then choose Invert to access the panel.
Dataset Inverter panel

Align Axis of Inertia

This new option, which is available in the Region of Interest pop-up menu, lets you
automatically align the axis of inertia of a selected region of interest with the axis ofinertia of another region of interest.

Look at Center of Mass
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The new option automatically aligns the center of mass of the selected region ofinterest in the current 2D scene views. You should note that the center of mass iscalculated from the labeled voxels contained within the bounding box of the region ofinterest.

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20 Release Notes Version 3.5
New Features

Visual Effects for Regions of Interest
This Dragonfly release includes a series of visual effects that can be applied to a regionof interest to enhance 3D visualizations of segmented features. Visual effects forregions of interest are available at the bottom of the Data Properties and Settings
panel, as shown below.
Visual effects for regions of interest

The visual effects available for regions of interest, and their associated properties, aredescribed in the following table.
Visual effects and properties for regions of interest
ExampleDescription

Original ROI

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

Clip

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

Edge Contrast

If selected, the intensity values of image data that correspond to the region ofinterest will be modulated with the values of their gradient modulus to produce animage in which edges are emphasized and other features are semi-transparent.

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The degree of contrast can be adjusted with the Contrast slider, as shown below.

Dragonfly Release Notes

Release Notes Version 3.5
New Features

ExampleFill

Description
If selected, voxels that correspond to the region of interest will be filled with asolid color.
To select a fill color, click the color swatch and then choose a color in the Colordialog.

LUT andAbsolute LUT

If selected, a lookup table function (LUT) or an absolute LUT will be applied toimage data that corresponds to the region of interest. LUTs and Absolute LUTs
determine how regions within specific arrays of intensity are highlighted and how
color is applied.
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 specificvalues 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.
Window LevelingIf selected, new window level values can be applied to image data that
corresponds to the region of interest.

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

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22 Release Notes Version 3.5
New Features

New Options for Multi‐ROIs
A number of new options are available in Dragonfly 3.5 for working with multi-ROIs. You
can copy scalar values from one multi-ROI to another, as well as delete scalar values.
These new features are described in the following topics.

Copy Scalar Values

This additional option for Dragonfly 3.5, which is available in the Multi-ROI pop-up
menu, lets you copy selected measurements contained within a multi-ROI to anothermulti-ROI.
You can choose the object that includes the scalar values you want to copy to theselected multi-ROI in the Choose a scalar value dialog.
Choose a scalar value dialog

Delete Scalar Values

This new option for Dragonfly 3.5, which is available in the Multi-ROI pop-up menu, lets
you delete selected measurements from multi-ROIs.

Orthographic Projection Mode
Dragonfly now offers the opportunity to view objects in both perspective andorthographic projection modes. In the familiar and default perspective mode, objects
are subject to foreshortening and will appear smaller as their distance from the camera
increases. In the parallel projection of orthographic mode, there is no foreshortening or
vanishing point and dimensions can be communicated unambiguously.
Although perspective viewpoints can provide more information about depth and often
tend to appear more realistic, orthographic viewpoints can make it much easier tocompare objects, such as the parts of a molecule, as there is no question about how theviewpoint may affect the perception of distance or size. In addition, a scale bar is

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available for orthographic views.

Dragonfly Release Notes

Release Notes Version 3.5
New Features

Perspective (on left) vs. orthographic (on right) projections

While working, you can easily switch between orthographic and perspective modes to
get a better sense of an object. Orthographic projection mode is selectable on the
Scene’s Views Properties panel and in the pop-up menu for 3D views. You can alsochoose Orthographic as the default projection mode (see 3D Views Preferences on
page 40).

NOTE Some lighting controls, such as shadowing and material properties, are not available fororthographic projections.

Scale Bar for Orthographic Views

A floating scale bar is available for 3D views showing orthographic projections to show
the relative size of an object. If required, you can re-position the scale bar by dragging
it anywhere inside the view, as well as set its length.

Scene View Orientation Panel
The options in the new Scene View Orientation panel, shown below, let you view andprecisely adjust the angles of rotation — Yaw, Pitch, and Roll — of a selected 2D or 3D
view, as well as to modify the position of the camera. Additional options for 2D views let
you navigate to the different slices contained in volumetric image data.

