D RAGONFLY 2020.1
R ELEASE N OTESCOPYRIGHT© 2020 Object Research Systems (ORS) Inc. All rights reserved.
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Portions of Dragonfly’s 3D engine licensed from the University of Münster.
Dragonfly is intended for research use only. It is NOT a medical device.

Title
Dragonfly Release Notes
Release date2020-05-20
Reference number TM021-A-07

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

Contents
This document describes the new features, product enhancements, and otherimprovements implemented in the Dragonfly and Dragonfly Pro 2020.1 software
release. You should read these release notes before you install this new version.

New Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7

Next Generation Rendering Engine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
New Rendering Capabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Correlative Workflows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Enabling the New Engine and Setting Defaults. . . . . . . . . . . . . . . . . . . . . . . . . 10
Scene's Views Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3D Presets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
3D Settings Panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Segmentation Wizard. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Key Features and Benefits. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Input Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Models Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Settings Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Bone Analysis Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Bone Analysis Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Plug Analysis Wizard. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Plug Analysis Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Plug Measurements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Plug Porosity Slice Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Pore Network Modeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

CT Reconstruction Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Reconstruction Algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Pre and Post‐Processing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

TM021-A-07

MC X‐Ray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
New Options for Multi‐ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Background Class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Scalar Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Labeling Multi‐ROIs with the Painter Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Options for Selected Classes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Creating New Multi‐ROIs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Creating Dense Multi‐ROIs from ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Creating Dense Multi‐ROIs from Multi‐ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . 30
2D Watershed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Creating Images from Selected Scalars. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Object Research Systems

4 Contents

New Features and Product Enhancements

Measurements for 2D Multi‐ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Tortuosity Distributions for Graphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Plotting Tortuosity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Plotting Throat‐Weighted Tortuosity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Computing Shortest Distances on Graphs . . . . . . . . . . . . . . . . . . . . . . . . . 33
Configured Actions for Computing Shortest Distances. . . . . . . . . . . . . . . . . . . . 34

Import Graph from CSV . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Probing Graph Scalar Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Scalar Values for Meshes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Translation for Scalar Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Image Filtering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Apply to Selected Slices Only . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Additive Noise Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Find Path Between ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Euler Characteristic Number . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Structured Grids Comparator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Processed Image Comparator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Segmentation Comparator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Distributed Tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Creating Image Masks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Auto Synchronization Between 2D and 3D Views . . . . . . . . . . . . . . . . . . . . 42
Import Images from Hitachi SEM. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Export Images as DICOM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Exporting Screenshots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Export Screenshots from Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Export Screenshots with Transparent Backgrounds. . . . . . . . . . . . . . . . . . . . . . 44

Export Meshes with Color . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Context Groups. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Widget Observer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Configured Actions for the Widget Observer . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Product Enhancements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .47

Refactored Menu Bar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Deep Learning Improvements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

New Class Pattern . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Class Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Multi‐Input and Multi‐Slice Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Training . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Selectable GPU for Deep Learning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

Improvements for Machine Learning Segmentation . . . . . . . . . . . . . . . . . . . 52

Constrain Ellipse Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Custom Captions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

Additional Options for Shapes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Selectable Sizes and Orientation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Extract Structured Grids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

Dragonfly Release Notes Version 2020.1

TM021-A-07

Edit Deep Model Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Automated Segmentations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Dataset Sampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Export Histogram Data in CSV . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Changes for Annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

Contents
New Features and Product Enhancements

Application of 3D Visual Effects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Scene’s Views Properties Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
3D Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Updates for the Organizer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Organizer Preferences. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Pop‐Up Menu Items . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

Managing User Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Licensing for Optional Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Academic Licensing Requests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Proxy Server Settings for License Activations . . . . . . . . . . . . . . . . . . . . . . . 61
Mapping for Configured Actions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Developer Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

Menu Bar Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .63

File Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Workflows Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Artificial Intelligence Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Utilities Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Developer Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Help Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Changes to Contextual Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .66

Data Properties and Settings Panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Dataset Pop‐Up Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Annotation Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
ROI Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Multi‐ROI Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Mesh Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Shape Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Vector Field Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Graph Pop‐Up Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

Views Pop‐Up Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Preferences Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Views Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Configurable Actions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Miscellaneous . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Organizer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73

Changes to the System Requirements. . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

Extending Dragonfly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73

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Requesting New Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73
Getting Help. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .74

Learning Dragonfly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Dragonfly Workshops . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

Reporting Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

Object Research Systems

56 Contents

New Features and Product Enhancements

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Dragonfly Release Notes Version 2020.1

New Features
Next Generation Rendering Engine

New Features

The 2020.1 software release for Dragonfly and Dragonfly Pro provides the following
new features. See Product Enhancements on page 47 for information about all theenhancements for Deep Learning, Machine Learning, and automated segmentation, as
well as improvements for managing user data and projects.

Next Generation Rendering Engine
Bring your real-world materials to life and produce stunning renderings for animatedsequences and publication-quality images. The 2020.1 Dragonfly software release
introduces the next generation of 3D rendering for the high-definition visualization ofscientific and industrial data. More powerful than ever, Dragonfly's new renderingengine delivers faster ray tracing, cleaner sampling, and more accurate lighting andshadowing — all within automated steps that save you valuable time.
In addition, the new engine’s interactivity controls for balancing performance and speed
for different quality graphic cards let you quickly amend scenes, adjust lighting and focus,
and change material properties. Below are just a couple of examples of the renderingresults you can expect in the Dragonfly 2020.1 software release.
Previous results (on left) and with Dragonfly’s new rendering engine (on right)

TM021-A-07

Soybean sample. Data courtesy of Keith Duncan (Donald Danforth Plant Science Center).

Detail of wooden gothic prayer bead. Data courtesy of the University of Western Ontario.

Object Research Systems

7

8 New Features

Next Generation Rendering Engine

New Rendering Capabilities
Below are some examples of the new capabilities for visualizing regions of interest andfor combining regions of interest with graphs. You should note that this renderingengine does not require image data to show an ROI in a 3D view.
New rendering capabilities for regions of interest and other objects

TM021-A-07

Segmented ceramic matrix composite. Courtesy of Aly Badran (University of Colorado).

Segmented solid oxide fuel cell with three‐phase boundary graph. Courtesy of Aaron Stebner(Colorado School of Mines).

Dragonfly Release Notes Version 2020.1

New Features
Next Generation Rendering Engine

Below is an additional example of the capabilities of the new rendering engine for
combining multiple objects in a single 3D view.
Thickness meshThickness mesh of an induced fracture in Berea sandstone core. Courtesy of Zuleima Karpyn, Penn
State University. Dataset available on the Digital Rocks portal (https://www.digitalrocksportal.org/).

Correlative Workflows
User who apply several microscopy techniques to single samples should notice that
correlative workflows with the new rendering are greatly improved. Challenges for
rendering low and high resolution datasets with large size differences at acceptablespeeds have been addressed and resolved. Instead of having to render all datasets atthe setting of the high-resolution dataset, the new rendering engine can render then ata constant rate of 10 to 15 frames per second (FPS). With Dragonfly’s legacy renderingengine, rendering a single frame could take up to 30 seconds whenever the size
difference in the correlative datasets was more than an order of magnitude.

N OTE Correlative workflows allow microscopists to study samples at much greater ranges ofTM021-A-07

magnification than with a single technique. Conducting an initial low-magnification
inspection of a sample to identify specific regions of interest can also generate muchgreater ranges of information about the samples at different scales.

N OTE Examining multiple overlapping datasets in 3D can still affect rendering performance with
the new engine. You should choose your interactivity settings appropriately (see Scene's
Views Properties on page 11) when working with multiple volumes and objects in thesame 3D view.

Object Research Systems

910 New Features

Next Generation Rendering Engine

Enabling the New Engine and Setting Defaults
A number of new items, circled below, are available in the 3D Settings preferences toenable the new rendering engine and to set its defaults.
Click the Preferences button on the Status bar or choose File > Preferences on themenu bar to open the Preferences dialog. Then choose Views | 3D Settings in the
Preferences dialog to view the 3D Settings preferences.
New rendering engine preferences

Use new rendering engine… Lets you toggle between the new rendering engine and thelegacy version. You should note that a restart will be required after changing therendering engine.

Default preset… Lets you select the 3D preset that will be applied by default (see 3D

Presets on page 13).

Gamma correction… Lets you select the gamma correction setting that will be applied

automatically.

Interactivity… Lets you choose an Interactivity option, which lets you balance quality

and speed for different grade graphic cards at every stage of the visualization workflow(see Scene's Views Properties on page 11).

Break during motion… If checked, the quality of visualizations will be decreased during

manipulations, but will then return to the set quality when at rest (see Scene's Views

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Properties on page 11).

Dragonfly Release Notes Version 2020.1

New Features
Next Generation Rendering Engine

Scene's Views Properties
A number of new options for adjusting interactivity and focus, as well as for adding
virtual floors, are available in the updated Scene's Views Properties panel, shown

below, for the new rendering engine.
Scene's Views Properties panel

New items in the Scene's Views Properties panel for the next generation renderingengine are described below. Changes to previous items, which are marked with *, arealso summarized.
Changes to the Scene’s Views Properties panel
Description
Orthographic projection*

Lighting and shadowing controls are available for orthographic projections with the new rendering engine.

Break during motion*

If checked, the quality of visualizations will be decreased during manipulations by increasing the size ofthe raycasting steps. For example, when panning, rotating, or adjusting window leveling. Visualizations
will return to the set quality when at rest. In general, selecting this option may help reduce delays whenworking with large datasets.

N OTE Was previously available as Lower quality in motion.
If checked, a delineated edge will be applied to the labeled voxels of visible regions of interest. Thissetting can help visualizations in which object boundaries are indistinct.

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Edge detect only ROIs

Object Research Systems

1112 New Features

Next Generation Rendering Engine

Description
Virtual floor

If checked, a virtual floor computed from the “Up” position of the camera will be automatically added to theview. As shown in the screen capture below, objects can cast realistic shadows on the 'virtual floor'.

N OTE The color of the virtual floor can be selected as a preference (see Views Preferences on page 71).

N OTE Computing virtual floors can be expensive as it is not a hardware accelerated feature andinteractivity performance will likely decrease. You should apply this feature only when you need to take aseries of screenshots or to record an animated sequence.
Interactivity

Each Interactivity option for Dragonfly’s new rendering engine offers the optimum balance of quality andspeed for different grade graphic cards and for different stages of visualization workflows.
Best quality… Retains the best quality visualizations during manipulations before returning to the set
quality.
Quality… Retains good quality visualizations for more limited graphic cards. You can also use this mode
when you’re nearing the final stages of your visualization process to quickly change and amend yourscene, enhance lighting, and change material properties.
Balanced… Provides a good balance between quality and speed.
Speed… This mode is ideal when working with lower quality graphic cards.
Fastest with lighting… Lets you quickly make manipulations without any discernible delay, while stillretaining current lighting.
Fastest without lighting… Lets you quickly make manipulations without any discernible delay, without
the current lighting applied. Use this mode to speed up your visualization workflow from the beginningwith almost instant feedback.

