D RAGONFLY 2020.2
R ELEASE N OTESCOPYRIGHT© 2020 Object Research Systems (ORS) Inc. All rights reserved.
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Title
Dragonfly Release Notes
Release date2020-09-28
Reference number TM021-A-08

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 2020.2 software
release. You should read these release notes before you install this new version.

New Features and Product Enhancements . . . . . . . . . . . . . . . . . . . . . . .5
Segmentation Wizard. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Model Generation Strategy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Support for Multi‐Slice Inputs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Support for Multi‐Modality Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Edit Training Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Training Progress . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Access the Wizard from the Menu Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Deep Learning Tool. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Custom Deep Model Architectures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Apply Options. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Automation and Macros . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Extract Object History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Macro Player . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Macro Builder Blocks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

CT Reconstruction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Center of Rotation Finder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Detector Spacing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Multi‐ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Separate Connected Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Process Islands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Export Classes as Thickness Meshes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Remove Shape from Class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Opacity Settings for Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Morphological Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

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ROIs and Multi‐ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Thresholding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Adjustable Contour Thickness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

ROI Painter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Image Filtering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Create Rulers Between Points . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Pick and Move Annotations in 3D. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Align View with Least Mean Square . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

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4 Contents

New Features and Product Enhancements

Shapes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Graphs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Rendering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Meshes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Camera Pivot Point . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Movie Maker. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Licensing Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Plug Analysis Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Universal Net Project. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .30

How to Participate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Menu Bar Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .32
Artificial Intelligence Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Changes to Contextual Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .32

Data Properties and Settings Panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Dataset Pop‐Up Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Annotation Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
ROI Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Multi‐ROI Pop‐Up Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Mesh Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Shape Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Vector Field Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Graph Pop‐Up Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Preferences Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35

Views Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Configurable Actions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Miscellaneous . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .36

Extending Dragonfly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .36
Requesting New Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .36
Learning Dragonfly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .36

Dragonfly Workshops. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

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Reporting Issues. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37

Dragonfly Release Notes Version 2020.2

New Features and Product Enhancements
Segmentation Wizard

New Features and Product Enhancements

The 2020.2 software release for Dragonfly and Dragonfly Pro provides the following

new features and product enhancements for the Segmentation Wizard, Deep Learning,
automation, CT reconstruction, and other features.

Segmentation Wizard
This Dragonfly release features a number of significant advancements for the
Segmentation Wizard, which provides an easy-to-use, guided workflow for
implementing powerful deep learning and machine learning segmentation of multidimensional images.

Model Generation Strategy
This new option for the Segmentation Wizard lets you choose a model generation
strategy when training is first started, as well as which models to include in subsequent
training cycles.
The Model Generation Strategy dialog, shown below, first appears when you click Trainin the Segmentation Wizard. You should note that the dialog will continue to appear for
additional training cycles as long as any strategy can still generate more models.
Model Generation Strategy dialog

You can do the following in the Model Generation Strategy dialog:• Select a strategy for the current Segmentation Wizard session. You should note that
additional strategies will be implemented in future product releases.
• Select a model to view its parameters.

TM021-A-08• Move models between the Available models list and the Selected models list, eitherwith the right and left arrows or by drag-and-drop. Only selected models will be
trained in the current training cycle.
• Delete models from the selected strategy for the current Segmentation Wizard
session. You can do this to streamline model training.

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56 Contents

New Features and Product Enhancements

Support for Multi‐Slice Inputs
Available in the Model Generator dialog, this new option for the Segmentation Wizard lets
you increase the input dimension of the training dataset(s) from a single slice to multiple
slices.
Click the Generate New Model button on the Models tab to open the Model Generator

dialog. Choose 3D as the Input dimension and then select the number of slices. This
option is circled on the following screen capture.
Model Generator dialog

You should note that the reference slice for multi-slice training is automatically set as
the middle slice for the number of slices selected and that the spacing or offset between
slices is set to 1. In this case, slices are taken sequentially. Dragonfly’s Deep Learning
Tool and Machine Learning Segmentation Tool provide more control for selecting thereference slice and spacing.

N OTE Currently, only U-Net 3D is a fully 3D model that uses 3D convolutions. The number of

input slices for this model is determined by the input size, which must be cubic. For
example, 32x32x32. U-Net uses 2D convolutions, but can take 3D input patches forwhich you can choose the number of slices. You should also note that in somecases, 3D models can be more reliable for segmentation tasks.

