D RAGONFLY 4.1
R ELEASE N OTESCOPYRIGHT© 2019 Object Research Systems (ORS) Inc. All rights reserved.
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Title
Dragonfly Release Notes
Release date2019-05-13
Reference number TM021-A-06

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

Release Notes
Version 4.1
This document describes the new features, product enhancements, and otherimprovements implemented in the Dragonfly and Dragonfly Pro 4.1 software release.
You should read these release notes carefully before you install this new version.

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

Pore Network Modeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Pore Network Modeling Plugins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Area and Depth Probe Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Depth Probing with Annotation Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
New Segmentation Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
New Options for Editing Regions of Interest . . . . . . . . . . . . . . . . . . . . . . . . . 9
New Options for Segmented Regions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Interfacial Meshes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Three‐Phase Boundaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Get Skeleton of ROI as Graph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Anisotropy Computations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Smoothing Operation for ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Export Dataset Mask. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Graph Analysis Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
New Options for Box Shapes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Edit Visual Box. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

New Image Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

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Gradient‐Domain Fusion Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Ring Artifact Removal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Filter Updates. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Histogram Comparer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Object Descriptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Application Recorder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Export Animated GIFs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Apply W/L and Gamma Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Developer Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Script Runner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
File Loader Generator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Product Enhancements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25

Bone Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Guided Segmentation Steps. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Inputs for Computing Global Measurements. . . . . . . . . . . . . . . . . . . . . . . . . . . 26

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4 Release Notes Version 4.1
Contents

Masking for Computations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Deep Learning Improvements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Model Evaluation Tool. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Clip Box Updates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Automatic Rotations for 3D Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Visibility Toggles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Visual Planes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Window Leveling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Configurable Window Leveling Text Annotation . . . . . . . . . . . . . . . . . . . . . . . . 31

Move Tool Update. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
3D Modeling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Graph Appearance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Export Graph to ROI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Import DICOM Images for Linux . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Auto Updates for the Organizer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Scene’s Views Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Configurable Axis Indicator. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Developer Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Menu Bar Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .36

File Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Tools Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Developer Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Changes to Contextual Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37

Data Properties and Settings Panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Dataset Pop‐Up Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Annotation Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
ROI Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Multi‐ROI Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Mesh Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Shape Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Vector Field Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Graph Pop‐Up Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Views Pop‐Up Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

2D Views Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
3D Views Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Preferences Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .40

System Requirements Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42

Extending Dragonfly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
Requesting New Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
Getting Help. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43

Learning Dragonfly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Dragonfly Workshops . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Reporting Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Dragonfly Release Notes

TM021-A-06

Views Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Configurable Actions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Miscellaneous . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Plugins Toolbar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Release Notes Version 4.1
New Features ‐ Pore Network Modeling

New Features

The 4.1 software release for Dragonfly and Dragonfly Pro provides the following newfeatures. For information about enhancements for Deep Learning and Bone Analysis, aswell as improvements for window leveling, visual planes, 3D modeling, and otherchanges, see Product Enhancements on page 25.

Pore Network Modeling
The 4.1 release includes the full integration of OpenPNM, which provides porous media
researchers with a ready-made framework for performing a wide range of pore network
simulations. The concept of pore network modeling is to represent a porous material asa network or graph of pores, which form the nodes and throats that form theconnections or edges. In a traditional pore network, the pores are the void spaces
between solid objects. However, Dragonfly’s pore network model can consider
connected void space or solid space and even multiple phases within each space.
Choose Tools > Pore Network Modeling on the menu bar to open the OpenPNM tab on

the left sidebar. The pore network modeling workspace is shown below.

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Pore network modeling workspace

Networks are usually “extracted” from images, in which the space is divided into
regions, thereby reducing the complexity of the space and degrees of freedom forsimulation. Direct numerical simulation techniques typically consider every voxel in theimage, whereas pore network models group neighboring voxels together and treat themas larger regions with common properties. This allows for rapid calculations, especiallyfor multiphase flows that are governed by capillary forces. Pore network models are

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56 Release Notes Version 4.1

New Features ‐ Pore Network Modeling

especially suitable for linear transport and percolation problems, and can also provide
estimations of flow at the sub-pore scale.
Fluid flow simulations use the extracted information about the pore regions such as thediameter of an inscribed sphere, cross-sectional area, and volume. The simulations
then use analytical solutions for flow in pipes of equivalent dimensions and shapes tobuild a set of linear algebraic equations of the form Ax + b = 0. The ‘A’s are theconductances of the connecting throats, the ‘b’s are a combination of the boundary
conditions and source terms in the pores, while ‘x’ is the quantity of interest such asconcentration of oxygen in air. The equations are cast into an adjacency matrix andsolved using common matrix inversion techniques.

NOTE The theory of pore network modeling and details of the software are presented in:
Gostick et al., OpenPNM: A pore network modeling package, Computing in
Science & Engineering, 18, 4, (60-74), (2016).

Pore Network Modeling Plugins
The new plugins included in this Dragonfly release for pore network modeling are:Generators… The Image Generator plugin can be used when tomography data is notavailable. This plugin uses PoreSpy generators functions for generating artificial imagesof porous materials for testing, validation, debugging, and illustration purposes. Go tohttps://porespy.readthedocs.io/en/master/modules/generators.html for more
information about PoreSpy generators.