N OT E Interactive rendering automatically updates rendered images in real time as you make changes inyour scene. It is a great aid in modifying and transforming objects, tweaking material properties, adjusting
lighting and the camera, and virtually any part of the rendered scene.
You should also note that some settings, such as maximized quality, cubic interpolation, gradient filtering,and virtual floors, can lead to rendering delays. For more speed, you can turn off some of these GPUintensive features until your visualization workflow is complete.
Lighting settings*

You should note the following changes for the Lighting settings:• The new Deepen shadows setting lets you choose to apply deep shadows, or if not selected, to apply
less harsh shadows.
• The material properties item ‘Shininess” is deprecated for the new rendering engine.
• The material property items 'Specular' and 'Diffuse' have been moved to the 3D settings panel and are
configurable for each object in the view (see 3D Settings Panel on page 13).

Dragonfly Release Notes Version 2020.1

TM021-A-07• The lighting items 'Shadow precision' and 'Spotlight' are deprecated for the new rendering engine.

New Features
Next Generation Rendering Engine

Description
Focus settings

You should note the following new items for adjusting the Focus settings:
Close up… If selected, reduces the minimum focusing distance of the camera. This lets you focus moreclosely to your subject, which gives you greater magnification.
Strength… Lets you adjust the amount of blur applied to the foreground and background areas that areoutside of the center of focus. You should note that unfocusing image areas can help make a feature ofinterest stand out.

Global volume opacity

Lets you adjust the opacity of all image data in a 3D view that does not correspond to the labeled voxels ofvisible regions of interest and visible multi-ROI classes.

N OTE The opacity of the highlight applied to selected regions of interest and multi-ROIs, as well as theimage data that corresponds to labeled voxels, are adjustable in the 3D opacity panel on the Data
Properties and Settings panel, as shown below.

3D Presets
A new set of 3D presets are available for Dragonfly’s new rendering engine that let you
quickly create optimized renderings of different materials and samples with a minimumof manipulations. These options are available in Presets drop-down menu on the 3D

presets panel, shown below.
3D presets panel

3D presets are groups of lighting and material settings that are optimized for particular
data types or materials, such as organic tissue, bone, and solids. For the best
performance with Dragonfly 2020.1, you should select the 3D preset that is the mostsuitable for your typical data as the default setting (see Enabling the New Engine andSetting Defaults on page 10 and Views Preferences on page 71). In addition to the preinstalled 3D presets, you can also create your own presets.

3D Settings Panel
A number of new options for adjusting the material properties of selected objects andfor filtering image data are available in the 3D settings panel, which is available on theright sidebar and is shown below.

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3D settings panel

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14 New Features

Next Generation Rendering Engine

New items in the 3D settings panel for the next generation rendering engine aredescribed below. Changes to previous items, which are marked with *, are also
summarized.
3D settings panel changes
Description
Solidity

Lets you vary the solidity, or opaqueness, of the voxels of the selected object. You should note that thisnon-linear function is applied at every step of the raycasting process in contrast to opacity, which is alinear function that determines the transparency of an object.

Diffuse*Determines the strength of diffuse light reflected from the surfaces of objects and is a characteristic oflight absorbed by surfaces. Increasing this property with the Diffuse slider will result in object surfaces
being more defined.

N OTE In most cases, you should adjust either Opacity or Solidity with their respective sliders.

N OTE Was previously part of the Scene View's Properties. And is now selectable for each object within a
3D view.
Specular*

Determines the strength of specular reflections originating from the surfaces of an object and is acharacteristic of light reflected from shiny surfaces. Increasing this property with the Specular slider will
result in increased reflections. You should note that specular effects will be affected by the Specular
boost setting, if this settings is selected.

N OTE Was previously part of the Scene View's Properties. And is now selectable for each object within a
3D view.
Shininess*

Determines how much the smooth surfaces of an object reflect light. Increasing shininess will result insurfaces that reflect more light and is usually adjusted in conjunction with Specular.

N OTE Was previously part of the Scene View's Properties. And is now selectable for each object within a
3D view.
Unsharp

If checked, objects in the view will be sharpened by increasing contrast along edges and other highfrequency components.

N OTE The term Unsharp comes from a darkroom technique used in traditional film-based photography inwhich an unsharp or smoothed version of an image is subtracted from the original one.
Tone mapping

Tone mapping maps one set of colors to another to approximate the appearance of high-dynamic-range
images in a medium that has a more limited dynamic range. In Dragonfly, it can be applied to brighten
datasets that appear too dark.

Filtered gradientIf checked, this option will smooth the gradient calculated for lighting. Very similar to tricubic filtering, but
applied to the gradient with the effect of smoothing areas with abrupt intensity changes.

MedianIf checked, objects will be smoothed by median filtering. When applied, pixel values are replaced with themedian of itself and their neighbors. This can help remove noise while still preserving boundaries.

Specular boost

If checked, adjustments to the Specular setting will be greater.

3D LUT*You should notice that LUTs, which determine how regions within specific arrays of intensity arehighlighted and how color is applied, are more accurately mapped to the selected window leveling range
when using the new rendering engine. In comparison to the previous rendering engine, 3D LUTs areapplied to the whole data range while leveling is applied as a pass-through.

N OTE An image gradient is a directional change in the intensity or color in an image.

N OTE Some 3D settings, such as cubic interpolation, gradient filtering, and high quality, canlead to rendering delays. For more speed, you can turn off some of these GPU-intensive
features until your visualization workflow is complete.

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N OTE Applied LUTs can be edited interactively to optimize visualizations.

New Features
Segmentation Wizard

Segmentation Wizard
Dragonfly’s new Segmentation Wizard provides an easy-to-use, guided workflow for
implementing powerful deep learning and classical machine learning segmentation ofmulti-dimensional images. With the Segmentation Wizard, you simply paint thedifferent features of interest within a limited subset of your image data and then trainmodels to identify objects according to a predefined set of rules. The most promisingmodel can then be fine-tuned and exported for repeated segmentation tasks. Thisempowers any user to achieve robust and reproducible segmentation results that are
not influenced by user bias.
Right-click the image data you need to segment in the Data Properties and Settings
panel and then choose Segmentation Wizard in the pop-up menu to open the

Segmentation Wizard context, shown below. The workspace includes a large views area
in which you can label the voxels within a frame and preview model predictions, as wellas panels on the right side that include the Input, Models, and Settings tabs.
Segmentation Wizard

N OTE The Segmentation Wizard requires a Deep Learning license. Refer to the topic Licensing
TM021-A-07

for Optional Features on page 60 for information about the availability of the optionalfeatures for Dragonfly 2020.1.

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16 New Features

Segmentation Wizard

Key Features and Benefits
Just some of the many key features and benefits of the Segmentation Wizard are listed
below.
• Automatically splits available data into Training, Evaluation, and Test sets.
• Works on frames that are created automatically on the visible part of the data.
• Users apply their specific knowledge to identify features of interest by labeling alimited subset of the image data that is defined by frames. Advanced knowledge ofmachine learning and deep learning algorithms is not required.
• Direct and quick feedback with previews of model predictions. New frames can be
filled automatically with the best model prediction, based on the highest-ranked
prediction.
• Models can be fine-tuned by correcting the most-promising prediction.

Input Tab
The Input tab on the Segmentation Wizard panel, shown below, provides theopportunity to add frames on the image data and to define classes. Labeling features ofinterest within frames can be accomplished with the ROI Painter tools. Frames can also
be filled from previously segmented multi-ROIs.

N OTE Refer to the topic New Options for Multi-ROIs on page 27 for information about the new
options for working with multi-ROIs in Dragonfly 2020.1.

Dragonfly Release Notes Version 2020.1

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Input tab about

New Features
Segmentation Wizard

Models Tab
The options on the Models tab let you enable or disable models, import trained models,
as well as to save models for use with the Segment with AI feature (see AutomatedSegmentations on page 55).
Models tab

Settings Tab
The options on the Settings tab, shown below, let you set your training preferences.
Settings tab

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You can choose to have new frames filled automatically with the best model prediction,
as well as determine when model training will be stopped.

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18 New Features

Bone Analysis Wizard

Bone Analysis Wizard
Designed for the evaluation of high-resolution micro-CT samples of bone specimens,
Dragonfly’s new Bone Analysis Wizard provides 3D vector-based mappings ofanisotropy magnitude and directionality and 3D scalar-based mappings of bone volume
fraction. In addition, an automated separation of cortical and trabecular bone drives thecalculation of common morphometric indices that provide researchers with quantitativedescriptions of bone micro-architecture.
Right-click the image data from a bone study in the Data Properties and Settings panel
and then choose Bone Analysis Wizard in the pop-up to open the Bone Analysis Wizard,

shown below.

Bone Analysis wizard

N OTE Bone Analysis is a separately licensed feature for Dragonfly 2020.1. Refer to the topic

Licensing for Optional Features on page 60 for information about the availability of all
the optional features for Dragonfly.

Bone Analysis Workflow
A series of self-guided segmentation steps let you close cortical pores and vascularcortical and trabecular bone, computing morphometric measurements, and generating
3D vector-based mappings of anisotropy magnitude and directionality and 3D scalarbased mappings of bone volume fraction. Observations and measurements areappended automatically to detailed reports.

Dragonfly Release Notes Version 2020.1

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inlets and fill an initial bone segmentation before proceeding to the separation of theNew Features
Bone Analysis Wizard

Bone segmentation and filling… The first step in the workflow lets you segment the
selected bone image and fill the initial segmentation.

Filled bone separation… The second step of the guided segmentation, shown below, lets
you choose a segmentation method ― Buie or Kohler ― for separating filled bone into

cortical and trabecular components.

Compute global measurements… The inputs for computing global measurements, as
described by Bouxsein et al.*, are shown in the following screen capture. These

measurements rely on input cortical bone and trabecular bone segmentations, which
offers the opportunity to edit automated bone segmentations, as well as to input any
region of interest that satisfies the requirements.

TM021-A-07* Bouxsein, M.L. et al. Guidelines for assessment of bone microstructure in rodents using microcomputed tomography. J Bone Miner Res 25, 2010.

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20 New Features

Bone Analysis Wizard

Global Measurements dialog

N OTE You can apply a mask to limit the area in which the selected global measurements will becomputed.

Compute scalar and vector fields… The parameters to compute scalar values of volume

thickness and vector fields of anisotropy are available as the next step in a bone

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analysis workflow.