Support for Multi‐Modality Models
In some cases, you may want to choose multiple inputs for the training data added to
the Segmentation Wizard. For example, when you are working with data fromsimultaneous image acquisition systems you might want to select each modality as an
input. You can now select multiple inputs for the Segmentation Wizard, either in the
Data Selection dialog if you start the wizard from the menu item (see Access the Wizard

In both cases, the number of modalities for Deep Learning and Machine Learningmodels is generated automatically. However, you should note that you can choose
different feature trees for Machine Learning models in the Model Generator dialog, asshown in the following screen capture.

Dragonfly Release Notes Version 2020.2

TM021-A-08

from the Menu Bar on page 10), or by selecting the multiple inputs in the Data
Properties and Settings panel and then opening the wizard from the contextual menu.

New Features and Product Enhancements
Segmentation Wizard

Model Generator dialog

You should note the following whenever you work with multi-modality models:• All input datasets must be registered and have the same geometry and shape.
• While labeling classes, you can switch the dataset in the view with the Next Imageand Previous Image buttons on the Input tab, circled below, as well as with keyboard

shortcuts ‘Show Next Image Modality’ and ‘Show Previous Image Modality’ (seeTM021-A-08

Configurable Actions on page 35).

• Defined ranges for each dataset will be retained whenever you navigate between the
different input images. You should also note that the opacity of the range highlight is
now selectable (see Thresholding on page 22).
• Reopened Segmentation Wizard sessions will open automatically on the last modalitythat was visible in the workspace.

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8 New Features and Product Enhancements
Segmentation Wizard

Edit Training Parameters
As an additional improvement for the Segmentation Wizard in Dragonfly 2020.2, you
can now edit the training parameters of Deep Models. Right-click the Deep Model you
need to edit on the Model tab and then choose Update Training Parameters in the pop-

up menu to open the Training Parameters dialog, shown below.
Training Parameters dialog

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N OTE Refer to the Dragonfly Help system for information about loss functions, optimization
algorithms, and the data augmentation settings. These topics are available in Deep
Learning in the section on Artificial Intelligence .

Dragonfly Release Notes Version 2020.2

New Features and Product Enhancements
Segmentation Wizard

Training Progress
The Training Progress dialog for the Segmentation Wizard was updated for this productrelease to provide more detailed feedback about the real-time status of training foreach model selected for the current training cycle. An example of the feedback provided
when training a U-Net deep learning model is shown in the following screen capture.
You can also monitor progress in List view, which provides the details of each epoch.
Training dialog

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N OTE The option to cancel training was also updated to let you choose to either cancel all

training or to cancel training for the current model only. These options are available in the
Action Confirmation dialog, as shown below, which appears whenever you click Cancel
or Stop during training.

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910 New Features and Product Enhancements
Deep Learning Tool

Access the Wizard from the Menu Bar
This software release provides to option to open the Segmentation Wizard from either
selected datasets or from the menu bar.
Choose Artificial Intelligence > Segmentation Wizard on the menu bar to first open the

Data Selection dialog, shown below. You can then select the image or images you want
to include in the current Segmentation Wizard session.
Data Selection dialog

Deep Learning Tool
The following enhancements are available for the Deep Learning Tool in Dragonfly
2020.2.

Custom Deep Model Architectures
Dragonfly’s Deep Learning Tool now supports custom deep model architectures formodels that do not follow standard architectures, for example YOLOv3, and for new
workflows, such as noise-to-noise models.

Apply Options
The Apply options for trained models have been updated to let you choose to process all
slices, marked slices, or to limit processing within an ROI mask. These options areshown below, as they appear in the Deep Learning Tool dialog.

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Deep Learning Tool dialog

Dragonfly Release Notes Version 2020.2

New Features and Product Enhancements
Automation and Macros

Automation and Macros
This software release provides a number of new features and updates for automating
workflows.

Extract Object History
The new Extract Action Log from Object feature for Dragonfly 2020.2 lets you automatecomplex scenarios that make use of multiple tools by extracting an object’s history as a
macro. Extracted macros can then be replayed to create a new or modified object byapplying the logged operations.
Do the following to extract the history of an object and play the logged operations:
1. Create or modify the required object with Dragonfly’s extensive toolset.
For example, you could experiment with a recipe that creates regions of interest
within selected ranges and then overwrites them on a small portion of a dataset.
2. Right-click the required object in the Data Properties and Settings panel and thenchoose Extract Action Log from Object in the pop-up menu.

A macro is generated with the name “Filtered session history of session YYYY-MMDD-HH-MM-SS for object xx”, where object xx is the item from which the history
was extracted.