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Scene View Orientation panel

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24 Release Notes Version 3.5
New Features

Auto Processing
The Auto Process Stack feature for Dragonfly 3.5 enables real-time automatic
processing of serial section 2D stack experiments. Instead of having to wait for theentire image stack to be available, you can set required operations — such as filtering,
registration, classification, or any operation saved in a macro — to be applied
automatically to new images as they arrive and interactively monitor the results as the3D image channel grows.
Choose Tools > Auto Process Stack to open the Auto Process Stack panel.
Auto Process Stack panel

It’s possible to indicate the time interval at which you’d like to have Dragonfly check for
new images, as well as to select tasks that have been saved from previous jobs.
Applicable tasks include classification with a saved classifier, slice alignment with
Dragonfly’s powerful matching methods, image filtering, and operations saved in amacro file.
When you’re ready, simply click the Start the Auto Process button. As new images

become available in the monitored folder, Dragonfly will process then according to thedefined parameters and integrate them into a 3D image channel that can be volume

NOTE This feature is available only for TIFF images and for operations that use a single

channel. All images must have the same pixel size and the same matrix dimensions.

NOTE The Auto Process Stack feature is not included in the standard Dragonfly installer.
Contact Object Research Systems to request a copy of this module.

Dragonfly Release Notes

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rendered with a lookup table (LUT). If necessary, image stacks can be re-processed.

Release Notes Version 3.5
New Features

2D View Text Annotations
This Dragonfly release includes additional text annotations for rotating 2D scene viewsaround its Z axis (Roll) and for navigating between the time steps of time-enabled
image data. These text annotations are circled below.
Text annotations for 2D views

Advanced Options and New Filters for Image Processing
A number of new options and filters are available in Dragonfly 3.5 for processing image
data.

Advanced Options

The Advanced Options for image processing let you process multi-scale images inselected operations, as well as select different geometries and data types for yourimage processing outputs. You should note that multi-scale images are images withdifferent geometries and/or image spacing.
To enable the Advanced Options, check Advanced Options in the Operations box, as
shown below.

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Advanced Options for image processing

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26 Release Notes Version 3.5
New Features

New Filters

The following new filters are available in this software release.

Frangi Filter… The newly added Frangi filter is typically used to detect vessel-like or
tube-like structures and fibers in volumetric image data. The screenshots below

demonstrate the results of applying the Frangi filter to the image data of lung tissue ona coronary computed tomography (CT) scan.
Original image in MIP mode (left) and result after processing with Frangi filter (right)

Frequency Domain Filters… Two new filters, Discrete Fourier Transform and Inverse
Discrete Fourier Transform, are available for working in the frequency domain.

Gradient and Divergence Filters… Available for Arithmetic operations, these filters aredesigned to extract information from images. The Gradient filter shows how quickly
intensity values change from pixel to pixel, while the Divergence filter, which is theinverse of the Gradient filter, indicates minor gray scale variations.

Default Output for Arithmetic Operations

With this software release, all calculations and the default output for arithmetic
operations are automatically set to the float data type. There is no longer any need toformat operations with a decimal, such as 2.0*A, to avoid wrapping. You should notethat if you select integer as the output data type, calculations will still be done in float,
but results may be clipped.

Modified Filters

Two previously available filters for detecting edges — Prewitt and Scharr — now default

to a combined mode, in which horizontal and vertical edges are extracted. You shouldnote that options for detecting horizontal and vertical edges separately are still available
for these filters.

New Options for Image Data
New functions are available in Dragonfly 3.5 for extracting datasets from marked slices,

New Dataset from Marked Slices

Lets you extract a new dataset from the marked image slices of volumetric image data.

Normalize Histogram

Lets you normalize the histogram of a selected dataset to the histogram of anotherdataset.

Dragonfly Release Notes

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normalizing image data to a reference, and overwriting dataset values.

Release Notes Version 3.5
New Features

Overwrite Dataset

Lets you overwrite the intersecting values of a selected dataset with the values ofanother dataset.

New Options for Selected Objects
The following new options are available for image data, regions of interest, multi-ROIs,
and meshes in the Data Properties and Settings panel pop-up menus.