Dragonfly Release Notes Version 2020.1

New Features
Bone Analysis Wizard

Compute scalar and vector fields

Prepare Screenshots and Notes… A multiple screenshots panel is available on the left

sidebar to collect screen captures that can be included in generated reports. Metadata
can be easily integrated in reports by clicking the Define Image Metadata button on theMultiple Screenshots panel. The Multiple Screenshots panel (on top) and Image
Metadata dialog are shown below.

Generate Report… Lets you generate a report in the PDF file format, which is

automatically formatted with a header that includes the project title, job ID, author(s),contact information, and creation date. You can also add your institution’s logo.
Computed global measurements and screen captures taken during the current session

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will also be included in the report. You should note that reports use a LaTeX templatethat can be easily modified for specific requirements.

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22 New Features

Plug Analysis Wizard

Plug Analysis Wizard
Dragonfly’s new wizard for Plug Analysis provides a dedicated workflow for analyzingcore plugs acquired from rock samples and other porous media. It includes powerfulalgorithms that support segmentation with Deep Learning and built-in automation for
quantitatively extracting computations that add weight to observations from corematerial. Analysis results can be quickly appended to detailed reports that can include
screen captures, graphs, and other supporting material. Choose Workflows > Plug
Analysis on the menu bar to open the Plug Analyzer, shown below. You can also open
the Plug Analysis Wizard from the dataset pop-up menu.
Plug Analysis module

N OTE Plug Analysis is a separately licensed feature for Dragonfly 2020.1 and is not bundledwith non-commercial licenses. Refer to the topic Licensing for Optional Features on
page 60 for information about the availability of all the optional features for Dragonfly.

Plug Analysis Workflow
computation steps described below.

Pre‐processing… The first step in the workflow lets you perform the basic pre-processing tasks of beam hardening correction and cropping with a cylinder on axial
and longitudinal views of the loaded image data.

Segmentation… Lets you choose an Otsu threshold, Deep Learning model, or to apply amanual range to perform the basic segmentation of the plug components.

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The Plug Analysis workflow includes the pre-processing, segmentation, editing, andNew Features
Plug Analysis Wizard

Correct segmentation… The opportunity to correct the automated segmentation by

applying morphological operators, filling inner areas, or with Dragonfly’s ROI Paintertools is then available at this next step of the workflow.

Box editing… The Box Editing step lets you adjust the input and output boxes forcomputing tortuosity and throat-weighted tortuosity from the graph of plug porosity.

Calculations… Lets you choose the measurements and computations you need to add
fully analyze your core sample (see Plug Measurements on page 23).

Prepare screenshots and notes… A multiple screenshots panel, shown below, is available
on the right sidebar to collect screen captures for generated reports. Notes can beeasily integrated in a report by clicking the Define Image Metadata button.

Reporting… Lets you generate reports in the PDF file format, which are automaticallyformatted with a header that includes the project title, job ID, author(s), contact

information, and creation date. Screen captures taken during the current session,
thickness mesh measurements, distributions of pore sizes and tortuosity, as well as
plug porosity measurements can also be included in reports. You should note thatreports use a LaTeX template that can be easily modified for specific requirements.

Plug Measurements
The analysis capabilities of the dedicated Plug Analysis module are listed below.
Plug Analysis measurements

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Description
Plug porosity

You can compute plug porosity for each XY slice within the segmented image data on the Slice Analysis
tab (see Plug Porosity Slice Analysis on page 24).

Thickness mesh

Computes color-coded meshes that show referential values of the local thickness. Thickness is calculated
as the diameter of a hypothetical sphere that fits within each boundary point and is the same ascomputing the volume thickness on the ROI and sampling it on the vertices of the mesh.

Volume thickness

Computes and generates scalar-based maps of volume thickness.

Shortest path distance map

Computes and generates scalar-based maps of the shortest path distance from the input box to the output
box defined at the Box editing step of the workflow.

Sparse Graph

Computes and generates sparse graphs that include edge scalar measurements of Euclidean length andvertex scalar measurements of pore diameter.

Dense Graph

Computes and generates dense graphs that include edge scalar measurements of Euclidean length andvertex scalar measurements of segment tortuosity, segment length, segment index, segment Euclidean
length, pore diameter, Dijkstra Euclidean, Dijkstra Throat Weighted.
The following distributions are also available for reporting as follows:

Pore size distribution… Plots pore size distribution within the dense graph.

Tortuosity… Plots tortuosity within the dense graph (see Tortuosity Distributions for Graphs on page 32).

Throat‐weighted tortuosity… Plots the distribution of throat-weighted tortuosity within the dense graph(see Tortuosity Distributions for Graphs on page 32).

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24 New Features

Plug Analysis Wizard

Plug Porosity Slice Analysis
This parameter for slice-by-slice analysis lets you compute plug porosity for each XY
slice within the volumetric data. The plug porosity percentage of the region of interest iscomputed as: [(total labeled voxels)/(total all voxels)]*100.
Click the Slice Analysis tab on the right sidebar to open the Slice Analysis panel. You

can then choose the Plug Porosity measurement and click the Compute button to

generate the results and plotted graph shown below. Select the Add Slice Analysis

results to report option if want to include this analysis in your generated report.
Slice Analysis panel

If required, you can customize and save the figure, as well as export the results to a
CSV file for further processing. Plug Porosity measurements are also available in themain application for detailed slice analyses of any reformatted view.

Pore Network Modeling
generate and extract pore network models based on 3D image data. The previously
released Pore Network Modeling module for Dragonfly provides valuable insights intopore and throat size distributions as a natural outcome of producing a network model.

Dragonfly Release Notes Version 2020.1

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Go further with other unique Dragonfly capabilities, such as pore network modeling, toNew Features
CT Reconstruction Module

CT Reconstruction Module
The CT Reconstruction module for Dragonfly 2020.1 provides for the tomographic

reconstruction of cone-beam projections with RTK, an open-source software based on
the Insight Toolkit (ITK), and parallel-beam projections using TomoPy, an open-source
Python package for tomographic data processing and image reconstruction. CT
Reconstruction provides benchmarked reconstruction algorithms, selectable
reconstruction parameters, iterative methods, and previews for verifying selected
settings. Extensive knowledge about the integrated image reconstruction algorithms is
not required to obtain optimal results with CT Reconstruction.
Choose Workflows > CT Reconstruction on the menu bar to open the CT Reconstruction

dialogs, shown below.

CT Reconstruction options for cone beam and parallel beam acquisitions

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N OTE The CT Reconstruction module is only available as Beta in this software release.

Reconstruction Algorithms
CT Reconstruction includes the benchmarked Feldkamp-David-Kress (FDK) algorithm
for cone-beam acquisitions, and Fourier grid reconstruction ('gridrec') and algebraic
reconstruction techniques ('art') for parallel-beam. Geometry readers are provided forcommercial scanners from Nikon, KA Imaging, and North Star Imaging.

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26 New Features
MC X‐RayPre and Post‐Processing
Basic operators for reconstruction include flat and dark-field correction and medianfiltering, while GPU acceleration provides fast processing of large data sizes.
Downstream, Dragonfly's extensive image processing toolbox includes beam-hardening
correction, ring artifact removal, noise reduction, and image stack alignment. Batch
processing allows reconstruction jobs to be run sequentially without operator input.

MC X‐RayMC X-Ray simulates electron scattering in materials in order to correlate X-Ray emission
to composition in quantitative X-ray microanalysis. By simulating X-ray spectra, it ispossible to establish the optimum conditions to perform a specific analysis, as well as toestablish detection limits or to explore possible peak overlaps.
MC X-Ray can compute the complete X-ray spectra from the simulation of electron
scattering in solids of various types of geometries and allows for up to 256 different
regions in the materials having the shape of spheres, cylinders, and combinations ofhorizontal and vertical planes. All of these regions can have a different composition.
Choose Workflows > MC X‐Ray Simulator to open the MC X-Ray dialog, shown below.

N OTE The MC X-Ray module is only available as Beta in this software release.
Additional features of MC X-Ray include bright-field, dark-field, and high angle annulardark-field detectors, as well as the display of electron trajectories, electron and energy
distribution at the specimen surfaces, transmitted electrons distribution, and energy
loss distribution.

Dragonfly Release Notes Version 2020.1

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Physical Models tab on the MC X‐Ray dialog

New Features
New Options for Multi‐ROIs

New Options for Multi‐ROIs
The 2020.1 software release introduces the concept of editable multi-ROIs. This meansthat you can create and label classes directly on a multi-ROI instead of working on
multiple regions of interest and then creating the multi-ROI.
As shown in the following screen capture, the new Classes and scalar information box

on the Data Properties and Settings panel for selected multi-ROIs indicates the name ofeach class in the multi-ROI, the number of labeled voxels, and the color assigned toeach class. If available, you can also view scalar information related to each class. In
addition, you can show or hide any class by toggling the visibility control.
Classes and scalar information for multi‐ROIs

N OTE The Pick tool lets you visually select a class within a view.
Background Class
If this option is enabled, labeled voxels that are removed from any class, as well as
unlabeled voxels that are painted, will be added automatically to the set backgroundclass.
Do the following to set a class as the background for a multi-ROI:• Name the class that you intend to set as the background, recommended.
• Drag the class to the Background class box and drop it when the “+” appears withyour cursor.

TM021-A-07• To remove the background class, check the None option.

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28 New Features

New Options for Multi‐ROIs

Scalar Information
Scalar information related to each class in a multi-ROI, whether it was generated orimported, appears in the Classes and scalar information list and is selectable in the

Scalar information box that is circled below.
Scalar information box

Labeling Multi‐ROIs with the Painter Tools
You can use the tools available on the ROI Painter panel, shown below, to manuallylabel the voxels of each class in a multi-ROI.
ROI Painter panel

N OTE The labeled voxels of the classes in a multi-ROI cannot intersect. For example, if you arelabeling voxels as 'Class 1' and paint over the labeled voxels of another class, then thosevoxels will be automatically labeled as 'Class 1'.

In cases in which a feature of interest was misidentified as belonging to another class,for example by the Segmentation Wizard during model training, you can edit labels in'Exclusive' mode. In this mode, only labeled voxels within the selected classes will beaffected by painting. For example, if you select classes A and B and then add to class A,
only voxels labeled as class B will be automatically relabeled as class A.
You can also edit the labels of each class within a multi-ROI by applying morphological
Additional options are available in the Classes and scalar information pop-up menu tolabel all non-intersected voxels, clear classes, and import the labels of a region ofinterest (see Options for Selected Classes on page 29).

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operators and other operations, such as filling inner areas and adding clipped regions.