3. Open the Macro Player. The macro can be edited, if required, and then played. You
should note that if your experiment was applied to a small portion of a dataset, you
can remove the cropping block so that the logged operations are applied to the full
dataset.

Principle of Operation
When a new session is started or a session is loaded, the tag “Session started” is added
to the Action log with the current date and time. This serves as the session ID. If
objects are loaded, the identity of those objects (GUID) are written in a starting
inventory in the Action log, with logger variable names.
The session history is saved whenever a session is saved, and includes everything fromthe end of the Action log up to the last “Session started” entry. The starting inventory is
also saved, as well as the ending inventory, with the identity of the objects saved withthe session (GUID) and the logger variable names. You should note that when a session
is loaded, the past history is recovered and the history of the current session is kept asa separate history.
When an object history is extracted, the whole history of the session is taken from theend to the beginning, one session history at a time:
1. The text of the current Action Log is taken and separated in a macro.
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2. The name of the variable (for example, “ROI-05”) to extract from the Action Log is
obtained from the GUID found in the ending inventory.
3. The blocks are analyzed from the end to the beginning and for each block, thefollowing are retrieved:•

The non-constant declared input variables.

•

The names of the variables part of non-constant declared input variable
collections.

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1112 New Features and Product Enhancements
Automation and Macros•

The assigned variables.

•

The declared output variables.

•

The assignments of declared output variables collections.

•

If there is at least one of these names found in the dependence, that block is kept
as follows:
The full block is kept “as is”, unless only assignments are required, in which casethe code is stripped to keep only pure assignments, or loading occurs, in whichcase the assignment is replaced by a call to an macro block with the UUID of themacro of the history of that object.
The declared input variables and the names found in the declared input variables
collections are added in the set of dependent variables to look for in preceding
blocks.
The declared input variables, the names of variables found in declared input
variable collections, the declared outputs variables and the names of thevariables found as assignments of declared output variable collections are addedin a set of variables that could be deleted.

You should note that when the evaluation of the blocks is done for a single session
history, the logger variables found in the starting inventory are identified and passed tothe previous session history using their GUID. A second pass is done through the whole
list of blocks to identify the pure deletion blocks to keep, that is, those affecting thevariables present in the whole history.

Keep Object History

A new preference, “Keep object history”, is available in the Miscellaneous settings tosave the object history in exported *.ORSObject formatted files. You should note thatsaving object histories can time-consuming and that the GUID of all objects is always
preserved when a session is saved or loaded.

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Miscellaneous preferences

Dragonfly Release Notes Version 2020.2

New Features and Product Enhancements
Automation and Macros

Macro Player
The Macro Player now features an expandable tree view that lets you dive-into macro
blocks extracted from object histories (see Extract Object History on page 11) and for
macros that call other macros. As shown in the following screen capture, you can
expand a block to view each individual step within it.
Choose Utilities > Macro Player on the menu bar to open the Macro Player, shown

below. You can expand and collapse blocks as required.
Macro Player

N OTE You can use the Parameter Editor at any step in an expanded macro block to edit a

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logged operation.

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14 New Features and Product Enhancements
Automation and Macros

The reformatted Macro Player also now includes the options to pause or stop the
execution of a macro block. For example, for macros exported from the Macro Builder.
These controls appear in the Stop macro execution dialog, as shown below, whenever

you play a macro.
Macro Player

Macro Builder Blocks
This product release also includes new blocks for the Macro Builder, which aredescribed below.

Prompt user for… Available in both Literals and Dragonfly > Value Chooser, this block

can be added to prompt users to select an object, such as a dataset, shape, region ofinterest, multi-ROI, mesh, annotation, vector filed, graph, or overlay, when a macro is
executed. You can customize the prompt and the title of the message box.

Pause execution… This new block can be found under Miscellaneous and when added,

will make the Macro Player pause at that point. For example, a pause could be added toa macro that extracts a number of cropped regions or sub-volumes. The pause would

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allow users to select a region.

Dragonfly Release Notes Version 2020.2

New Features and Product Enhancements
Automation and Macros

Choose Utilities > Macro Builder on the menu to open the Macro Builder dialog. The

additional options for the Prompt user for block are circled below.

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Macro Builder dialog

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16 New Features and Product Enhancements
CT Reconstruction

CT Reconstruction
This software release provides a number of enhancements for reconstructing cone
beam and parallel beam projections with the CT Reconstruction module.