Network Extraction… Although abstract pore network models can be constructed using

cubic lattices for the pore positions and other constructions, such as Delaunay

tessellations, the most useful type of network model is extracted from an image.
The Network Extraction plugin takes a dataset, ROI, or multi-ROI as an input to extract a
network. The extraction uses PoreSpy’s SNOW (Sub-Network of an Over-segmented
Watershed) network extraction algorithm. Details of the algorithm can be found in: Jeff
T. Gostick, Versatile and efficient pore network extraction method using marker-based
watershed segmentation, Physical Review E 96, 2, (2017).
Importantly, the algorithm accurately captures the size and shape of the pores across awide range of porosity, which is the fraction of voxels in the image assigned to aparticular phase. The above manuscript details how experimental percolation data wasmatched for a wide variety of materials including sandstone with 20% porosity andhighly anisotropic fibrous material with 75% porosity.

Network Diagnostics… This plugin provides a simple way to run diagnostic simulations

for the effective properties of the network without specifying boundary conditions.

Boundary Selector… The Boundary Selector plugin lets you select boundaries for

Simulations… The Simulations plugin allows for greater control over the simulation

variables, compared with the Network Diagnostics plugin.

Workspace Manager… This plugin is provided for cases in which OpenPNM, an advanced
open source pore network modeling package, is required for very complex simulations.
The Workspace Manager lets you save objects generated in Dragonfly and then open
them using OpenPNM scripts. Go to http://openpnm.org/ to learn more about OpenPNM.

Dragonfly Release Notes

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performing simulations using the multi-ROI image created during network extraction.

Release Notes Version 4.1
New Features ‐ Area and Depth Probe Tools

Area and Depth Probe Tools
This Dragonfly release provides the option to probe 2D and 3D neighborhoods of image
data, multi-ROIs, and meshes and then extract measurements such as voxel counts,
mean value, and the standard deviation of probed voxels, as well as the scalar values
assigned to multi-ROI labels and to the vertex indexes of scalar meshes. The area anddepth probe tools are applicable to 2D views in any oblique, and are also available forprobing 3D views.
The new area and depth probe tools are available on the updated Probe panel, shown
below.
Probe panel

Refer to the table below for information about the new Probe tools.
Probe tools
Description
Disk Probe… Reports the position and values of the selected circular neighborhood that isaligned with the current view.
Square Probe… Reports the position and values of the selected square neighborhood that isaligned with the current view.
Sphere Probe… Reports the position and values of the selected spherical neighborhood thatis aligned with the current view.

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Cube Probe… Reports the position and values of the selected cubic neighborhood that isaligned with the current view.

NOTE When probing neighborhoods, the diameter of the Disk or Sphere probe, as well as theside measurement of the Square or Cube probe, is selectable. Refer to the Dragonfly
Help system for more information about the Probe measurements and for information
about the configured actions for the Probe tools.

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8 Release Notes Version 4.1

New Features ‐ Depth Probing with Annotation Tools

Depth Probing with Annotation Tools
In addition to the depth probe tools available on the Probe panel (see Area and Depth
Probe Tools on page 7), this software release provides the option to apply an Averaging
mode to profile intensity perpendicular to a ruler or path within a disk or square.
The Averaging mode for rulers and paths, as well as a selectable diameter, is available
in the updated Intensity Profile dialog, shown below.
Intensity Profile dialog

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NOTE You can show the “unaveraged” minimum and maximum values as a series of dottedlines on the profile by selecting the Extra lines option Individual minimum andmaximum.

Dragonfly Release Notes

Release Notes Version 4.1
New Features ‐ New Segmentation Options

New Segmentation Options
The updated Range box, shown below, now includes options to automatically set ranges
defined by the Otsu threshold.
Range box

Lower Otsu… Automatically sets the defined range between 0 and the Otsu threshold.
Upper Otsu… Automatically sets the defined range between the Otsu threshold and the
maximum value in the data range.

NOTE The reformatted Range box, in which you can define intensity domains for thresholdsegmentations and for editing regions of interest, also provides more responsive
performance and additional information, such as the selected sample’s data range andthe range of plotted values on the histogram.

New Options for Editing Regions of Interest
To edit a segmentation, you can now automatically re-assign labeled voxels from one
region to interest to another with the Brush tools. For example, in cases in which an
automated bone segmentation resulted in voxels corresponding to trabecular bone
being erroneously labeled as cortical bone or vice versa. In the example below, corticalbone (highlighted in yellow) was mistakenly assigned to the trabecular regions.

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Automated segmentation result

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910 Release Notes Version 4.1

New Features ‐ New Options for Editing Regions of Interest

NOTE You can also choose to work in the newly introduced Exclusive mode with the Brushtools. In this mode, only the labeled voxels belonging to the selected regions of interest
will be affected when painting. This option is available on the ROI Painter panel as shown
below.

Do the following to re-assign labeled voxels from one ROI to another:1.

Select the 2D view in which you plan to edit the regions of interest.

2.

Select the required regions of interest on the Data Properties and Settings panel.
The selected ROIs are identified as (A) and (B).

3.

Select a 2D or 3D Brush on the ROI Painter panel.

4.

Select the Exclusive option, if required.
In this mode, painting will only be applied to the labeled voxels of the selected
regions of interest. Unlabeled voxels will not be painted.

5.

Do the following, as required:• Add and re-assign labeled voxels to ROI (A) from ROI (B) by holding down LEFTCTRL (or your configured Add with key) and then painting.
As shown below, only labeled voxels highlighted in yellow are re-assigned tothose highlighted in blue when painting in Exclusive mode. Unlabeled voxels are
not painted.

LEFT SHIFT (or your configured Remove with key) and then painting.

Dragonfly Release Notes

TM021-A-06• Remove and re-assign labeled voxels from ROI(A) to ROI(B) by holding downRelease Notes Version 4.1
New Features ‐ New Options for Segmented Regions

New Options for Segmented Regions
A number of new options, such as interfacial mesh generation, extraction of threephase boundaries, anisotropy computations, and smoothing, are available in thissoftware release for regions of interest.