New Features
New Options for Multi‐ROIs

Options for Selected Classes
Contextual menu items for single selections and multiple-class selections let you fully
segment the multi-ROI, as well as clear, delete, and merge classes. You can also extractclasses as ROIs for other purposes.
Single selection (on left) and multiple (on right) options

Creating New Multi‐ROIs
The options to create a new multi-ROI with a selectable number of classes is available
from the ROI Tools panel. Click the New button in the Basics box to open the New

Region of Interest dialog, shown below.
New Region of Interest dialog

Creating Dense Multi‐ROIs from ROIs
The option to create new multi-ROIs, in which the labeled voxels of each selected ROI is
assigned to a class and all unlabeled or 'complementary' voxels are labeled as anadditional class, is available from the pop-up menu for selected regions of interest. For
example, if you create a multi-ROI from five regions of interest, then the dense multiROI will contain six classes and will be fully segmented.
As shown in the following illustration, in which the labeled voxels of three regions ofintersect, the selection order determines how labeled voxels are distributed in the
resulting classes of the multi-ROI. Unlabeled voxels are assigned to an additional class.

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Intersecting ROIs and resulting dense multi‐ROIs

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30 New Features

New Options for Multi‐ROIs

You should note that dense multi-ROIs are often selected as the output for training
deep learning models.

Creating Dense Multi‐ROIs from Multi‐ROIs
The option to create new multi-ROIs, in which all unlabeled or 'complementary' voxels
are labeled and assigned to a new class, is now available from the pop-up menu for
selected multi-ROIs. For example, if you create a dense multi-ROI from a multi-ROI
that contains five classes, then the dense multi-ROI will contain six classes and will befully segmented.

2D Watershed
In cases in which you need to prepare training data for Deep Learning, you can performa watershed segmentation on a single slice of a labeled multi-ROI.
Right-click the required multi-ROI in the Data Properties and Settings panel and thenchoose 2D Watershed in the pop-up menu. You will then need to choose a region ofinterest for computing a distance map, as well as a landscape for computing thewatershed. The result will be a fully segmented, single-slice multi-ROI.

Creating Images from Selected Scalars
This new option for multi-ROIs automatically creates an image for each scalar value
checked in the Select Desired Scalars dialog, shown below
Select Scalars dialog.

The result is series of new images in which data values correspond to the scalar valuesof labeled voxels.

N OTE Images are generated in the FLOAT data type, which stores double-precision floating-

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point numbers with up to 17 significant digits.

Dragonfly Release Notes Version 2020.1

New Features
Measurements for 2D Multi‐ROIs

Measurements for 2D Multi‐ROIs
A number of new options are available in this software release for measuring theproperties of the labeled regions, or connected components, on 2D multi-ROIs.
Right-click a multi-ROI in the Data Properties and Settings panel and then choose

Connected Components > Analysis in the pop-up menu to start your analysis. The
following properties can then be selected in the Statistical Properties dialog in the
Object Analysis module.

Statistical Properties for 2D multi‐ROIs

Descriptions of the selectable statistical properties for 2D multi-ROIs are available in
the following table.
Selectable statistical properties for 2D multi‐ROIs
Description
2D Area

The area of the labeled pixels in the region, reported in (default units)2.

2D Bounding Box Area

The area of the bounding box that encloses the labeled pixels in the region, reported as (default units)2.

2D Convex Area

The area of the convex hull image, which is the smallest convex polygon that encloses the region.

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Reported in (default units)2.
2D Eccentricity

Eccentricity of the ellipse that has the same second-moments as the region. The eccentricity is the ratio of
the focal distance (distance between focal points) over the major axis length. The value is in the interval[0, 1]. When it is 0, the ellipse becomes a circle.

2D Equivalent Diameter

The diameter of a circle with the same area as the region, reported in default units.

2D Euler Number

Euler characteristic of the region.

2D Extent

Ratio of pixels in the region to pixels in the total bounding box. Computed as:

2D Filled Area

The area of all pixels — both labeled and unlabeled — in the region which describes the area of the filled

2D Area / 2D Bounding Box Area.
region. Reported in (default units)2.
2D Major Axis Length

The length of the major axis of the ellipse that has the same normalized second central moments as theregion. Reported in default units.

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32 New Features

Tortuosity Distributions for Graphs

Description
2D Minor Axis Length

The length of the minor axis of the ellipse that has the same normalized second central moments as theregion. Reported in default units.

2D Orientation

Angle between the 0th axis (rows) and the major axis of the ellipse that has the same second moments as
the region, ranging from -pi/2 to pi/2 counter-clockwise. Reported in degrees or radians.

2D Perimeter

Perimeter of object which approximates the contour as a line through the centers of border pixels using a4-connectivity. Reported in default units.

2D Solidity

Ratio of pixels in the region to pixels of the convex hull image.

Tortuosity Distributions for Graphs
As a new feature for computed graphs, you can plot the distribution of graph tortuosity
and throat-weighted tortuosity between input and output boxes. You should note thatthe tortuosity factor is a measure of the departure of a porous medium from the ideal
system made of straight and parallel capillaries.
Histograms of tortuosity and throat‐weighted tortuosity

Plotting Tortuosity
Do the following to plot the distribution of tortuosity within a graph of porous media:• Add box shapes to define the input and output of the segment of the graph that you• Right-click the graph in the Data Properties and Settings panel and then choose Plot

Graph Tortuosity in the pop-up menu.

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want to plot.

New Features
Computing Shortest Distances on Graphs• Choose the input and output boxes, as shown below.

• Click OK to plot the tortuosity within the selected segment of the graph.

Plotting Throat‐Weighted Tortuosity
Do the following to plot the distribution of throat-weighted tortuosity within a graph ofporous media:• Add box shapes to define the input and output of the segment of the graph that you
want to plot.
• Right-click the graph in the Data Properties and Settings panel and then choose Plot

Graph Throat‐Weighted Tortuosity in the pop-up menu.

• Choose the graph region of interest, as well as the input and output boxes, as shown
below.

• Click OK to plot the throat-weighted tortuosity within the selected segment of thegraph.

Computing Shortest Distances on Graphs
This software release provides the option to compute the shortest distance between two
selected nodes on a graph and to then extract additional scalar values within thatinterval. Choose Utilities > Start Graph Shortest Path on the menu bar to open theGraph Shortest Path dialog, shown below.

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Graph Shortest Path dialog

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34 New Features

Computing Shortest Distances on Graphs

Do the following to compute the shortest distance between two selected nodes:• Pick a path-starting vertex and a path-ending vertex with the Pick tool.

• Choose a measurement in the Edge measurement drop-down menu.
• Click the Compute path button.

The shortest path between the selected vertices is computed automatically and theEdge LUT measurement is updated to highlight the computed path, as shown below.

In addition, specific measurements extracted from the edges within the path appear
in the Graph Shortest Path dialog. These include the total of the selected
measurements, the minimum, maximum, and mean values, as well as the variance.
• If available, you can choose other edge measurements to examine in the Current slot
drop-down menu, as shown below.

Configured Actions for Computing Shortest Distances
Configured actions for computing distances
Description
Pick path ending vertex

Configured action for picking the path-ending vertex.

Pick path starting vertex

Configured action for picking the path-starting vertex.

Pick vertices

Configured action for entering vertex-picking mode.

Switch to pick end vertex

Configured action for switching to pick path-ending vertex mode.

Switch to pick start vertex

Configured action for switching to pick path-starting vertex mode.

Dragonfly Release Notes Version 2020.1

TM021-A-07

The following configured actions are available for picking vertices with the Pick tool.

New Features
Import Graph from CSV

Import Graph from CSVThis new option, which is available on the File menu, lets you import a graph saved in

the comma-separated values (*.csv extension) file format.

Probing Graph Scalar Values
You can now view the scalar values of graph edges and/or nodes, as well as assigned
index numbers, in 3D views with the Probe tool. Results are displayed on the Probepanel, as shown below.
Probe panel

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N OTE The Probe panel is available by default on the left sidebar on the Main tab.

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36 New Features

Scalar Values for Meshes

Scalar Values for Meshes
This software release includes the option to add additional scalar values, such ascurvature, normal angles with the Z-axis, or a constant, to meshes.
Right-click a mesh in the Data Properties and Settings panel and then choose therequired option in the pop-up menu. The computed scalar value will appear in the

Scalar information group box, as shown below, and will be displayed on the legend.
Scalar information

You should note that you can map values to any LUT. In the following example, thedefault blue-green-yellow LUT was selected for mapping normal angles with the Z axis.
Normal angles with Z axis

Translation for Scalar Values
If required, you can apply a linear transformation, with or without an offset, to selectedmesh scalar data. Right-click the mesh in the Data Properties and Settings panel andthen choose Apply Translation to Scalar Values in the pop-up menu. You can thenchoose the scalar values slot that you need to modify in the Choose a Scalar Values
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Slo t dialog, as well as the slope value and offset in the following dialogs.

Dragonfly Release Notes Version 2020.1

New Features
Image Filtering

Image Filtering
A number of new options, as well as additional filters, are available in this software
release for processing and filtering image data.

Apply to Selected Slices Only
As an update for image processing, you can now restrict the application of a filter orarithmetic operation to selected image slices. For example, to correct an anomaly that
only appears a limited number of slices on a 3D image.
Do the following to apply filtering to selected slices only:• Mark the image slices to which you want to restrict processing.

N OTE Right-click inside the view of the original data and then choose Show Marked
Slices Indicator in the pop-up menu to view the options for marking image slices.
• Choose Apply > On selected slices in the Output box on the Image Processing panel,as shown below.

• Choose the slices, or a range of slices, on which the selected operation should beapplied in the Selected Slices dialog, as shown below.

N OTE You can also extract a dataset of selected slices only by checking the Discard
other slices option.

Additive Noise Filter
The new Additive Noise filter lets you artificially add noise to an image. Deliberately
corrupting an image with noise lets you test the resistance of an image processing

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operator to noise and assess the performance of various noise reduction filters anddenoising models.

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3738 New Features
Image Filtering

The result of adding noise to a grayscale image is show below on an intensity profile.

The following options are available for the Additive noise filter in the Image Processing
panel.
Options for additive noise

Distribution… Lets you choose a distribution for the added noise — Uniform absolute,
Uniform relative, and Gaussian.

Range… Lets you choose the range of data within which noise will be added. For

example, at a range of 100 with a ‘Uniform relative’ distribution, noise will be added

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within ±50 of the original data.

Dragonfly Release Notes Version 2020.1

New Features
Find Path Between ROIs

Find Path Between ROIs
This new option for Dragonfly 2020.1 lets you define the connectivity of the strongest
path between two regions of interest.
Path ROIs computed with varying geometrical biases

Do the following to compute a path ROI between two ROIs:•

Define the start and end nodes as regions of interest and then create a mask ROI
to contain the path, recommended.

•
•
•
•

Right-click the image data on which you want to compute the path and thenchoose Find Path ROI Between ROIs in the pop-up menu.

Choose the starting point ROI and end point ROI in the Choose an ROI dialog.

Choose an ROI as the mask, recommended, and then click OK .