Center of Rotation Finder
You can now choose from a number of algorithms to find the center of rotation forreconstructing parallel beam projections, as well as preview the results of centers ofrotation computed from different offsets for both parallel and cone beam projections.
Choose Workflows > CT Reconstruction to start the CT Reconstruction module. The
option to open the CT Rotation Finder dialog is highlighted on the screen capture

below.

CT Reconstruction dialog

Options to find and preview centers of rotation are available in the CT Rotation Finder
dialog, as shown below for parallel beam projections.

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CT Rotation Finder dialog

Dragonfly Release Notes Version 2020.2

New Features and Product Enhancements
CT Reconstruction

You can do the following in the CT Rotation Finder dialog:• Choose an algorithm to automatically find the rotation axis location for parallel beam
projections. These include using Nghia Vo’s method, entropy error, and finding theoffset between the first projection and a mirrored projection 180 degrees apart using
phase correlation in Fourier space.
• Preview the results of applying manual offsets from the center value computed fromthe size of the dataset.
• Generate previews from any slice in the projection dataset.
• For comparison purposes, the histograms of generated previews can be evaluated in
the Compare Histograms dialog, shown below.

• Select the best preview and then export the rotation center to the CT Reconstruction
dialog. You can also export a number of previews, which will include the center ofrotation value. Whenever you need to test the selected parameters for areconstruction engine, you can generate a number of previews at different settings
and then import the inputs from the best preview. For comparison purposes, you canplot the intensity profiles of the previews along a ruler or compare their histograms.

N OTE Although the center of rotation is computed automatically from the source and detector

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offset settings for cone beam projections, it is recommended that you use the CT Rotation
Finder if your previews or reconstructions are not satisfactory.

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18 New Features and Product Enhancements
Multi‐ROIs

Detector Spacing
When importing the acquisition parameters for cone beam projections, detector spacing
is now parsed automatically from the selected metadata file. This parameter is circled
below.
CT Reconstruction acquisition parameters for cone beam

Multi‐ROIs
A number of new options for multi-ROIs — Separate Connected Components, Process

Islands, Export Class as Thickness Mesh , and Remove Shape from Class — areavailable in the contextual menu for selected classes, as shown below. These options
are described in the following text.

Separate Connected Components
As a new option for multi-ROIs in Dragonfly 2020.2, you can separate the connectedcomponents, such as fibers, vesicles, and puncti, within a class or selected classes.
Separation is done based on connectivity — 6-connected or 26-connected. In image
processing, connectivity is the way in which voxels in 3-dimensional images relate to

Dragonfly Release Notes Version 2020.2

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Classes pop‐up menu

New Features and Product Enhancements
Multi‐ROIs

their neighbors and are labeled as separate components. You should note that a set ofvoxels in an image that are connected to each other is often called a connectedcomponent.

6‐connected… Propagation is done by strictly using the 6 faces adjacent to the current
seed and will result in the maximum number of connected components.

26‐connected… Propagation is done in all directions, using the 6 faces, 12 edges, and 8

corners adjacent to the current seed. This will result in the fewest number of connectedcomponents.

N OTE In either case, each separated component will be assigned to a new label.

Process Islands
In cases in which you need to refine threshold segmentation results or need to isolate
objects of a certain size, you can now remove small objects from a selected class, aswell as isolate larger objects. These operations can be based on voxel counts or byrank.
The options for processing islands within a selected class are shown in the screen
capture below and are described in the following text.
Options for processing Islands

Right-click a class in the Classes and scalar information box and then choose Process
Islands in the pop-up menu. You can then choose to remove or keep objects as

described below.

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Remove by Voxel Count (6‐connected or 26‐connected)… Removes all objects, as

determined by the 6-connected or 26-connected method, that have a voxel count lower
than a selected threshold. Voxel counts can be selected in the Minimal Voxel Countdialog.

Keep by Voxel Count (6‐connected or 26‐connected)… Keeps all objects, as determinedby the 6-connected or 26-connected method, that have a voxel count higher than aselected threshold. Voxel counts can be selected in the Maximal Voxel Count dialog.

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20 New Features and Product Enhancements
Multi‐ROIs

Remove by Largest (6‐connected or 26‐connected)… Removes a selected number ofthe largest connected components, as determined by the 6-connected or 26-connected
method and as ranked by voxel count. The number of components to remove can beselected in the Remove Biggest Count dialog.

Keep by Largest (6‐connected or 26‐connected)… Keeps a selected number of thelargest connected components, as determined by the 6-connected or 26-connected
method and as ranked by voxel count. The number of components to retain can beselected in the Isolate Biggest Count dialog.