Interfacial Meshes
Normal, sampled, or cubic meshes that describe interfacial surfaces, which can be
defined as the point of contact between two phases, can be generated for selected
regions of interest or multi-ROIs. Right-click the required regions of interest or multiROIs in the Data Properties and Settings panel and then choose 3D Modeling >Generate Interfacial Mesh in the pop-up menu to compute the mesh. You can choose amesh type in the Generate an Interfacial Mesh dialog, shown below.
Generate an interfacial mesh dialog

An example of an interfacial mesh extracted for a segmented phase is shown in thefollowing screen capture.
Interfacial mesh
images in:

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NOTE If more than two regions of interest or multi-ROIs are selected, the interfacial surface

generated will be between the first object selected (A) and the union of all other selected
objects (B + C + D…).

NOTE Interfacial mesh representations are approximations only and computed surfaces may

not correspond to the actual surface. Computing interfacial surfaces from regions ofinterest, which are performed in 3D with interpolated surfaces, is the recommended
alternative for an analysis. In some cases, smoothing a mesh may help to align surface
measurements to those computed from regions of interest.

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12 Release Notes Version 4.1

New Features ‐ New Options for Segmented Regions

Three‐Phase Boundaries
This Dragonfly release includes the option to extract graphs of the three-phaseboundary shared between selected regions of interest and to compute pore throat
thickness. The concept of a three-phase boundary (TPB) is most commonly described infuel cell literature and employed in research, especially with respect to solid oxide fuelcells and polymer electrolyte membrane fuel cells. The TPB concept postulates thathydrogen oxidation and oxygen reduction reactions can only occur at confined spatialsites where electrolyte, gas, and electrically connected catalyst regions contact.
To extract a three-phase boundary graph, select the regions of interest that describe
the three phases and then choose 3D Modeling > Extract Three‐Phase Boundary Graphin the pop-up menu. If you additionally need to compute throat thickness, choose 3D

Modeling > Extract Three‐Phase Boundary Graph and Compute Throat Thickness.

Extract three‐phase boundary options for regions of interest

The result is a three-phase boundary graph that can be examined in a 3D view.

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Three‐phase boundary graph

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Release Notes Version 4.1
New Features ‐ New Options for Segmented Regions

Information and settings related to the graph are available on the Data Properties andSettings panel, as shown in the following screen capture. You should note that scalarvalues related to computed throat thicknesses are available in the Graph settings box
and that these values can be further examined with the help of the Measurement
Inspector.
Properties for three‐phase boundary graphs

NOTE You can further analyze graphs with Dragonfly’s new Graph Analysis tool (see Graph

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Analysis Tool on page 18).

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14 Release Notes Version 4.1

New Features ‐ New Options for Segmented Regions

Get Skeleton of ROI as Graph
This new option for regions of interest automatically creates a graph in which thesegments contained within the skeletonized region of interest are assigned to edges
and vertices. The scalar values of Segment Index, Segment Euclidean Length, Segment
Length, and Segment Tortuosity are also computed automatically and available for
evaluation.
Right-click the required region of interest and then choose 3D Modeling > Get Skeleton
of ROI as Graph to create a graph from an ROI, as shown below.
Graph of skeleton of an ROINOTE The additional options of adding a constant vertex measurement or vertex connectivities

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measurement is available in the pop-up for graphs, as shown below.

You should also note that applying a constant to the vertex radius measurement canfacilitate the evaluation of some graphs.

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Release Notes Version 4.1
New Features ‐ New Options for Segmented Regions

Information about the selected graph, as well as the graph settings, are available on the
Data Properties and Settings panel, as shown below.
Graph information and settings

NOTE You can also evaluate graphs with the help of Dragonfly’s Measurement Inspector. Rightclick the graph and then choose Measurement Inspector in the pop-up menu to open the
Inspector tab on the right sidebar.

NOTE You can further analyze graphs with Dragonfly’s new Graph Analysis tool (see Graph

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Analysis Tool on page 18).

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16 Release Notes Version 4.1

New Features ‐ New Options for Segmented Regions

Anisotropy Computations
This software release provides the opportunity compute anisotropy, which is a measureof how highly oriented substructures are within a volume, using the mean intercept
length (MIL) or star volume distribution (SVD) method. To compute anisotropy, rightclick the required region of interest and then choose Compute Anisotropy Using > MeanIntercept Length (MIL) or Compute Anisotropy Using > Star Volume Distribution (SVD)
in the pop-up menu. The result appears in a message box after the computation iscomplete.
Anisotropy computation

NOTE For an isotropic (perfectly oriented) system, the degree of anisotropy (DA) is equal to 0.

As the system becomes more anisotropic (less well-oriented), the DA increases to somevalue less than 1.

The settings for computing the degree of anisotropy, for example of segmented
trabecular bone, are available in the Set Anisotropy Parameters dialogs, shown below.
Set Anisotropy Parameters dialogs

Refer to the table below for a description of the settings applicable to anisotropy
computations.
Settings for computing anisotropy

Dragonfly Release Notes

Max iterations

Is the maximum number of random points in the sample that will be analyzed. Fitting
will stop automatically after this number is completed or if the coefficient of variation(tolerance) is reached.

Sampling (m)Is the resolution, or distance between subsequent samples along each vector. You
should note that the entered value can be equal to the voxel size of the input regionof interest.

Orientations

Is the number of lines to analyze per sampling sphere.

Min iterations

Is the minimum number of random points in the sample that will be analyzed.