Select a geometrical bias and then click OK the compute the path.

The new path ROI appears in the Data Properties and Settings panel.

Euler Characteristic Number
Euler Characteristic numbers provide topological characteristics of various classes ofgeometric figures based only on a relationship between the numbers of vertices (V),edges (E), and faces (F) of the figure. This number, given by V - E + F, is the same for
all figures whose boundaries are composed of the same number of connected pieces.
To compute the Euler characteristic number, right-click a region of interest or graph in
the Data Properties and Settings panel and then choose Get Euler Characteristic

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Number in the pop-up menu. The result appears in an Information dialog.

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3940 New Features

Structured Grids Comparator

Structured Grids Comparator
The new Structured Grids Comparator for Dragonfly 2020.1 lets you evaluate thequality of processed image data and segmentations with a number of metrics.
Choose Structured Grids Comparator in the Utilities menu to open the Structured Grids

Comparator dialog. You can then select a ground truth, mask, and the required metrics

to evaluate your data. You should note that results are cumulative and can be exported
in the comma-separated values (*.csv extension) file format for further analysis orarchiving.

N OTE The structured grids that you choose to compare must have the same size and shape, as
well as the same resolution.

Processed Image Comparator
For processed image data, you can select metrics such as Mean Squared Error (MSE),
Normalized Root Mean Square Error (NRMSE), Peak Signal-to-Noise Ratio (PSNR), andStructural Similarity Index (SSIM), to evaluate the quality of images generated bydenoising deep learning models or that were processed by filtering or any otheroperation.
Structured Grids Comparator results for processed image data

N OTE You can open the Processed Image Comparator from the Data Properties and Settings
panel by multi-selecting the ground truth and processed image data, right-clicking, andthen choosing Open Processed Image Comparator in the pop-up menu.

Segmentation Comparator
For regions of interest and multi-ROIs, you can select metrics such as Accuracy, Diceevaluate the quality of machine learning and deep learning segmentation models.

Dragonfly Release Notes Version 2020.1

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Similarity Coefficient (DICE), False Negatives (FN), False Positives (FP), and others toNew Features
Distributed Tasks

Segmentation Comparator results for evaluating a multi‐ROIN OTE You can open the Segmentation Comparator from the Data Properties and Settings panel
by multi-selecting the ground truth and segmentation of interest, right-clicking, and thenchoosing Open Segmentation Comparator in the pop-up menu.

Distributed Tasks
This new option for Dragonfly 2020.1 lets you dispatch demanding tasks, such asreconstructing cone-beam projections, simulating X-ray emissions, and training deepmodels, to multiple machines.
Choose Preferences > Distributed Tasks to open the preferences for selecting a task
database connection.

Distributed Tasks preferences

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N OTE This module is standard for Dragonfly HPC and is also available on demand for holders ofmultiple Dragonfly and Dragonfly Pro commercial licenses. It is not available for free noncommercial licenses.

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42 New Features

Creating Image Masks

Creating Image Masks
This new option for Dragonfly 2020.1 lets you quickly create an ROI mask forprocessing image data. Right-click the required image data in the Data Properties andSettings panel and then choose Create Mask in the pop-up to open the Create Mask
panel, shown below.
Create Mask panel

The resulting mask will be a new region of interest with the same shape as the selected
image data and that is fully labeled within the selected dimension and increment.

Auto Synchronization Between 2D and 3D Views
With the Auto Synchronization option for Dragonfly 2020.1, you can automatically

update the slice position of all the MPR views in the current scene to wherever you
clicked in the 3D view.

N OTE The configured action for this option is “Center MPR 2D views from 3D pick” (seeConfigurable Actions on page 71).

Import Images from Hitachi SEM
Support for importing images acquired with Hitachi scanning electron microscopes isavailable in this software release. Simply add the required TIFF file to Dragonfly's
Image Loader and the application will apply the information available in theaccompanying “image_file_name.txt” file to correctly import your Hitachi SEM
acquisitions.

N OTE See Measurements for 2D Multi-ROIs on page 31 for information about the new options

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are available in this software release for measuring the properties of the labeled regions
on 2D multi-ROIs.

Dragonfly Release Notes Version 2020.1

New Features
Export Images as DICOM

Export Images as DICOM
This software release provides the option to export images in the DICOM format.
Whenever you export images in the DICOM format, you can choose the images to beexported and an export destination.
Choose Export > As DICOM in the Data Properties and Settings panel to open the

Export as DICOM Images dialog, shown below.
Export as DICOM Images dialog

N OTE Digital Imaging and Communications in Medicine (DICOM) is a standard for handling,storing, printing, and transmitting information in medical imaging. It includes a file format
definition and a network communications protocol that uses TCP/IP to communicate
between systems. DICOM files (*.dcm extension) can be exchanged between two entities
that are capable of receiving images and data in DICOM format.

Exporting Screenshots
A number of additional options are available for exporting screenshots of 2D and 3D
views. These new options are described below.

Export Screenshots from Views
The option to export screenshots is now available from the contextual menus for 2D and
3D views, as shown below.

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View contextual menu

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Export Meshes with Color

Export Screenshots with Transparent Backgrounds
The option to export screenshots from 3D views with a transparent background isavailable in this software release. Select Alpha background in the Screenshot Sizedialog, shown below, to export the image in the PNG and TIFF file formats with atransparent background.
Screenshot Size dialog

Export Meshes with Color
The option to export scalar meshes with colors preserved is now available for the VRML(*.wrl extension) file format. Right-click the mesh you need to export and then choose

Export > Mesh to File with Colors in the pop-up menu.
N OTE Importing meshes exported with color in the VRML file format is not yet supported by
Dragonfly.

Context Groups
This software release provides the option to save and load ‘context groups’, which
define the workspace of contexts ― such as the Segmentation, Plug Analyzer, or Bone
Analysis Wizards ― and include all objects associated with the context. This lets you
resume working within a specialized workflow after exiting the context or Dragonfly
without having to import the required objects or to repeat computational steps.
Context groups appear on the Data Properties and Settings panel in the main context,
as shown below.

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Context group in the Data Properties and Settings panel (circled)

To load a context from the main application window, right-click the required group in
the Data Properties and Settings panel and then choose Reopen in the pop-up menu.

Dragonfly Release Notes Version 2020.1

New Features
Widget Observer

You can also import a context group from a saved session. Choose File > Import

Object(s) on the menu bar and then select the ORSSession (*.ORSSession extension)

file with the required session group. You can then select the group that you want toimport in the Select Objects dialog.
Select Objects dialog

Widget ObserverThis new software developer tool helps you to troubleshoot issues, such as unequal
panel sizes, misaligned icons, and missing styles, by letting you examine the propertiesof the parents and childs of a selected widget.
Choose Developer > Widget Observer on the menu bar to open the Widget Observer

panel, shown below.
Widget Observer panel

You can then open a single Widget Observer or Graph Observer, as shown in thefollowing screen captures. To view the properties of a widget you can enter the object
ID or use a configured action to show the properties of the selected instance of class

TM021-A-07(see Configured Actions for the Widget Observer on page 46).

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46 New Features

Widget Observer

Widget Observer and Graph Observer dialogs

Configured Actions for the Widget Observer
The following configured actions are available for opening the Widget Observer panel
and associated dialogs.
Configured actions for the Widget Observer
Description
Opens the Widget Observer panel on the right sidebar.

Start Widget Observer (graph) on
widget at cursor

Opens the Graph Observer and displays the properties of the selected instance of a class. For
example, ‘OrsPythonPlugins.OrsBasicManipulate.mainform.mainform’.

Start Widget Observer (single widget)on widget at cursor

Opens the Widget Observer and displays the properties of the selected instance of a class. For
example, ‘OrsPythonPlugins.OrsBasicManipulate.mainform.mainform’.

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Open the Widget Observer

Dragonfly Release Notes Version 2020.1

Product Enhancements
Refactored Menu Bar

Product Enhancements

This release provides the following product enhancements for Dragonfly 2020.1.
Information about new features, such as the Segmentation Wizard, Plug Analysis, andthe CT Reconstruction, as well newly implemented options for multi-ROIs and graphs, isavailable in the topic New Features on page 7.

Refactored Menu Bar
One of the first changes you should notice in Dragonfly 2020.1 is the refactored menubar, shown below.
Menu barRefactoring was implemented to help make finding the items that you need for yourworkflows easier and quicker. For details about the items available on the menu bar, see
Menu Bar Changes on page 63.

Deep Learning Improvements
This software release features a number of enhancements and other changes for Deep
Learning. These modifications are summarized below.

New Class Pattern• Deep models are now divided into two types — Regression and Segmentation. There
are no longer separate categories for binary and multi-class segmentations. The
Model Generator was updated to support only two model types.
• Segmentation deep models now only accept multi-ROIs as the target output andproduce multi-ROIs as previews and segmentations.

N OTE Refer to the topic New Options for Multi-ROIs on page 27 for information about

TM021-A-07

creating and labeling classes directly in multi-ROIs and other options.

• Segmentation class settings — visibility, name, and color — are now part of the deepmodel. Default settings are created to be consistent with old versions.
• The number of classes — Class count — selected for a segmentation model in the
Model Generator dialog and the number of classes in the output target multi-ROI
must be the same. In previous versions, the model assumed that output multi-ROIs
contained an additional unspecified background class. For example, the output multi-

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48 Product Enhancements

Deep Learning Improvements

ROI for a segmentation model with a Class count of four previously needed to contain
only three classes.

Class models that previously required multi‐ROIs with three classes (left), now needmulti‐ROIs with four classes (right), as shown above.
• Masks are auto generated from labeled voxels.
• Training patches have to be 100% labeled to be included in training, not 50% aspreviously.
• The method by which data is sampled for training has been changed — fromgenerated patches sampling to grid sampling.

Class Settings
Class settings are now displayed in a table on Model Overview screen, as shown below,

even if model is not loaded. If required, class names and assigned colors can be edited
here.

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Class settings

Dragonfly Release Notes Version 2020.1

Product Enhancements
Deep Learning Improvements

Multi‐Input and Multi‐Slice Models
Dragonfly’s Deep Learning tool now supports multiple inputs, as well as multi-slice
models. These options can be selected in the Model Generator dialog as the Input countand Input dimension options and then configured on the Model Training panel.
Model Generator dialog (above) and Model Training panel (below)

Training
The following changes are implemented for training deep models:• The default training parameters are now selected more carefully.
• No more global shared parameters, such as data augmentation, validation, and so on.
All training parameters are saved as a file in the model folder each time that a modelis trained.
• Training log history can be displayed from the Model contextual menu, as shown

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below.