N OTE Components with an identical voxel count are considered as unique objects when they
are ranked.

Export Classes as Thickness Meshes
For analysis purposes, you can now export selected classes as color-coded thickness
meshes that show referential values of the local thickness between boundary points.
Thickness is calculated as the diameter of a hypothetical sphere that fits within eachboundary point. The measurements available in the Scalar information box on the Data
Properties and Settings panel include the minimum and maximum values of the local
thickness. You can also filter displayed ranges in the Measurement Inspector.
Do the following to export a class or classes as a thickness mesh:
1. Right-click the required class or selected classes in the Classes and scalar
information box and then do one of the following:••

Choose Export Class as a Thickness Mesh to export the mesh without sampling.
Choose Export Class as a Sampled Thickness Mesh to export the mesh withsampling. You can then select the required sampling values for the X, Y, and Z
axes in the Export as Sampled Thickness Mesh dialog.

2. Do the following if you need to smooth the mesh for export:•

Choose a smoothing method — Laplacian Smoothing or Hamming Windowed

Smoothing .

N OTE You can adjust additional properties for Hamming Windowed Smoothing in

the Advanced Parameters dialog. Click the Advanced Properties button to open
the dialog.

•

Choose the number of iterations required.

3. Click the OK button to export the selected class or classes as a thickness mesh.
When processing is complete, the exported thickness mesh will appear on the Data
Properties and Settings panel. Thickness meshes can be examined in 2D and 3D

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views.

Dragonfly Release Notes Version 2020.2

New Features and Product Enhancements
Multi‐ROIs

Remove Shape from ClassThis new option for selected classes lets you clear all labeled voxels within a shape. Do
the following to modify the labeling of a class within a shape:
1. Create the required shape, such as a box, capsule, cylinder, or sphere.
2. Right-click the required multi-ROI class in the Classes and scalar information box
and then choose Remove Shape from Class in the pop-up menu.
3. Select the shape you created in the Choose a Shape dialog and click OK .

Opacity Settings for Labels
Available in both the main context and in the Segmentation Wizard, this new option forvisualizing multi-ROIs lets you adjust the opacity of each labeled class independently.
Click the Opacity

icon in the classes list to open the Opacity slider, as shown below.

You can then adjust opacity from 0 to 100 percent with the slider.
Opacity slider for multi‐ROI classes

N OTE Whenever you change the opacity of a class, the global opacity settings selected in theTM021-A-08

2D opacity and 3D opacity boxes will not be applied. However, you can right-click a classwith an individually set opacity and then choose Use Global Opacity in the pop-up menu
to reinstate the global opacity settings.

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22 New Features and Product Enhancements
ROIs and Multi‐ROIs

Morphological Operations
This software release adds support for applying morphological operations, such as

Dilate, Erode, Close, Open, and Smooth, to selected multi-ROI classes. In addition,
operations such as Fill inner areas , are also enabled for multi-ROI classes. These
options are available in the Morphological operations and Operations boxes on the

Segment tab, as shown below, and in the ROI Tools panel in the Segmentation Wizard.
Morphological operations and Operations boxes

N OTE Whenever multiple classes are selected, Dilate, Erode, and other operations will be
executed in order selected, for example, A then B then C.

ROIs and Multi‐ROIs
A number of new options are available for applying thresholds for creating and painting
regions of interest and multi-ROIs, as well as for visualizing ROIs and multi-ROIs in 2D
views.

Thresholding
You can now control the opacity of the selected range highlight when defining a domain
of intensity on 2D views for creating threshold segmentations and for working with the
ROI Painter tools.
Choose the image that will provide the intensity range in the Image drop-down menu
and the adjust the opacity of range highlight with the Opacity slider, as shown below.

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Range box

Dragonfly Release Notes Version 2020.2

New Features and Product Enhancements
ROI PainterAdjustable Contour Thickness
This software release provides the option to adjust the thickness of the contours of an
ROI or multi-ROI that is shown as outlines in the 2D views of a scene. Select therequired ROI or multi-ROI and then check the Show only contour in the 2D settings box

on the Data Properties and Settings panel. You can then adjust the thickness of thecontour with the Contour thickness slider, as shown below.
2D settings

ROI PainterTo facilitate painting in 3D views with the Brush tools, the size of the brush is now
shown while you work.
Spherical Brush tool in 3D view

N OTE Brush sizes can be adjusted with your mouse scroll wheel.