Radius (m)Is the radius of the sampling sphere, which determines the length of each sampling
vector.

Tolerance

Is the coefficient of variation. Sampling new random points will continue until eithera coefficient of variation equal to the tolerance is reached or the maximum numberof iterations is completed.

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Description

Release Notes Version 4.1
New Features ‐ New Options for Segmented Regions

Smoothing Operation for ROIs
In some cases, such as after creating a threshold segmentation, it may be necessary tosmooth a region of interest by removing noise from the surface of an object. This
software release provides a new morphological operation for smoothing ROIs in theMorphological operations box, shown below, which is available on the ROI Tools panel.
Morphological operations

The precise effect of the smoothing operation is determined by the selected structuring
element. If the Range option is also selected, the operation will be limited to the defined
range. An example of smoothing is show in the following screen captures.
Original ROI (left) and smoothed ROI (right)

Export Dataset Mask
It can often be necessary, or useful, to restrict measurements or processing to a subsetof the data that needs to be analyzed. This software release provides the option toexport a subvolume of a dataset that only includes data values that intersect with thelabeled voxels of a selected region of interest.
This option is available in the Dataset operations box on the ROI Tools panel, as shown
below.

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Export option

NOTE Dataset masks are exported in the shape of the selected region of interest.

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18 Release Notes Version 4.1

New Features ‐ Graph Analysis Tool

Graph Analysis Tool
Included in this software release is a Beta version of Dragonfly’s new Graph Analysis
tool. This module lets you conduct a detailed analysis of a selected graph, such asplotting angles between graph edges and node-type abundance, as well as prune
graphs in cases in which nodes or links are not compliant with the graph properties.
To open the Graph Analysis tool, right-click the graph you need to analyze and thenchoose Graph Analysis in the pop-up menu. The screen captures below include theGraph Analysis and the Graph Analysis Histogram dialogs.

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Graph Analysis dialogs

Dragonfly Release Notes

Release Notes Version 4.1
New Features ‐ New Options for Box Shapes

New Options for Box Shapes
A number of new options for automatically resizing boxes to a selected 3D object are
now available in the Shape contextual menu and include the following:

Grow to Contain 3D Object… Expands the box to fully enclose the bounding box of theselected 3D object. In this case, the box will not be contracted or reoriented.

Wrap 3D Object… Resizes and/or reorients the box to tightly wrap the bounding box ofthe selected 3D object.

You can select the 3D object — such as a mesh, dataset, region of interest, or multi-ROI— that you want to contain or wrap to in the Choose a 3D Object dialog, shown below.
Choose a 3D Object dialog

Edit Visual Box
In some post-processing and analysis operations, it might be necessary to modify thespacing of a Box shape or to create a box with a specific granularity. For example, whenchoosing a box for computing vector fields describing anisotropy for a bone analysis.
To open the Edit Visual Box dialog, shown below, right-click the required Box shape andthen choose Edit Visual Box in the pop-up menu.

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Edit Visual Box dialog

NOTE You can also edit the advanced properties of a box, such as its position in space ororientation.

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20 Release Notes Version 4.1

New Features ‐ New Image Filters

New Image Filters
The following new filters are available in this software release for processing image data
and for training deep learning models and classifiers for trainable segmentation.

Gradient‐Domain Fusion Filter
The new gradient-domain fusion filter helps remove inter-image discontinuties, while
preserving intra-image detail, from registered image stacks acquired from modalities
such as scanning electron microscopy (SEM). You should note that gradient-domain
fusion filtering is a two-step process. First, anisotropic smoothing is applied byconvoluting the image stack with an anisotropic Gaussian with low variance in XY and ahigher one is Z. This step removes both low and high frequencies. Then, Poisson
blending is applied to restore the high frequencies by fusing the high frequency of theoriginal image and the lower one of the smoothed data by doing a frequency space
blend.
The result of gradient-domain fusion filtering is illustrated in the example on thefollowing page.
Original data (left) and preview after gradient‐domain fusion filtering (right)

Ring Artifact Removal
Ring artifacts can be a common issue affecting CT image systems and often correspondto detector defects. These artifacts usually appear at fixed positions and form a circle(360 degrees scan) or half circle (180 degrees scan) on tomographic slices. The bestsolution is to avoid these artifacts at the source. However, in cases in which only
reconstructed slices are available, a new Ring Removal filter is available in this

NOTE For more information about his new filter, refer to: https://tomopy.readthedocs.io/en/
latest/api/tomopy.misc.corr.html#tomopy.misc.corr.remove_ring.

Dragonfly Release Notes

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Dragonfly release.

Release Notes Version 4.1
New Features ‐ Histogram Comparer

Filter Updates
Some users have reported that the previews for the K-Means filters can be
unpredictable and that results might not match previews. This was due to a random
centroid initialization and random reassignment. In the updated version of these filters,
the centroid initialization is now deterministic, not random.

Histogram ComparerThis software release adds the option to directly the compare the histograms of multiple
datasets, as shown below. To compare histograms, select the required datasets in the
Data Properties and Settings panel and then choose Compare Histograms .
Histogram Comparator

Object Descriptions
You can now add a description to any object, including image data, regions of interest,
meshes, graphs, and others. Right-click the required object and then choose Add

Object Description to open the dialog shown below.

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Object Description dialog

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22 Release Notes Version 4.1

New Features ‐ Application Recorder

Application RecorderThis release features a simple, easy-to-use application recorder that lets you
automatically record your full screen while working with Dragonfly. The application
recorder, which could be used to make tutorial videos or to illustrate issues you may
experience when working with Dragonfly, does the following:•

Records full screen in high-quality resolution and full color.