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50 Product Enhancements

Deep Learning Improvements• The TensorBoard callback is now always used and was removed from the UI. This
callback writes a log for TensorBoard, which lets you to visualize dynamic graphs ofyour training and test metrics, as well as activation histograms for the different layers
in your model. TensorBoard is a visualization tool provided with TensorFlow.
• The Training Progress bar, shown below, was updated to provide more detailed

TM021-A-07

feedback about the real-time status of training.

Dragonfly Release Notes Version 2020.1

Product Enhancements
Deep Learning Improvements

You can also view training progress and the results of each epoch in a list view, asshown below.

• Models can be unloaded to release GPU memory.
• Model status was expanded with additional descriptors — Not loaded — and colorcoding for easy identification.

Selectable GPU for Deep Learning
A new preference for selecting a specific GPU device to use for Deep Learning is now
available in cases in which you have multiple GPUs and need to set one of them for
Deep Learning.
Go to Preferences > Miscellaneous to open the preferences for the available GPU

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cards, circled below.

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52 Product Enhancements

Improvements for Machine Learning Segmentation

Improvements for Machine Learning Segmentation
The Machine Learning Segmentation Tool, which provides classical machine learning
segmentation of multi-dimensional images and was previously referred to as theSegmentation Trainer, was reformatted for this software release to mirror the look andfeel of Dragonfly’s Deep Learning Tool.
Choose Artificial Intelligence > Machine Learning Segmentation on the menu bar toopen the Machine Learning Segmentation dialog, shown below.
Machine Learning Segmentation dialog

Changes implemented for machine learning segmentation include the following:• Some items were re-distributed on the Model, Input, Method, and Results tabs.
• Class definitions, including name, color, and visibility, are available on the Model
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Overview panel.

Dragonfly Release Notes Version 2020.1

Product Enhancements
Improvements for Machine Learning Segmentation• The number of training voxels that intersect with the applied mask is indicated on the

Input panel, as shown below.

• Output targets are now multi-ROIs, not ROIs.

N OTE Refer to the topic New Options for Multi-ROIs on page 27 for information about

creating and labeling classes directly in multi-ROIs and other options.

Edit Deep Model Filters
Additional changes to the Machine Learning Segmentation Tool include the option toedit deep model filters, such as activation maps.
Right-click a Deep Model filter in the Features tree on the Method tab and then choose

Edit in the pop-up menu to open the Feature Preset dialog, shown on the following

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page. You can then edit the filter parameters.

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54 Product Enhancements

Improvements for Machine Learning Segmentation

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Feature Presets dialog

Dragonfly Release Notes Version 2020.1

Product Enhancements
Automated Segmentations

Automated Segmentations
A number of updates for automated segmentations are available in this software releasein the Segment with AI feature. The updated panel, which replaces the one previously

available as Segment with Classifier, is available on the Segment tab on the left sidebar

by default.

Segment with AI panel

The changes implemented for segmenting image data with the Segment with AI featureare summarized below.
• Models are sorted by class count and are no longer separated between deep models
and machine learning classifiers.
• You can view the name and associated color of each class in a selected model, as well
as set visibility for previews, in the Classes box.

• Regression models have been removed. You should note that these models areavailable in the Comprehensive filters for image processing.
• For 3D models, you can choose the reference slice and spacing for applying previews
and segmenting the selected data. These options are available as shown below.

TM021-A-07• The option to segment all slices or selected slices, as well as to apply the model withina mask are now available, as shown below.

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56 Product Enhancements
Dataset Sampler

Dataset Sampler
As an added option for modifying data, you can now downsample and upsample by arandom factor. Right-click the data you need to modify and then choose Modify andTransform > Sample in the pop-up menu to open the Dataset Sampler panel.
Dataset Sampler panel

Export Histogram Data in CSVThis software release provides the opportunity to export histogram data in the commaseparated values (*.csv extension) file format for further analysis or archiving.
This option is available for histograms computed from:• Image data and regions of interest and in the Compare Histograms dialog.
• The Object Analysis dialog, when in histogram view. For example, the histogram of
Phi versus Theta.
• The Histographic Segmentation dialog. For example, image data versus the Sobel 3Dof the image data.
• The Slice Analysis panel.
Click the Export to CSV button, as shown below, from any of the above to export
histogram data in the CSV file format.

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Export to CSV option for histograms

Dragonfly Release Notes Version 2020.1

Product Enhancements
Changes for Annotations

Changes for Annotations
The changes described below are available for annotations, such as rulers, angles, andregions, in the Dragonfly 2020.1 software release.

Constrain Ellipse Tool
You can now constrain the Ellipse tool to a circle by configuring a keyboard shortcut for
the action ‘Constrain ellipse to be round ’.

Custom Captions
In this software version, you can add custom captions to rulers, angles, and otherannotations. Custom captions are available in the Properties box on the Data Properties
and Settings panel for selected annotations.
To create a custom caption, choose Custom in the Caption drop-down menu and thenenter a caption in the Custom caption edit box.
Annotation properties

Additional Options for Shapes
The following options are now available for Shapes in this software release.

Selectable Sizes and Orientation
The software release adds the options to automatically align boxes, capsules, cylinders,and spheres with a selected dataset, as well as to set the dimensions of a shape. These
options are available on the Data Properties and Settings panel for selected shapes, as
shown below.

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Size panel

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5758 Product Enhancements

Application of 3D Visual Effects

Extract Structured Grids
The option to extracted structured grids from a dataset is now available for capsules,
cylinders, and spheres. This feature was previously limited to boxes.
Right-click the required shape in the Data Properties and Settings panel and thenchoose Extract Structured Grid in the pop-up menu to open the Choose a Name and a

Dataset dialog, shown below. You can then enter a name for the extracted structured
grid and the object from which the intersecting data values will be extracted.
Choose a Name and a Dataset dialog

Application of 3D Visual Effects
For single shapes, such as a box or visual plane, you can now set applied 3D visual
effects to the inside or outside of different objects. This can be particularly useful whencreating animated sequences with Dragonfly’s Movie Maker.
In the example below, clipping was applied to the inside of a box for a thickness meshand to the outside of the same box for the corresponding image data.

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Clip applied inside and outside of multiple objects

Dragonfly Release Notes Version 2020.1

Product Enhancements
Scene’s Views Properties Panel

Scene’s Views Properties Panel
A number of new items and additional changes were implemented for the Scene’s Views
Properties panel to accommodate the advanced capabilities of the new rendering engine
for Dragonfly 2020.1. These changes are itemized in the topic Scene's Views Properties
on page 11.

3D Settings
A number of new options are available for adjusting the visualization of image data andother objects in the 3D settings box on the Data Properties and Settings panel whenusing the new rendering engine for Dragonfly 2020.1. These changes are itemized in
the topic 3D Settings Panel on page 13.

Updates for the Organizer
A set of new preferences and pop-up menu items are available for the Organizer in thissoftware release. In addition, an updated progress bar now shows the progress of filedownloads.

Organizer Preferences
The following preferences are available for the Organizer.

Start the Organizer automatically… If selected, the Organizer will appear automatically

onscreen whenever you start Dragonfly.

Synchronize object names with Properties list… If selected, object names will be

synchronized between the Organizer and the Properties list.

Pop‐Up Menu Items
The following contextual menu item is available for objects selected in the Organizer:

Show File in New File Browser… Opens your file browser at that location of the selected

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item.

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5960 Product Enhancements
Managing User DataManaging User Data
Previous Dragonfly releases offered the option to add descriptions to selected objects,
such as image data, regions of interest, meshes, and so on. This software releaseprovides the additional option to add any number of field names and associated values
to an object description.
Right-click an item in the Data Properties and Settings panel and then choose Manage

User Data in the pop-up menu to open the User Data dialog, shown below.
User Data dialog

N OTE Object descriptions entered in previous Dragonfly versions will be migrated automaticallyto the new dialog. The ‘Manage User Data’ item was previously named ‘Edit Object
Description’.

Licensing for Optional Features
You should note that commercial users will require a separate license for each optionalfeature that is available for Dragonfly 2020.1. These features include the following:•

Deep Learning… Includes the Deep Learning Tool , with which you can train deepmodels for image segmentation and regression tasks. Also included with thisfeature is the Segmentation Wizard, which provides an easy-to-use, guided
workflow for implementing deep learning and classical machine learning

segmentation of multi-dimensional images (see Segmentation Wizard on page
15).
You should note that additional features, such as Segment with AI, will be limited
to classical machine learning models without a license for Deep Learning.

•

Auto Process… Enables real-time processing of serial section 2D stack

experiments. You should note that Auto Process is now a standard feature for•Dragonfly Pro.

Bone Analysis… This feature is designed for the evaluation of high-resolution
Hyperspectral Image Analysis… Facilitates the interactive visualization,
manipulation, and analysis of hyperspectral images.

•

Image Stitcher… Lets you precisely combine, or stitch, overlapping 2D or 3D

image tiles to create a single high-resolution image that is beyond the normal

resolution of a microscope’s field of view.
•

Organizer… Provides an easy way to organize, manage, and share data andanalysis results.

Dragonfly Release Notes Version 2020.1

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micro-CT image data of bone specimens (see Bone Analysis Wizard on page 18).

•

Product Enhancements
Academic Licensing Requests•

Plug Analysis… This new feature for Dragonfly provides a dedicated workflow foranalyzing core plugs acquired from rock samples and other porous media (seePlug Analysis Wizard on page 22).

N OTE The optional features listed above for Dragonfly 2020.1, except for Plug Analysis, arebundled with non-commercial licenses and do not require any additional activation keys.

Academic Licensing Requests
You should note that starting with version 2020.1, academic licensing requests can bemade directly from Dragonfly.
Choose Help > Request Non‐Commercial License on the menu bar to open the Request

Non-Commercial License dialog, shown below.
Request Non‐Commercial License dialog

N OTE You must provide your credentials and a photo of the ID issued by your institution, as wellas complete the online survey, to request a non-commercial license.

Proxy Server Settings for License Activations
In most cases, systems must be connected to the Internet to activate a Dragonfly
license. If the Internet connection at your facility runs through a proxy, you can now
configure a proxy server in the Proxy Configuration dialog, shown below, whenever you

activate a Dragonfly license.

To open the Proxy Configuration dialog, click the Configure Proxy button, shown below,
in the Activate Product dialog.

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Proxy Configuration dialog

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62 Product Enhancements

Mapping for Configured Actions

Mapping for Configured Actions
You can now include the Menu key when you configure a shortcut for a configured

action. This new option is circled on the screen capture of the Configure Action dialog

and is shown below.
Configure Action dialog

Developer Documentation
The developer documentation for Dragonfly has been updated for version 2020.1.
Choose Developer > Developer Documentation on the menu bar to open theTM021-A-07

documentation system.

Dragonfly Release Notes Version 2020.1

Menu Bar Changes
File Menu

Menu Bar Changes

The following changes and new items for the refactored menu bar are implemented for
Dragonfly 2020.1.