Image Filtering
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The following updates are available for filtering image data in Dragonfly 2020.2.

Mean shift… Multi-threading is now available for the Mean Shift filter, which should

result in faster computations. You should note that mean shift filtering can be used foredge-preserving smoothing and is based on a data clustering algorithm.

Adaptive… The Gaussian method implemented in the Adaptive filter for thresholding

has been replaced with a more robust method from another library.

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24 New Features and Product Enhancements
Annotations

Annotations
A number of new options for working with annotations are available in this productrelease. These are described below.

Create Rulers Between Points
As a new feature for Dragonfly 2020.2, you can now create a ruler between two
selected points. Do the following to create a ruler between two points:
1. Select two points within a Points set, either in a 2D view or in the Points list.
2. Right-click the Points set in the Data Properties and Settings panel and then choose

Create a Ruler Between Two Points in the pop-up menu.

The ruler that connects the two selected points is added to the list of objects in the
Data Properties and Settings panel.

Pick and Move Annotations in 3D
In this software release, you can now re-position rulers and points in 3D views, as
shown below.
Selected ruler in a 3D view

Align View with Least Mean SquareThis new option for Dragonfly 2020.2 lets you align a 2D view with the landmarks
defined with a Points set. The alignment is done by minimizing the sum of the squared

Select the required 2D view and then right-click a Points set in the Data Properties andSettings panel and then choose Align Current View with Least Mean Square in the pop-up view to align the selected view.

N OTE You will need to add at least three points to a Points set to enable this option.

Dragonfly Release Notes Version 2020.2

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residuals, which is equal to the mean displacement.

New Features and Product Enhancements
ShapesShapesThe new Shape properties box on the Data Properties and Settings panel, shown below,groups together new settings for shapes, as well as the visual effect options available inprevious Dragonfly versions.
The new options for adjusting shapes, which include Density and Thickness , are circled
on the following screen capture.
Shape properties

Density… Lets you control the spacing within the grid that defines capsules, cylinders,and spheres. Applicable to 3D views only.

Thickness… Lets you control the thickness of the shape outline in 2D and 3D views andTM021-A-08

the thickness of the grid in 3D views.

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26 New Features and Product Enhancements
GraphsGraphs
A number of improvements for viewing and evaluating graphs are included in thissoftware release. These include improved rendering and additional settings forcustomizing the 3D view of a graph.

RenderingSome of the improvements for visualizing graphs include better depth sorting whenzooming, rounder nodes, and superior rendering edges on top of vertices. An exampleof these enhancements is shown in the following screen capture.
Sparse graph created from a pore network model

Settings
Other options for evaluating graphs include using a constant vertex measurement,
which can help reveal details that are obscured by segments with larger radii.
The Use constant vertex measurement option is available on the Data Properties andTM021-A-08

Settings panel in the Settings box and is circled on the following screen capture.

Dragonfly Release Notes Version 2020.2

New Features and Product Enhancements
GraphsGraph settings

The following example shows the advantage of applying a constant vertex radius whenevaluating a graph. You should note that the vertex radius can be adjusted with theslider.

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Before (left) and after (right) applying a constant vertex radiusObject Research Systems

27

28 New Features and Product Enhancements
MeshesMeshesFor evaluating meshes in 3D views, this Dragonfly release includes the option to adjust
the thickness of edges whenever Wireframes or Outlined is selected as the Fill mode.
This new Thickness slider is available in the Mesh settings box, as shown below.
Mesh settings

Camera Pivot Point
In previous Dragonfly releases, it was only possible to change the camera pivot point in
the 2D views of a scene. You can now adjust the pivot point in the 3D view of a scene.
Select the Pivot Point tool on the Manipulate panel, as shown below, and then adjust

the pivot point as required in any view.
Manipulate panel

Look at Pivot Point… This new configured action lets you automatically center thecamera on the pivot point in 3D views.

Movie Maker
This new release also features a number of improvements and enhancements for theMovie Maker.

Rotation options… The option to add rotations around an object’s axis instead of thecamera axis is now available in the Rotation Options dialog, shown below. To open the
dialog, click the Rotate button on the Movie Panel panel. You will then need to click the

Rotate around the object’s axis button, circled below, to change the default rotation

around the camera axis. You can then select the required rotation.

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Rotation Options dialog

Dragonfly Release Notes Version 2020.2

New Features and Product Enhancements
Licensing Changes

Licensing Changes
The following licensing changes are effective as of the Dragonfly 2020.2 release.