•

Mouse highlighting spotlights the location of the cursor.

•

Recordings can be saved in the MPEG4 (*.mp4 extension), AVI (*.avi extension),and GIF (*.gif extension) file formats.

Choose Tools > Application Recorder on the menu bar to open the Recorder panel,shown below.
Recorder panel

Export Animated GIFs
The option to export animations and application recordings in the animated GIF fileformat (*.gif extension) is now available from the 2D Animation panel, the Movie Maker,
and from the Application Recorder.

NOTE When exporting an animated GIF, Dragonfly will first render the full sequence as an

MPEG and then calculate the best color palette for the animated GIF, which is limited to
256 colors. The temporary MPEG will not be retained in memory.

Apply W/L and Gamma Values
In some cases, you may want to apply the window leveling settings and gamma value
you selected for reviewing images to exported image data. This new option, circled
below, is available in the Save As dialog when you choose to export images.

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Save As options

NOTE This is available only for Dragonfly Pro. Contact Object Research Systems for
information about the availability of this version of Dragonfly.

Dragonfly Release Notes

Release Notes Version 4.1
New Features ‐ Developer Tools

Developer Tools
A number of new tools designed for developers, such as the Script Runner and File
Loader Generator, are available in this software release.

Script Runner
The new Script Runner is a tool designed to execute custom code. It can be used for
introspection purposes on any Python object in the application, such as class instances,
widgets, or ROIs. It can also be used to evaluate code snippets or to debug a few lines
of code that is used in a file-based extension, such as a generic menu item. This tool issimilar to the Python console for its ability to execute any code. Multiple scripts can be
kept and recovered after the application is restarted. Moreover, the Script Runnerprovides options to repeat the execution of the provided script, enabling live
introspection of objects being manipulated while the script is run.
Choose Developer > Script Runner on the menu bar to open the Script Runner dialog,
shown below.

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Script Runner dialog

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24 Release Notes Version 4.1

New Features ‐ Developer Tools

File Loader Generator
The new File Loader Generator generates a file canvas from the provided parametersrecognized as a File Loader extension. A File Loader extension allows developers to loada dataset having a specific file format.
Choose Developer > File Loader Generator on the menu bar to open the File Loader

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Generator dialog.

Dragonfly Release Notes

Release Notes Version 4.1
Product Enhancements ‐ Bone Analysis

Product Enhancements

This release provides the following product enhancements for Dragonfly. Information
about new features, such as depth probing, image filters, and the application recorder,
as well newly implemented options for pore network modeling and segmented regions,is available in the topic New Features on page 5.

Bone Analysis
Dragonfly 4.1 includes a number of improvements for the Bone Analysis module. Theseenhancements include guided segmentation steps, expanded inputs for computing
global measurements, and masking to limit lengthy computations.

Guided Segmentation Steps
A series of guided segmentation steps were added to the Bone Analysis dialog that let
you close cortical pores and vascular inlets and fill an initial bone segmentation before
proceeding to the separation of the cortical and trabecular bone.
The first step of the new guided segmentation scheme is shown below.
Filling bone segmentations

The second step of the guided segmentation, shown below, lets you choose asegmentation method for separating filled bone into cortical and trabecularcomponents.

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Segmenting cortical and trabecular bone

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26 Release Notes Version 4.1

Product Enhancements ‐ Bone Analysis

Inputs for Computing Global Measurements
The workflow of Bone Analysis has been changed so that global measurement
computations now rely on input cortical bone and trabecular bone segmentations,instead of the previously automated cortical and trabecular area segmentations. Thischange offers the opportunity to edit automated bone segmentations, as well as to
input any region of interest that satisfies the requirements.
The new inputs for computing global measurements are shown in the following screen
capture.
Inputs for computing global measurements

Masking for Computations
You can now apply a mask to limit the area in which average trabecular separation
thickness will be computed.

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Mask for computing average trabecular separation

Dragonfly Release Notes

Release Notes Version 4.1
Product Enhancements ‐ Deep Learning Improvements

Deep Learning Improvements
This software release features a number of enhancements for Deep Learning, including
the following:• Custom loss function/metrics, including weighted categorical cross-entropy, Dice,
PSNR, SSIM, and Jaccard similarity coefficient.
• Support for loading/saving a model with custom layers, loss functions, and evaluation
metrics.
• Use of the first layers of a Deep Model to compute feature vectors in the
Segmentation Trainer.

Model Evaluation Tool
To help evaluate Deep Learning segmentation quality, this software release features amodel evaluation tool that lets you compare different models with selected metrics,
such as binary cross entropy, mean absolute error, and Poisson for regression, as wellas Jacard similarity, accuracy, and Dice for binary segmentation.
Choose Tools > Deep Learning Model Evaluation Tool on the menu bar to the open the
Model Evaluation dialog, as shown below.

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Model Evaluation dialog

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28 Release Notes Version 4.1

Product Enhancements ‐ Clip Box Updates

Clip Box Updates
Updates for the Clip box, shown in the following screen capture, let you add X, Y, and Z
axis markers, as well as labels that show the length measurements for each axis or
graduated “tick marks” that are aligned on the border of the box. You can also now
choose to show or hide the grid lines and box borders.
Clip box

The additional settings for the Clip box are available on the Data Properties and Settings
panel, shown below.

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Clip settings

Dragonfly Release Notes

Release Notes Version 4.1
Product Enhancements ‐ Automatic Rotations for 3D Views

Clip box settings
Description
Grid lines

If checked, grid lines will be shown on the Clip box.

Borders

If checked, the borders of the Clip box will be shown.

Axis

If checked, the X, Y, and Z axes will be identified and shown on the Clip box.