File Menu
The new items listed below are available for the File menu. Other changes are also
noted.

File menu changes
Description
Import Graph from CSV*

Lets you import a graph that was saved in the comma-separated values (*.csv extension) file format.

User Profile

Opens the User Profile dialog, in which you can enter your name and contact information, as well as add
a copyright notice.

N OTE Was originally available in the Help menu.
* New for version 2020.1.

Workflows Menu
This new menu contains items originally available in the Tools menu, as well as anumber of new items.
Workflows menu
Description
Image Filtering

Opens the Image Filtering module, in which you can process images using standard image filters, deeplearning models, and arithmetic operations.

Active Contour

Opens the Active Contour module, in which you can quickly and efficiently perform segmentation tasks
using the active contour model.

Histographic Segmentation

Open the Histographic Segmentation module, in which you can quickly segment image data by
selecting clustered data values.

Hyperspectral Image
Analysis

Opens the HyperChannels panel on the left sidebar. This module facilitates the interactive visualization,
manipulation, and analysis of hyperspectral images.

Pore Network ModelingOpens the Pore Network Modeling module, which provides a ready-made framework for performing awide range of pore network simulations.

Plug Analysis*

Opens the Plug Analysis wizard, which provides a dedicated workflow for analyzing core plugs acquired
from rock samples and other porous media (see Plug Analysis Wizard on page 22).

CT Reconstruction*

Opens the CT Reconstruction module, which provides tomographic reconstruction of cone-beam andparallel-beam acquisitions (see CT Reconstruction Module on page 25).

MC X-Ray Simulator*

Opens the MC X‐Ray module, which can simulate electron scattering in materials in order to correlate XRay emission to composition in quantitative X-ray microanalysis (see MC X-Ray on page 26).

TM021-A-07* New for version 2020.1.

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Artificial Intelligence Menu

Artificial Intelligence Menu
This new menu contains items originally available in the Tools menu, as well as anumber of new items.
Artificial Intelligence menu
Description
Machine Learning
Segmentation

Opens the Machine Learning Segmentation Tool , which is an advanced machine learning plug-in forimage segmentation.

Deep Learning Model
Evaluation Tool

Opens the Model Evaluation dialog, in which you can compare the results of different deep models withselected metrics.

Deep Learning Tool

Opens the Deep Learning Tool, with which you can train deep models for image segmentation andregression tasks.

N OTE Was previously named ‘Segmentation Trainer’.

Utilities Menu
This new menu contains items originally available in the Tools menu, as well as anumber of new items.
Utilities menu
Opens the Auto Process Stack panel on the right sidebar, which enables real-time automatic processingof serial section 2D stack experiments.

Macro Builder

Opens the Macro Builder, which provides an intuitive, visual way to build and edit complex macros or to
combine multiple macros for batching.

Macro Player

Opens the Macro Player, in which you can record and play macros.

Screen Recorder

Opens the Screen Recorder dialog, which lets you start recording your full screen while working with
Dragonfly.

Camera Position
Bookmarker

Opens the Camera Position Bookmarker, in which you can bookmark and apply camera positions.

Opacity Console

Opens the Opacity Setting dialog, in which you adjust the opacity of multiple objects.

Action Log Viewer

Opens the Action Log Viewer console, in which you view all the actions that were performed during thecurrent session.

Python Console

Opens the Python console, which provides a quick way to execute commands and explore possibilities
that can be pasted into larger scripts.

Report Generator*

Opens the Report Generator panel on the left sidebar, in which you can generate a report from saved
XML data.

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

Start Command Prompt

Opens the Command Prompt window, which lets you access the Python environment from Dragonfly.

Start Command Prompt (asAdministrator)

Opens the Command Prompt window in Administrator mode.

Open All Users Folder in FileBrowser

Automatically opens the Dragonfly directory with the Python All Users Extensions folder in your installedfile manager.

Open Current Users Folder
in File Browser

Automatically opens the Dragonfly directory with the Python Users Extensions folder in your installed file
manager.

Infinite Toolbox

Opens Dragonfly's Infinite Toolbox , in which you can submit, browse, and download extensions that
implement new features and workflows.

Open Plugins

Lets you directly access plug-ins from a drop-down menu.

Dragonfly Release Notes Version 2020.1

TM021-A-07

Description
Auto Process StackMenu Bar Changes
Developer Menu

Description
Structured Grids
Comparator*

Opens the Structured Grids Comparator dialog, in which you can evaluate the quality of processed
image data, regions of interest, or multi-ROIs (see Structured Grids Comparator on page 40).

Graph Shortest Path*

Opens the Graph Shortest Path dialog, in which you can compute the shortest distance between two
selected nodes on a graph and then extract additional scalar values within that interval (see Computing
Shortest Distances on Graphs on page 33).

* New for version 2020.1.

Developer Menu
The new items listed below are available for the Developer menu. Other changes arealso noted.

Developer menu changes
Description
Developer Documentation

Opens the Dragonfly technical documentation package for developers.

Widget Observer

Opens the Widget Observer panel, from which you can examine the properties of the parents and childsof a selected widget (see Widget Observer on page 45).

Deep Model Architecture
Generator

Opens the Deep Model Architecture Generator dialog, in which you can create the architecture for a
new deep model.

FIle Loader Generator

Opens the File Loader Generator dialog, with which you can create a new file load option.

N OTE Was moved from the Help menu.

Help Menu
The new items listed below are available for the Help menu.
Help menu additions
Description
Opens the Request a Non‐Commercial License dialog, in which you can request a non-commercial
license (see Academic Licensing Requests on page 61).

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Request Non-Commercial
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66 Changes to Contextual Menus

Data Properties and Settings Panel

Changes to Contextual Menus

The following changes and new items for the contextual menus are implemented for
Dragonfly 2020.1.

Data Properties and Settings Panel
The following contextual menu items are now available for selected image data,
annotations, regions of interest, multi-ROIs, meshes, shapes, vector fields, and graphson the Data Properties and Settings panel.

Dataset Pop‐Up Menu
A number of new items, listed below, are available for the Dataset pop-up menu. Otherchanges, such as deprecated items, are also listed.
Dataset pop‐up menu changes
Description
Edit Object Description

Item deprecated. Replaced with ‘Manage User Data’.

Export as DICOM

Provides the option to export images in the DICOM format (see Export Images as DICOM on page 43).

Segment with AI

Replaces the item ‘Segment with Classifier’ (see Automated Segmentations on page 55).

Manage User Data

Opens the User Data dialog, in which you can add metadata to the selected item (see Managing User
Data on page 60).

Create Mask

Lets you quickly create an ROI mask with the same shape as the selected image data and that is fullylabeled within the selected dimension and increment. (see Creating Image Masks on page 42).

Find Path ROI Between
ROIs

Automatically computes the path linking two regions of interest (see Find Path Between ROIs on
page 39).

Bone Analysis Wizard

Opens the Bone Analysis Wizard , which is designed for the evaluation of high-resolution micro-CT
image data of bone specimens (see Bone Analysis Wizard on page 18).

Plug Analysis Wizard

Opens the Plug Analysis Wizard, which provides a dedicated workflow for analyzing core plugs
acquired from rock samples and other porous media (see Plug Analysis Wizard on page 22).

Segmentation Wizard

Opens the Segmentation Wizard , which provides an easy-to-use, guided workflow for implementing
powerful deep learning and classical machine learning segmentation of multi-dimensional images (seeSegmentation Wizard on page 15).

Open Processed Image
Comparator

Opens the Processing Image Comparator dialog, in which you can compare processed images with aground truth using selected metrics (see Structured Grids Comparator on page 40).

NOTE This option is available for multiple selections only.

Annotation Pop‐Up Menu
A number of new items, listed below, are available for the Annotation pop-up menu.

Annotation pop‐up menu changes
Description
Edit Object Description

Item deprecated. Replaced with ‘Manage User Data’.

Manage User Data

Opens the User Data dialog, in which you can add metadata to the selected item (see Managing User
Data on page 60).

Align Current View Normal*

Automatically aligns the normal of the current view with the selected ruler.

* Available only for rulers.

Dragonfly Release Notes Version 2020.1

TM021-A-07

Other changes are also noted.

Changes to Contextual Menus
Data Properties and Settings Panel

ROI Pop‐Up Menu
A number of new items, listed below, are available for the Region of Interest pop-up

menu. Other changes are also noted.
ROI pop‐up menu changes

Description
Edit Object Description

Item deprecated. Replaced with ‘Manage User Data’.

Create Dense Multi-ROI
from ROIs

Creates a new multi-ROI, in which the labeled voxels of each selected ROI is assigned to a class and all
unlabeled, or 'complementary' voxels, are labeled as an additional class (see Creating Dense Multi-ROIs
from ROIs on page 29).

Manage User Data

Opens the User Data dialog, in which you can add metadata to the selected item (see Managing User
Data on page 60).

Get Euler Characteristic
NumberAutomatically computes the Euler Characteristic number of the selected ROI (see Euler Characteristic
Number on page 39).

Open Segmentation
Comparator

Opens the Segmentation Comparator dialog, in which you can compare regions of interest with aground truth using selected metrics (see Structured Grids Comparator on page 40).

NOTE This option is available for multiple selections only.

Multi‐ROI Pop‐Up Menu
A number of new items, listed below, are available for the Multi‐ROI pop-up menu.
Other changes are also noted.
Multi‐ROI pop‐up menu changes
Description
Edit Object Description

Item deprecated. Replaced with ‘Manage User Data’.

Create Dense Multi-ROI

Creates a new multi-ROI, in which all unlabeled, or 'complementary' voxels, are labeled and assigned to a
new class (see Creating Dense Multi-ROIs from Multi-ROIs on page 30).

Compute Watershed 2D

Lets you perform a Watershed segmentation on a single slice of a multi-ROI (see 2D Watershed on
page 30).

Manage User Data

Opens the User Data dialog, in which you can add metadata to the selected item (see Managing User
Data on page 60).

Create Images from Scalars

Automatically creates an image for each scalar value checked in the Select Desired Scalars dialog(see Creating Images from Selected Scalars on page 30).

Fill Multi-ROI with New Class

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

Create Cubic Mesh

Item deprecated. Options to create meshes from multi-ROIs are available on the Segment tab on the left
sidebar.

Open Segmentation
Comparator

Opens the Segmentation Comparator dialog, in which you can compare multi-ROIs with a ground truth
using selected metrics (see Structured Grids Comparator on page 40).

TM021-A-07

NOTE This option is available for multiple selections only.

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68 Changes to Contextual Menus

Data Properties and Settings Panel

Mesh Pop‐Up Menu
A number of new contextual items, listed below, are available for meshes. Otherchanges are also noted.
Mesh pop‐up menu changes
Description
Export Mesh to File with
ColorsLets you export scalar meshes in the VRML (*.wrl extension) file format with vertex colors preserved.