Plug Analysis Wizard
The Plug Analysis wizard, which provides a dedicated workflow for analyzing core plugs
acquired from rock samples and other porous media, will now be bundled with noncommercial licenses and will not require an additional activation key. You should notethat commercial users require a separate license for each optional feature that is

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available for Dragonfly.

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30 Universal Net Project
Licensing Changes

Universal Net Project

The recently launched Universal Net Project is a collaboration between Object Research
Systems and µCT data contributors. The purpose of the project is to design and train a

deep neural network that will be capable of unsupervised or automated segmentation of
new random µCT datasets. To be able to do so, the network has to be trained on adiverse library of µCT data. Contributors are invited to enrich ORS’ existing library ofµCT data with scans representing diverse combinations of µCT equipment, acquisition
parameters, scan content, artifacts, and so on. This diversity is projected to enablebroad network training and the anticipated result is a generalized universal network
capable of precise segmentation. By participating in this project you will be contributing
to the success of your own future research and that of your colleagues.
You can access the Universal Net Project at bones.db.theobjects.com. The Directory
page of the repository is shown in the following screen capture.

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Universal Net Project

Dragonfly Release Notes Version 2020.2

Universal Net Project
How to Participate

How to Participate
If you want to participate in the Universal Net Project, you can join as one of the twocontributor types.

Full dataset contributor accounts… Are for participants who want to provide the projectwith their full scans. Provided data will be manually abridged and then made available

for download for manual segmentation by segmentation contributors. Segmented data
will then be used as training data for the network. You should note that segmentation
contributors will not have access to submitted full datasets.

Segmentation contributor accounts… Are for participants who want to help the projectby manually segmenting abridged data.

N OTE For users who want to create an account as a contributor of full datasets, the site

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administrator will need to review their credentials.

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3132 Menu Bar Changes

Artificial Intelligence Menu

Menu Bar Changes

New items for the menu bar implemented in Dragonfly 2020.2 are listed below.

Artificial Intelligence Menu
New items available on the Artificial Intelligence menu are listed below.
Artificial Intelligence menu
Description
Segmentation Wizard

Opens the Data Selector dialog, in which you can select the image or images that will be added to the
Segmentation Wizard before it launches (see Access the Wizard from the Menu Bar on page 10).

Changes to Contextual Menus

The following changes for the contextual menus are implemented in Dragonfly 2020.2.

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 in the Dataset pop-up menu.
Dataset pop‐up menu changes
Description
Extract Action Log from
ObjectExtracts the object’s history as a macro that can be replayed to create a new or modified object byapplying the logged operations (see Extract Object History on page 11).

Annotation Pop‐Up Menu
A number of new items, listed below, are available in the Annotation pop-up menu.
Annotation pop‐up menu changes
Description
Extract Action Log from
ObjectExtracts the object’s history as a macro that can be replayed to create a new or modified object byapplying the logged operations (see Extract Object History on page 11). You should note that this item isavailable for all annotations.

Align Current View with
Least Mean Square

Automatically aligns the selected 2D view with the landmarks defined with a Points set (see Align View
with Least Mean Square on page 24).

Create a Ruler Between Two
Selected Points

Automatically creates a ruler between two selected points (see Create Rulers Between Points on
page 24).

Dragonfly Release Notes Version 2020.2

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PointsChanges to Contextual Menus
Data Properties and Settings Panel

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

ROI pop‐up menu changes
Description
Extract Action Log from
ObjectExtracts the object’s history as a macro that can be replayed to create a new or modified object byapplying the logged operations (see Extract Object History on page 11).

Multi‐ROI Pop‐Up Menus
A number of new items, listed below, are available in the Multi‐ROI pop-up menu in the
Data Properties and Settings panel.
Multi‐ROI pop‐up menu changes
Description
Assign Unit to Scalar Values

Transforms selected scalar values by assigning a new unit to a measurement. For example, if a length
measurement is equal to 0.0025 meters and you assign centimeters as the unit to the scalar value, thenthe measurement shown will be 0.25 meters. You should note that measurements will always appear inyour selected units, for example 25 centimeters.

Extract Action Log from
ObjectExtracts the object’s history as a macro that can be replayed to create a new or modified object byapplying the logged operations (see Extract Object History on page 11).

New items are also available in the pop-up menu for selected classes in the Classes andscalar information box. These are listed in the following table.
Classes pop‐up menu changes
Description
Lets you separate the connected components within a selected class or classes based on 6-connectedconnectivity (see Separate Connected Components on page 18).