Align Centroids

This pop-up menu item lets you automatically align the centroid of the selected object
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
Choose the object to align with dialog, as shown below.
Choose the object to align with dialog

Apply Transformations

To help maintain consistency when you work with multiple objects, you can apply thetransformations, such as translations and rotations, that were applied to a reference
object to another object. You should note that only objects that were translated and/or
rotated, will be available in the Choose an object dialog as the reference.
Choose an object dialog

Support for CZI Files
This software release provides support for importing and visualizing CZI files, a format
used by ZEISS microscopes to save data, such as image stacks and time lapse series.
Available for Dragonfly Pro only. Contact Object Research Systems for information

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about the availability of Dragonfly Pro.

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28 Release Notes Version 3.5

Product Enhancements and Other Changes

Product Enhancements and Other Changes

This release provides the following product enhancements for Dragonfly and Dragonfly
Pro. For information about new features, such as the Active Contour tools, overlays, andshapes, see New Features on page 5.

Updates for Aligning Image Slices
This Dragonfly release provides a number of powerful new options and tools forproperly aligning an image stack into a correct 3-dimensional model that ensuresaccurate image processing and analysis.
Choose Dataset Slices Registration in the Data Properties and Settings pop-up menu to

open the Slice Registration panel shown below.

Registration Methods

The following additional registration methods are available in this Dragonfly 3.5
software release.

Enhanced Correlation Coefficient… Implements an area-based alignment that builds on
intensity similarities.

Dragonfly Release Notes

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Slice Registration panel

Release Notes Version 3.5
Product Enhancements and Other Changes

Feature Base… Matches features between image slices by detecting corners, which areregions in the image with large variations in intensity in all directions. The preview for
Feature Base comparisons, shown below, stacks two images horizontally and draws
lines from the first image (the currently displayed slice in the workspace) to the next

slice and shows the best matches for the number of features requested for the preview.
Preview for Feature Base registration

Template Matching… Provides a method for searching for and finding the location of atemplate image in the larger images within the 3D image stack. This registration

method simply slides the template image over the input image (as in 2D convolution)and compares the template and patch of input image under the template image.
The preview for template matching, shown below, returns a grayscale image, in which
each pixel denotes how much the neighborhood of that pixel matches with thetemplate.

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Matching result for a detected template

Selection Box Options

A number of new options are available for the selection box, which provides a mask forthe registration inputs.

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30 Release Notes Version 3.5

Product Enhancements and Other Changes

Follow Template… The Follow Template option for selection boxes lets you add atemplate that will be applied to subsequent slices during processing. It is a type offloating selection box.
Template Matching option

Selectable Slice Ranges… The options in the Slice Range box, shown below, let you

select a range of images within the stack to which required transformations will becomputed. You should note that any transformation applied to the last slice in the range
will also be applied to the remaining slices in the image stack.
Slice Range option

Visual Effects for Clipped Regions
The Clip tool allows you to interactively clip image data, regions of interest, multi-ROIs,
and meshes along orthogonal planes in 3D views. This Dragonfly release introduces
additional visual effects, such as look-up table functions, edge contrast, and windowleveling, that can be applied to the clipped region of selected objects.
Visual effects for clipped regions are available on the Clip panel, as shown below.
Visual effects for clip boxes

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The following effects can be applied to the currently checked object or objects.

Dragonfly Release Notes

Release Notes Version 3.5
Product Enhancements and Other Changes

Clip effects and properties
ExampleClip

Description
If selected, the data of selected visual(s) that corresponds to theinside or outside of the Clip box will be clipped.
NOTE In this Dragonfly release, Clip is applied as the default setting
applied to volumetric image data, regions of interest, multi-ROIs, andmeshes. You may have to remove this visual effect when you create
exploded views.

Edge Contrast*

If selected, the intensity values of selected image data that
corresponds to the inside or outside of the Clip box will be modulatedwith the values of their gradient modulus to produce an image inwhich edges are emphasized and other features are semitransparent.
The degree of contrast can be adjusted with the Contrast slider, as
shown below.

Fill**

If selected, voxels contained within the inside or outside of the Clip
box will be filled with a solid color.

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To select a fill color, click the color swatch and then choose a color in
the Color dialog.