Label

Lets you choose what labels you want to appear on the Clip box.
None… If selected, no labels will be shown.
Ticks (2 Axes)… If selected, tick marks will be shown at intervals equal to the gridsize along two axes of the Clip box.
Ticks (3 Axes)… If selected, tick marks will be shown at intervals equal to the gridsize along the X, Y, and Z axes of the Clip box.
Length… If selected, the current length of each axis of the Clip box will be shown.
You should note that the initial Clip box applied to an unstructured grid, such as amesh or graph, will be padded by 1% for visualization purposes. If resized, the Clip
box will report the actual dimensions of the unstructured grid.

Lock text

If selected, text associated with the tick marks will not move when the camera isrotated.

NOTE You can select the default colors for the axis and tick marks in the Colors preferences, aswell as the default appearance of the Clip box in the 3D Settings preferences (see Views
Preferences on page 40).

Automatic Rotations for 3D Views
Automatic rotations for 3D views, which can included in animated sequences, areavailable in this software release. Right-click the required 3D view and then choose

Start Rotation in the pop-up menu. The rotation will start automatically from thecurrent pivot position.

A number of new configurable actions for spinning objects in a 3D view are alsoavailable. These include the following:

Spin an object in 3D… Lets you configure a keyboard shortcut to start a spin.
Stop 3D spin… Lets you configure a keyboard shortcut to stop spinning.
Switch to 3D spin mode… Lets you configure a keyboard shortcut to enter spin mode.

Visibility Toggles
This software release introduces as series of keyboard shortcuts that let you set all
objects selected in the Data Properties and Settings panel to non-visible or visible in thecurrent 2D scene views or to toggle the opacity of ROIs, multi-ROIs, and datasets
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selected in the Data Properties and Settings panel. See Configurable Actions on page 40
for a list of all new actions for toggling visibility.

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30 Release Notes Version 4.1

Product Enhancements ‐ Visual Planes

Visual Planes
In this software release, the Visual Plane panel has been removed and all planesettings, such as Show data, are now available on the Data Properties and Settings
panel. In addition a new option to add multiple planes with a single click is available on
the Shapes panel, shown below.
Shapes panel

Visual Plane options
Description
Adds three new planes to the Data Properties and Settings panel.

The options in the Plane settings box on the Data Properties and Settings panel let you
choose an initial orientation for the selected plane or to bind a plane with a selected 2D
view. You can also choose to show corresponding 2D data in the scene’s 3D view. As isthe case for all other shapes, you can choose the additional visual effects you want toapply to the selected plane in the Visual effects box.

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Visual Plane settings

Dragonfly Release Notes

Release Notes Version 4.1
Product Enhancements ‐ Window Leveling

Window LevelingThis software release features a reformatted Window Leveling panel that provides more
responsive performance, particularly when working in 3D views, and additional
information, such as the selected sample’s data range and the range of plotted values
on the histogram. The reformatted panel is shown below.
Window Leveling panel

NOTE This software release also features an update to PyQt from MatPlotLib for computing
histograms, which should result in quicker computations.

Configurable Window Leveling Text Annotation
New options for selecting a mode for the Window Leveling text annotation is available inthis software release, as shown below.
Window leveling text annotation options

You can choose to show the window width and center values (on left above) or theminimum and maximum values of the selected range (on right above). These options
are available in the Miscellaneous preferences, as shown in the following screen

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capture.

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32 Release Notes Version 4.1

Product Enhancements ‐ Move Tool Update

Miscellaneous preferences

Move Tool Update
An additional option — four-quadrants — is now available for manually registering
datasets with the Move tool. This option is circled below.
Move panel

If the option is selected, the 2D views in the workspace will be divided into four
quadrants, with the quadrants on the top left and bottom right showing one dataset andthe remaining quadrants showing the other dataset. This arrangement was
implemented to help align features within the selected datasets, as shown in thefollowing screen capture.

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2D views

Dragonfly Release Notes

Release Notes Version 4.1
Product Enhancements ‐ 3D Modeling

3D Modeling
A number of improvements, listed below, are available for 3D modeling in this software
release.

Graph Appearance
The rendering of graphs is dynamic in this software release, which means that when thedata includes a limited number of nodes, more vertices are displayed. Likewise, when
the data includes a large number of nodes, less vertices will be displayed. This is aimed
at helping to both accelerate and improve visualizations.

Export Graph to ROIThis software release provides the option to export a graph as a region of interest, asshown below.
Export graph to ROI option

Import DICOM Images for LinuxThe option to import DICOM images is now available for the Linux version of Dragonfly.
Choose File > Load DICOM Folder on the menu bar to open the Select DICOM Folder

dialog, shown below.

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Select DICOM Folder dialog

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34 Release Notes Version 4.1

Product Enhancements ‐ Auto Updates for the Organizer

Auto Updates for the Organizer
As an update for Dragonfly’s Organizer, you can now synchronize a project with changes
made in the workspace. For example, after editing a region of interest. As shown below,
simply click the Update All Objects button to save all of the changes that were made to

all of the objects opened from the current project.
Organizer dialog

Scene’s Views Properties
The option to apply anti-aliasing to 3D scene views, in order to smooth jagged edges on
curved lines and diagonals, is now available on the Scene’s Views Properties panel. This
option is circled below.

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Scene’s Views Properties panel

NOTE You should also notice additional improvements for setting the Lighting properties for 3D
views.