Separate Connected
Components (26-connected)

Lets you separate the connected components within a selected class or classes based on 26-connectedconnectivity (see Separate Connected Components on page 18).

Process Islands

Lets you remove small objects from a selected class, as well as isolate larger objects (see Process
Islands on page 19).

Extract Class as an ROI

Item renamed, was previously available as ‘Extract as ROI’.

Export Class as a Thickness
Mesh

Lets you export selected classes as color-coded thickness meshes that show referential values of thelocal thickness between boundary points(see Export Classes as Thickness Meshes on page 20).

Export Class as a Sampled
Thickness Mesh

Lets you export selected classes as sampled color-coded thickness meshes that show referential valuesof the local thickness between boundary points(see Export Classes as Thickness Meshes on page 20).

Remove Shape from Class

Lets you clear all labeled voxels within a selected shape (see Remove Shape from Class on page 21).

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Separate Connected
Components (6-connected)

Object Research Systems

3334 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.
Mesh pop‐up menu changes
Description
Assign Unit to Scalar Values

Transforms selected scalar values by assigning a new unit to a measurement. For example, if a length
measurement is equal to 0.0025 meters and you assign centimeters as the unit to the scalar value, thenthe measurement shown will be 0.25 meters. You should note that measurements will always appear inyour selected units, for example 25 centimeters.

Extract Action Log from
ObjectExtracts the object’s history as a macro that can be replayed to create a new or modified object byapplying the logged operations (see Extract Object History on page 11).

Shape Pop‐Up Menu
A number of new items, listed below, are available in the Shape pop-up menu.
Pop‐up menu changes for shapes
Description
Extract Action Log from
ObjectExtracts the object’s history as a macro that can be replayed to create a new or modified object byapplying the logged operations (see Extract Object History on page 11).

Vector Field Pop‐Up Menu
A number of new items, listed below, are available in the Vector Field pop-up menu.
Pop‐up menu changes for vector fields
Description
Extract Action Log from
ObjectExtracts the object’s history as a macro that can be replayed to create a new or modified object byapplying the logged operations (see Extract Object History on page 11).

Graph Pop‐Up Menu
A number of new items, listed below, are available in the Graph pop-up menu.
Pop‐up menu changes for graphs
Description
Transforms selected scalar values by assigning a new unit to a measurement. For example, if a length
measurement is equal to 0.0025 meters and you assign centimeters as the unit to the scalar value, thenthe measurement shown will be 0.25 meters. You should note that measurements will always appear inyour selected units, for example 25 centimeters.

Extract Action Log from
ObjectExtracts the object’s history as a macro that can be replayed to create a new or modified object byapplying the logged operations (see Extract Object History on page 11).

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Assign Unit to Scalar Values

Dragonfly Release Notes Version 2020.2

Preferences Changes
Views Preferences

Preferences Changes

A number of new items, listed below, and other changes have been implemented forsetting the application preferences.
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
2D Settings
ROI and Multi-ROI contour
thickness

Lets you select a default contour thickness, in screen percentage, for when regions of interest and multiROIs are shown as outlines in 2D views (see Adjustable Contour Thickness on page 23).

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

Inverts the defined range of the selected image for threshold segmentations and painting (seeThresholding on page 22).

Look at pivot

Centers the camera on the pivot point (see Camera Pivot Point on page 28).

Show next image modality

Changes the view in the Segmentation Wizard to the next image for multi-modality training (see Support
for Multi-Modality Models on page 6).

Show previous image
modality

Changes the view in the Segmentation Wizard to the previous image for multi-modality training (seeSupport for Multi-Modality Models on page 6).

Miscellaneous
Changes for the Miscellaneous preferences are indicated in the following table.
Miscellaneous preferences changes
Description
Saves the object history in exported *.ORSObject files (see Extract Object History on page 11).

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Keep object history

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36 System Requirements
Dragonfly Workshops

System Requirements

This release supports the base system requirements (see http://www.theobjects.com/
dragonfly/system-requirements.html).

Extending Dragonfly

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

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.

N OTE All scheduled Dragonfly workshops have been postponed or cancelled due to worries

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about the coronavirus pandemic. We will resume our workshop schedule as soon as
possible. You can check for updates at http://www.theobjects.com/dragonfly/
workshops.html.

Dragonfly Release Notes Version 2020.2

Reporting Issues
Dragonfly Workshops

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-08

Report an Issue on the menu bar.

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Dragonfly Release Notes Version 2020.2