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32 Release Notes Version 3.5

Product Enhancements and Other Changes

ExampleLUT andAbsolute LUT*

Description
If selected, a lookup table function (LUT) or absolute LUT will beapplied to selected data that corresponds to the inside or outside of
the Clip box. LUTs determine how regions within specific arrays ofintensity are highlighted and how color is applied.
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 mappedto specific values will be retained whenever leveling values arechanged. For regular LUT functions, colors will be remapped to therange of values defined by the window width.
Window Leveling*

If selected, independent window level values can be applied to thedata of selected visual(s) that corresponds to the inside or outside of
the Clip box.
The width of the window, as well as its center value, can be selectedwith the Width and Center sliders, as shown below.

* Applicable to selected image data and image data corresponding to selected regions of interest and multi-ROIs.

TM021-A-03** For image data, all voxels within the bounding box will be considered. For regions of interest and multi-ROIs, only labeled voxels will beconsidered. For meshes, only voxels that correspond to the surface of the mesh will be considered.

Dragonfly Release Notes

Release Notes Version 3.5
Product Enhancements and Other Changes

Measurement Inspector
The Measurement Inspector available for multi-ROIs and scalar meshes now includes a
Measurement range selector, circled below, that lets you select the range of data thatwill be plotted in the histogram.
Measurement Inspector

Options in the Measurement range box also let you copy the range of othermeasurements, either from the current multi-ROI or another multi-ROI, to the currently
selected measurement. You can also reset the range to the original values.

Export Options… Additional updates to the Measurement Inspector include Export

options in the In window and Out window rendering boxes, which let you create a new
multi-ROI that includes all of the labeled objects that correspond to the selected range.

3D Settings
This Dragonfly release includes a new setting — Hard gradient — for modifying theappearance of volumetric image data in 3D views. This option, circled below, isavailable in the 3D settings box on the Data Properties and Settings panel.

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3D settings

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34 Release Notes Version 3.5

Product Enhancements and Other Changes

Scene’s Views Properties
In addition to accelerated rendering that lets you to easily combine 3D renderings,
regions of interest, and meshes in the same 3D view, this Dragonfly release also
features new lighting controls and an auto-focus option.
These updates, circled below, are available on the Scene’s Views Properties panel.
Scene’s views properties for 3D views

Shadow Opacity

Lets you adjust the opacity of shadows cast on and by objects in 3D views.

Auto Focus

An Auto focus option is now available for automatically optimizing the focus of theTM021-A-03

camera within a 3D view.

Dragonfly Release Notes

Release Notes Version 3.5
Product Enhancements and Other Changes

Points Tool
A number of updates — Auto generate caption and Export — are available for the Points

tool in this software release.

Auto Generate Caption

Lets you automatically generate captions that show the position or value of each point
added to 2D and 3D views.
Options for generated captions

Data Export

Lets you export Points data in the CSV file format.

NOTE The new options for the Points tool also includes configurable control points (seeConfigurable Control Points for Annotation Tools on page 35).

Path Tool
Options for the Path tool now include the function to profile intensity along the fulllength of a selected path. The resulting profile intensity graph indicates the maximum,
minimum, and mean data values along the path.

NOTE The new options for the Path tool also includes configurable control points (seeConfigurable Control Points for Annotation Tools on page 35).

Configurable Control Points for Annotation Tools
You can now modify the appearance of the control points of an annotation by selecting
their size and style. These options, which are applicable to rulers, angles, regions, andpoints, are available in the Data Properties and Settings panel as shown below.

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Annotation properties

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36 Release Notes Version 3.5

Product Enhancements and Other Changes

Additional Support for Time‐Enabled Data
This Dragonfly release features additional support for importing and examining timeenabled data.

T Size for Importing Raw Data

For time-enabled data you can now enter the number of time steps in the T edit box,
circled below. You should note that changing the number of time steps willautomatically adjust the size of the image stack (Z axis).
Import Datasets dialog

Navigation Tools

This Dragonfly release includes additional options for navigating through time-enabled
datasets. These include a Time Step text annotation (see 2D View Text Annotations on
page 25) and a spin box, circled below, for moving between different time steps.

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2D Scene’s Views Properties panel

Dragonfly Release Notes

Release Notes Version 3.5
Product Enhancements and Other Changes

Export Options
The export options for the .ORSObject file format now let you choose to export multiple
objects as separate files or to include them in a single file.