Dragonfly Release Notes

Release Notes Version 4.1
Product Enhancements ‐ Configurable Axis Indicator

Configurable Axis Indicator
An additional representation for the Axis Indicator that appears in 3D views is available
in this software release. Right-click the 3D view and then choose Axis Indicator in the

pop-up menu. You can select Cube , Arrows , or None in the submenu.
Axis Indicator styles

NOTE You can choose a default appearance for the Axis Indicator in the 3D Settings
preferences (see Views Preferences on page 40).

Developer Documentation
The developer documentation for Dragonfly has been updated for version 4.1. Choose

Help > Dragonfly Developer Documentation on the menu bar to open theTM021-A-06

documentation system.

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36 Release Notes Version 4.1

Menu Bar Changes ‐ File Menu

Menu Bar Changes

The following changes and new items for the menu bar are implemented for Dragonfly
4.1.

File Menu
The new items listed below, and other changes, are available for the File menu.
File menu changes
Description
Import Selected Object(s)from FileLets you import selected objects from an ORS Object file (*.ORSObject extension) that contains multiple
objects. You can select all of the objects that you want to import in the Select Objects dialog, shown
below.

Tools Menu
The new items listed below, and other changes, are available for the Tools menu.
Tool menu changes
Description
Application Recorder

Opens the Recorder dialog, which lets you record your screen while working with Dragonfly (seeApplication Recorder on page 22).

Deep Learning Model
Evaluation Tool

Opens the Model Evaluation dialog (see Model Evaluation Tool on page 27).

Pore Network ModelingOpens the OpenPNM tab on the left sidebar (see Pore Network Modeling on page 5).

Developer Menu
The new items listed below, and other changes, are available for the Developer menu.
Developer menu changes

Opens the Script Runner dialog (see Script Runner on page 23).

File Loader Generator

Opens the File Loader Generator dialog (see File Loader Generator on page 24).

Dragonfly Release Notes

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Description
Script RunnerRelease Notes Version 4.1
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 4.1.

Data Properties and Settings Panel
The following contextual menu items are now available for datasets, annotations,regions of interest, multi-ROIs, meshes, shapes, vector fields, and graphs on 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.
Dataset pop‐up menu changes
Description
Compare Histograms

Available for multiple selections, this option lets you directly compare the histograms of selected datasets(see Histogram Comparer on page 21).

Edit Object Description

Lets you enter a description for the selected dataset (see Object Descriptions on page 21).

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

Lets you enter a description for the selected annotation (see Object Descriptions on page 21).

ROI Pop‐Up Menu
A number of new items, listed below, are available for the Region of Interest pop-up
menu. You should also note that the ROI pop-up menu was reformatted into groups,
such as Modify and Transform, Connected Components, and 3D Modeling, for easieraccess to the available options.
ROI pop‐up menu changes
Description
Edit Object Description

Lets you enter a description for the selected region of interest (see Object Descriptions on page 21).

Compute Anisotropy Using

Mean Intercept Length (MIL)… Lets you compute the degree of anisotropy for the selected region ofinterest using the mean intercept length (MIL) method (see Anisotropy Computations on page 16).

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Star Volume Distribution (SVD)… Lets you compute the degree of anisotropy for the selected region ofinterest using the star volume distribution (SVD) method (see Anisotropy Computations on page 16).

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38 Release Notes Version 4.1

Changes to Contextual Menus ‐ Data Properties and Settings Panel

Description
3D Modeling

Get Skeleton of ROI as Graph… Lets you create a graph of a skeletonized region of interest (see Get
Skeleton of ROI as Graph on page 14).
Generate Interfacial Mesh… Lets you generate an interfacial mesh from multiple regions of interest (seeInterfacial Meshes on page 11).
Extract Three-Phase Boundary Graph and Compute Throat Thickness… Lets you extract a graph ofthe three-phase boundary shared between selected regions of interest that includes scalar values of porethroat thickness (see Three-Phase Boundaries on page 12).
Extract Three-Phase Boundary Graph… Lets you extract a graph of the three-phase boundary shared
between selected regions of interest (see Three-Phase Boundaries on page 12).

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

Lets you enter a description for the selected multi-ROI (see Object Descriptions on page 21).

Generate Interfacial Mesh

Lets you generate an interfacial mesh from multiple multi-ROIs (see Interfacial Meshes on page 11).

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

Lets you enter a description for the selected mesh (see Object Descriptions on page 21).

Add a Constant Vertex
Measurement

Lets you add a constant vertex measurement to the selected mesh. The name of the measurement andits value can be entered in the Name and Value dialogs, respectively.

Shape Pop‐Up Menu
A number of new items, listed below, are available for the Shape pop-up menu.
Shape pop‐up menu changes
Description
Grow to Contain 3D Object*

Automatically expands a box to fully enclose the bounding box of a selected 3D object (see New Options
for Box Shapes on page 19).

Wrap 3D Object*

Automatically resizes and reorients a box to tightly wrap the bounding box of a selected 3D object (seeNew Options for Box Shapes on page 19).

Edit Visual Box*

Lets you modify the spacing of a Box shape or to create a box with a specific granularity (see Edit VisualBox on page 19).

Vector Field Pop‐Up Menu
A number of new items, listed below, are available for the Vector Field pop-up menu.
Pop‐up menu changes for vector fields
Description
Edit Object Description

Dragonfly Release Notes

Lets you enter a description for the selected vector field (see Object Descriptions on page 21).

TM021-A-06* Available for box shapes only.

Release Notes Version 4.1
Changes to Contextual Menus ‐ Views Pop‐Up Menus

Graph Pop‐Up Menu
A number of new items, listed below, are available for the Graph pop-up menus.
Pop‐up menu changes for graphs
Description
Edit Object Description

Lets you enter a description for the selected graph (see Object Descriptions on page 21).