Edit Object Description

Item deprecated. Replaced with ‘Manage User Data’.

Manage User Data

Opens the User Data dialog, in which you can add metadata to the selected item (see Managing User
Data on page 60).

Align Axis of Inertia

Lets you automatically align the axis of inertia of the current mesh with the axis of inertia of another mesh.

Add Vertex Normal Angle
from Z Axis Scalar Value

Automatically computes and adds normal angles from the Z-axis (see Scalar Values for Meshes on
page 36).

Apply Translation to Scalar
ValuesLets you apply a linear transformation, with or without an offset, to the values of the selected scalar type.

Compute GaussianCurvature

Automatically computes and adds scalar values of curvature calculated with the Gaussian method (seeScalar Values for Meshes on page 36).

Compute Mean Curvature

Automatically computes and adds scalar values of curvature calculated with the Mean method (seeScalar Values for Meshes on page 36).

Create Vertex Scalar
Distance from Mean Points

Automatically computes and adds scalar values of distances calculated from the mean position of a seriesof points.

N OTE You must first create a points series with the Point tool to enable this item.

Shape Pop‐Up Menu
A number of new items, listed below, are available for the Shape pop-up menu. Otherchanges are also noted.

Pop‐up menu changes for shapes
Description
Edit Object Description

Item deprecated. Replaced with ‘Manage User Data’.

Manage User Data

Opens the User Data dialog, in which you can add metadata to the selected item (see Managing User
Data on page 60).

Remove from Structured
Grid

This item does one of the following:• Removes all labeled voxels in the selected region of interest or multi-ROI that intersect with the voxels
contained in the subvolume defined by the current shape(s).
• Overwrites all voxels in the selected image data that intersect with the voxels contained in the
subvolume defined by the current shape(s). New values will be ‘0’.

TM021-A-07

N OTE This item was previously available only for regions of interest.

Dragonfly Release Notes Version 2020.1

Changes to Contextual Menus
Data Properties and Settings Panel

Vector Field Pop‐Up Menu
A number of new items, listed below, are available for the Vector Field pop-up menu.
Other changes are also noted.

Pop‐up menu changes for vector fields
Description
Edit Object Description

Item deprecated. Replaced with ‘Manage User Data’.

Manage User Data

Opens the User Data dialog, in which you can add multiple attributes to the selected data (see Managing
User Data on page 60).

Delete Selected Scalar
ValuesLets you delete selected measurements. You can select multiple scalar value slots when deleting scalar
information.

Import Scalar Values fromCSV File

Lets you import scalar values contained in a comma-separated values (*.csv extension) file. Scalar values
can imported from either an ORS-formatted CSV file, in which case all slots will be imported, or you canimport scalar slots one-by-one from a generic CSV file that contains the required IDs and corresponding
values.

Map Scalar Values From

Lets you map vertex scalar values contained within another object to the selected vector field.

Add a Constant Vertex
Measurement

Lets you add a constant vertex measurement to the selected vector field.

Apply Translation to Scalar
ValuesLets you apply a linear transformation, with or without an offset, to the values of the selected scalar type.

Export Data to CSV FileLets you export vector fields in the selected comma-separated values (*.csv extension) file format.

Graph Pop‐Up Menu
A number of new items, listed below, are available for the Graph pop-up menu. Otherchanges are also noted.

Pop‐up menu changes for graphs
Description
Edit Object Description

Item deprecated. Replaced with ‘Manage User Data’.

Manage User Data

Opens the User Data dialog, in which you can add multiple attributes to the selected data (see Managing
User Data on page 60).

Plot Graph Tortuosity

Lets you plot the tortuosity within a graph of porous media (see Plotting Tortuosity on page 32).

Plot Graph Throat Weighted
Tortuosity

Lets you plot the throat-weighted tortuosity within a graph of porous media (see Plotting Throat-Weighted
Tortuosity on page 33).

Copy in an ROI as Sphere
and Cylinder

Lets you copy a graph into a region of interest as labeled spheres and cylinders, with either a fixed radiusor radii computed from a selected scalar slot.

Apply Translation to Scalar
ValuesLets you apply a linear transformation, with or without an offset, to the values of the selected scalar type.

Create Vertex Scalar
Distance from Mean Points

Automatically computes and adds scalar values of distances calculated from the mean position of a seriesof points.

TM021-A-07

N OTE You must first create a points series with the Point tool to enable this item.
Get Euler Characteristic
NumberAutomatically computes the Euler Characteristic number of the selected graph (see Euler Characteristic
Number on page 39).

Create Euclidean Length
Scalar Values

Automatically adds measurements of Euclidean length to the edge scalar values.

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70 Changes to Contextual Menus
Views Pop‐Up Menus

Context Group Pop‐Up Menu
This new contextual menu is available for the context groups created when working
with the Segmentation, Bone Analysis, and Plug Analysis wizards.
Pop‐up menu for context groups
Description
ExportLets you export the selected context group in the ORS Object file format (*.ORSObject extension).

Extract Objects from Context
Group

Lets you extract selected objects from the context group. The objects included in the context group can beselected in the Select Objects dialog, shown below.

Execute Macro

Provides a shortcut for selecting macros that can be executed for the context.

Manage User Data

Opens the User Data dialog, in which you can add multiple attributes to the selected context (seeManaging User Data on page 60).

Reopen...

Lets you reopen the selected context and continue your workflow.

Views Pop‐Up Menus
A number of new options are available for the 2D and 3D views pop-up menus.
Views pop‐up menu changes
Description
Orthogonalize Other 2DViews*

Automatically resets all other 2D views in the current scene to be orthogonal to the current scene view.
For example, after you have created an oblique or double-oblique view.

Export Screenshot of View

Lets you export a screenshot of the current view — including its scale bar, legend, annotations, overlays,
and other objects that are visible onscreen — to a number of standard image file formats.

NOTE A no background option is available for exporting screenshots of 3D views (see Export
Screenshots with Transparent Backgrounds on page 44).

TM021-A-07* Available for 2D views only.

Dragonfly Release Notes Version 2020.1

Preferences Changes
Views Preferences

Preferences Changes

A number of new items, listed below, and other changes have been implemented for thesetting the application preferences. You should note that a new set of preferences for
the Organizer have also been added to the Preferences dialog.
Click Preferences on the Status bar or choose File > Preferences on the Menu bar toopen the Preferences dialog.

Views Preferences
Changes for the Views preferences are indicated in the following table.
Views preferences changes
Description
Colors
Virtual floor

Lets you choose a color for the virtual floor option for 3D views (see Scene's Views Properties on
page 11).

Fonts
User interface font size

Lets you choose a font size, in points, for interface elements such as panels, dialogs, and other controls.

3D Settings
Use new rendering engine

Lets you enable Dragonfly’s new rendering engine (see Enabling the New Engine and Setting Defaults on
page 10).

Default preset

Lets you set a default preset for 3D views whenever the new rendering engine is enabled.

Gamma correction

Lets you set a default Gamma correction for 3D views whenever the new rendering engine is enabled.

Interactivity

Lets you set a default Interactivity setting for 3D views whenever the new rendering engine is enabled.

Break during motion

Lets you set a short delay or interval before the requested quality is applied. This can avoid unnecessary
delays when making multiple changes to 3D views, such as rotation, pans, window leveling, and so on.

Configurable Actions
New items for the Configurable Actions preferences are indicated in the following table.
Configurable Actions changes

TM021-A-07

Description
Center MPR 2D views from
3D pick

Lets you automatically update the slice position of all MPR views in the scene to where you clicked in the3D view.

Constrain ellipse to be roundConstrain the Ellipse tool to a circle.

Open the Widget Observer

Opens the Widget Observer panel on the right sidebar (see Widget Observer on page 45).

Start Widget Observer(graph) on widget at cursor

Opens the Graph Observer and displays the properties of the selected instance of class. For example,‘OrsPythonPlugins.OrsBasicManipulate.mainform.mainform’.

Start Widget Observer(single widget) on widget at
cursorOpens the Widget Observer and displays the properties of the selected instance of class. For example,‘OrsPythonPlugins.OrsBasicManipulate.mainform.mainform’.

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72 Preferences Changes
Miscellaneous

Miscellaneous
Changes for the Miscellaneous preferences are indicated in the following table.
Miscellaneous preferences changes
Description
GPU card for Deep Learning

Lets you designate a specific GPU for deep learning (see Selectable GPU for Deep Learning on page 51).

Organizer
The new set of preferences for the Organizer is available in the 2020.1 software
release.

Organizer preferences
Description
If selected, the Organizer will appear automatically onscreen whenever you start Dragonfly.

Synchronize object nameswith Properties list

If selected, object names edited in the Data Properties and Settings panel with be updated automaticallyin the Organizer and vice-versa.

TM021-A-07

Start the Organizer
automaticallyDragonfly Release Notes Version 2020.1

System Requirements
Changes to the System Requirements

System Requirements

This release supports the base system requirements.

Changes to the System Requirements
Changes to the base system requirements are noted below.
System requirements changes
VersionChanges to system requirements

3.0.0

None.

3.1.0

None.

N OTE 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

None.

3.6.0

None.

4.0.0

None.

N OTE The Anaconda distribution was changed to version 5.2.0 for this software release. You should also
note that the current version of Python accessed by Dragonfly will be updated automatically to version
3.6.5 when you install this new release. In addition, the Anaconda distribution will be installed in the
ProgramData folder, as shown below, instead of the Program Files directory.

This change was implemented to allow users to update Dragonfly without running in Administrator mode.
If you are updating a previous installation, the current Anaconda distribution will be deleted from theProgram Files folder.
4.1.0

None.

2020.1None.

N OTE The current version of Python accessed by Dragonfly will be updated automatically to version 3.7.3
when you install this new release.

Extending Dragonfly

Dragonfly’s Infinite Toolbox, an open exchange platform for the Dragonfly user
community, lets you submit, browse, and download extensions that implement new

TM021-A-07

features and workflows for all of your image processing or analysis needs.
Choose Utilities > Infinite Toolbox on the menu bar to open Dragonfly’s Infinite Toolbox.

Requesting New Features

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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74 Getting Help

Learning Dragonfly

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.

Dragonfly Workshops
Our hands-on training workshops are a great way to get up and running quickly.
Combining in-depth instruction with class exercises, our product specialists will quickly
teach you how to use key Dragonfly features and functions to optimize your image
visualization and analysis tasks.
Check for upcoming workshops on our website at:
http://www.theobjects.com/dragonfly/workshops.html.

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 >TM021-A-07

Report an Issue on the menu bar.

Dragonfly Release Notes Version 2020.1

TM021-A-07

Getting Help
Reporting Issues

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TM021-A-07

76

Dragonfly Release Notes Version 2020.1