Visual Plane Panel
A number of modifications were made to the Visual Plane panel, shown below.
Visual Plane panel

In this Dragonfly release, Visual Planes will appear in the Data Properties and Settings
panel, where you can control the visibility of a visual plane and add effects such as clip,edge contrast, window leveling, and others (see Shapes Panel on page 8 for more
information about planes).

Support for 4K Displays
This software release features additional support for users who choose to work with 4K
displays.

Developer Documentation
The developer documentation for Dragonfly has been updated for version 3.5. Choose

Help > Dragonfly Developer Documentation on the menu bar to open theTM021-A-03

documentation system.

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38 Release Notes Version 3.5
Menu Item Changes

Menu Item Changes

The following changes and new menu items are implemented for Dragonfly 3.5.

Menu Bar Items

A number of new items, listed below, have been added to the File, Tools, and Developer
menus.
New menu bar items
Description
File menu
Open Plugins

Lets you directly access Dragonfly plugins from a drop-down menu.

Tools menu
Active Contour

Opens the Active Contour panel (see Active Contour on page 5).

Execute DOS CommandOpens the Command dialog, in which you can enter common DOS commands.

Developer menu
Instance Observer

Opens the Instance Observer panel. Refer to the Dragonfly developer documentation for more
information about the Instance Observer.

Profiler

Opens the Profiler panel, in which you can wrap a method dynamically and monitor the timing of an
operation. Refer to the Dragonfly developer documentation for more information about the Profiler.

Dataset Pop‐Up Menu

A number of new items, listed below, and other changes have been implemented for thedataset pop-up menu. These are listed below.
Dataset pop‐up menu changes
Description
Apply Registration to Other
Dataset(s)Lets you apply the transformations used to register a dataset to another dataset.

Align Centroid With

Lets you align the centroid of the selected dataset with a reference object (see Align Centroids on
page 27).

Apply Transformation From

Lets you apply transformations, such as translations and rotations, that were applied to a reference object
to the selected dataset (see Apply Transformations on page 27).

New Dataset from Marked
SlicesLets you extract a new dataset from marked image slices (see New Dataset from Marked Slices on
page 26).

Normalize Histogram

Lets you normalize the histogram of a selected dataset to the histogram of a reference dataset (seeNormalize Histogram on page 26).

Overwrite Dataset

Lets you overwrite the intersecting values of a dataset with the values of another dataset (see Overwrite
Dataset on page 27).

Annotation Menu

A number of new items, listed below, and other changes have been implemented for the

Annotation pop‐up menu changes
Description
Apply Transformation From

Dragonfly Release Notes

Lets you apply transformations, such as translations and rotations, that were applied to a reference object
to the selected annotation (see Apply Transformations on page 27).

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annotation pop-up menu. These are listed below.

Release Notes Version 3.5
Menu Item Changes

Region of Interest Menu

A number of new items, listed below, and other changes have been implemented for theregion of interest pop-up menu. These are listed below.
Region of interest pop‐up menu changes
Description
InvertLets you invert the axis representation(s) and values of a region of interest (see Invert on page 19).

Generate Contour Mesh

Lets you generate a contour mesh from a region of interest (see Generate Contour Mesh on page 18).

Align Centroid With

Lets you align the centroid of the selected region of interest with a reference object (see Align Centroids
on page 27).

Apply Transformation From

Lets you apply transformations, such as translations and rotations, that were applied to a reference object
to the selected region of interest (see Apply Transformations on page 27).

Create a Signed Distance
Map

Lets you create a signed distance map, in which the deviation between two regions of interest is shown asa colored map.

Align Axis of Inertia

Lets you align the axis of inertia of a region of interest with another ROI (see Align Axis of Inertia on
page 19).

Look at Center of Mass

Lets you automatically align the center of mass of a region of interest in the views of a scene (see Look atCenter of Mass on page 19).

New Binary Image from ROI

Automatically creates a new dataset(s) in which the labeled voxels in the selected region(s) of interest areassigned a value of 1 and unlabeled voxels are assigned a value of 0.

Resample Geometry

Was previously named Resample Shape.