Graph Analysis

Opens the Graph Analysis dialog, in which you can conduct detailed analyzes, such as plotting angles
between graph edges and node-type abundance, as well as prune graphs (see Graph Analysis Tool on
page 18).

Add a Constant Vertex
Measurement

Lets you add a constant vertex measurement to the selected graph. The name of the measurement andits value can be entered in the Name and Value dialogs, respectively.

Add Vertex Connectivities
Measurement

Lets you add vertex connectivities measurements to the selected graph.

Views Pop‐Up Menus
A number of new options are available for the views pop-up menus.

2D Views Pop‐Up Menu
A number of new items, listed below, are available for the 2D Views pop-up menu.
2D Views pop‐up menu changes
Description
Orthogonalize Other 2D
Views

Lets you set the 2D views in a scene to be orthogonal to a selected oblique or double-oblique view.

3D Views Pop‐Up Menu
A number of new items, listed below, are available for the 3D Views pop-up menu.
3D Views pop‐up menu changes
Description
Start Rotation

Lets you start an automated rotation of the view (see Automatic Rotations for 3D Views on page 29).
Lets you choose a style for the Axis Indicator (see Configurable Axis Indicator on page 35).

Hide Movie Maker

Lets you hide the Movie Maker panel in the selected 3D view. In this case, all thumbnails on the timeline
will be kept.

Close Movie Maker

Lets you close the Movie Maker panel in the selected 3D view. In this case, all thumbnails will be removed
from the timeline.

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Axis Indicator

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40 Release Notes Version 4.1

Preferences Changes ‐ Views Preferences

Preferences Changes

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

Views Preferences
Changes for the Views preferences are indicated in the following table.

Views preferences changes
Description
ColorsClip box

Lets you choose the default colors applied to the Clip box.
X axis… Lets you select the color used to identify the X axis.
Y axis… Lets you select the color used to identify the Y axis.
Z axis… Lets you select the color used to identify the Z axis.
Ticks color… Lets you select the color of the tick marks.
Plane color… Determines the color applied to the selected plane of a Clip box.

3D Settings
Axis indicator

Lets you choose the default appearance of the Axis Indicator.
Cube… If selected, the Axis Indicator will appear as a cube.
Arrows… If selected, the Axis Indicator will appear as a series of three interconnected arrows.
None… If selected, the Axis Indicator will not be shown.
Axis indicator size… Determines the size, in screen percentage, of the Axis Indicator.

Clip box

Lets you choose the default appearance of the Clip box.
Show grid lines… If selected, grid lines will appear by default on newly created Clip boxes.
Show border… If selected, borders will appear by default on newly created Clip boxes.
Show axis… If selected, axes will appear by default on newly created Clip boxes.
Show ticks… If selected, graduated “tick marks” will appear by default on newly created Clip boxes.
Axis size… Lets you choose the thickness of the axis lines.
The following settings are available in the Clip box ticks font box to customize the appearance of the clip
box tick marks:
Font… Lets you choose a font face for the tick marks.
Font size (in screen percentage)… Lets you choose a font size, relative to the resolution of the views in
the workspace, for the tick marks.
Minimum font size (in points)… Lets you set a minimum font size, in points, that determines how small
the tick marks can decrease when views are resized.

Configurable Actions
Configurable Actions preferences changes
Description
Set all selected objects nonvisible in 2D

Lets you configure a keyboard shortcut to set all objects selected in the Data Properties and Settings
panel to non-visible in the current 2D scene views.

Set all selected objects
visible in 2D

Lets you configure a keyboard shortcut to set all objects selected in the Data Properties and Settings
panel to visible in the current 2D scene views.

Dragonfly Release Notes

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Changes for the Configurable Actions preferences are indicated in the following table.

Release Notes Version 4.1
Preferences Changes ‐ Miscellaneous

Description
Toggle the 2D visibility of theselected object

Lets you configure a keyboard shortcut to toggle the visibility of all objects selected in the Data Properties
and Settings panel to visible in the current 2D scene views.

Toggle the 2D opacity of
selected ROIs, multi-ROIs,
and datasets

Lets you configure a keyboard shortcut to toggle the opacity of ROIs, multi-ROIs, and datasets selected in
the Data Properties and Settings panel or Opacity Settings dialog. Toggling will be between 0 and the set
opacity value.

Spin an object in 3D

Lets you configure a keyboard shortcut to start spinning objects in the selected 3D view.

Stop 3D spin

Lets you configure a keyboard shortcut to stop spinning.

Switch to 3D spin mode

Lets you configure a keyboard shortcut to enter spin mode.

Miscellaneous
Changes for the Miscellaneous preferences are indicated in the following table.
Miscellaneous preferences changes
Description
Window leveling text
annotation mode

Lets you choose the default mode — Show range or Show width and center — for the Window Levelingtext annotation (see Configurable Window Leveling Text Annotation on page 31).

Plugins Toolbar
This new set of preferences lets you configure the Plugins Toolbar panel with a selected
number of plugins.

TM021-A-06

Plugins Toolbar preferences

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42 Release Notes Version 4.1

System Requirements Changes ‐ Plugins Toolbar

System Requirements Changes

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

VersionChanges to system requirements

3.0.0

None.

3.1.0

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

3.5.0

None.

3.6.0

None.

4.0.0

None.
NOTE 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.

Extending Dragonfly

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

Requesting New Features

to an existing workflow.

Dragonfly Release Notes

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Let us know if you have a suggestion for a new feature, or an idea for an improvement

Release Notes Version 4.1
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-06

Report an Issue on the menu bar.

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Dragonfly Release Notes