Multi‐ROI Menu

A number of new items, listed below, and other changes have been implemented for themulti-ROI pop-up menu. These are listed below.
Multi‐ROI pop‐up menu changes
Description
InvertLets you invert the axis representation(s) of a multi-ROI (see Invert on page 19).

Delete Selected Scalar
ValuesLets you delete scalar measurements from a multi-ROI (see Delete Scalar Values on page 22).

Copy Scalar Values From

Lets you copy scalar values from one multi-ROI to another (see Copy Scalar Values on page 22).

Align Centroid With

Lets you align the centroid of the selected multi-ROI with a reference object (see Align Centroids on
page 27).

Apply Transformation From

Lets you apply transformations, such as translations and rotations, that were applied to a reference object
to the selected multi-ROI (see Apply Transformations on page 27).

Resample Geometry

Was previously named Resample Shape.

Mesh Pop‐Up Menu

A number of new items, listed below, and other changes have been implemented for the
pop-up menu for meshes. These are listed below.

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Mesh pop‐up menu changes
Description
Mesh Decimator

Lets you reduce the number of vertices, edges, and triangles in a mesh (see Mesh Decimator on
page 14).

Mesh Registration

Lets you register a mesh with a reference (see Mesh Registration on page 15).

Signed Deviation Map

Lets you create a signed distance map, in which the deviation between two meshes is shown as a coloredmap (see Deviation Maps on page 16).

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40 Release Notes Version 3.5
Preferences Changes

Description
Deviation Map

Lets you create a distance map, in which the deviation between two meshes is shown as a colored map(see Deviation Maps on page 16).

Delete a Scalar Value Slot*

Lets you delete selected measurements from scalar meshes (see Delete Scalar Values on page 17).

Map Scalar Values From

Lets you map scalar values contained in a mesh or multi-ROI to the selected mesh (see Map Scalar
Values on page 16).

Copy Scalar Values From

Lets you map scalar values contained in a mesh to the selected mesh (see Copy Scalar Values on
page 16).

Align Centroid With

Lets you align the centroid of the selected mesh with a reference object (see Align Centroids on page 27).

Apply Transformation From

Lets you apply transformations, such as translations and rotations, that were applied to a reference object
to the selected mesh (see Apply Transformations on page 27).

* Available only for meshes with scalar values.

Preferences Changes

Colors Preferences

Changes for the Colors preferences are indicated in the following table.
Colors preferences
Description
Shape lines

Lets you select the colors for selected and unselected shape lines (see Shapes Panel on page 8).

3D Views Preferences

A new set of preferences are available in this Dragonfly release for 3D views.
3D Views preferences
Description
Default to orthographic
perspective

If selected, 3D scene views will appear in Orthographic Projection mode by default (see Orthographic
Projection Mode on page 22).

Additional preferences changes are summarized below.

Configured Actions

The Configured Actions preferences now include a description of their associated state.

System Requirements Changes

This release supports the base system requirements. Any differences in thoserequirements are noted below.
System requirements changes
Changes to system requirements

3.0.0

None.

3.1.0

None.
NOTE Dragonfly 3.1 includes a new Anaconda distribution for Python. You should note that the current
version of Python accessed by Dragonfly will be updated automatically to version 3.6 when you install thisnew release.

3.5.0

Dragonfly Release Notes

None.

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VersionRelease Notes Version 3.5
Extending Dragonfly

Extending Dragonfly

Dragonfly’s Infinite Toolbox, an open exchange platform for the Dragonfly user
community, lets you submit, browse, and download extensions that implement newfeatures and workflows for all of your image processing or analysis needs.
Choose Tools > Infinite Toolbox on the menu bar to open Dragonfly’s Infinite Toolbox.

Getting Help

Learning Dragonfly
Just by taking a quick look around www.theobjects.com/dragonfly, you’ll find somegreat free resources, such as our latest instructional videos, recorded webinars, anduser forums.

Reporting Issues
Dragonfly includes an integrated reporting module that lets you include comments andother information along with generated DMP and log files whenever you encounter anissue that results in a crash or application freeze.
Send Report to ORS dialog

You should note that you can also report an issue at any time by choosing Help >Report an Issue on the menu bar.

Request a New Feature
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Let us know if you have a suggestion for a new feature, or an idea for an improvement
to an existing workflow.

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Dragonfly Release Notes