D RAGONFLY R ELEASE N OTESV ERSION 4.0

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Title
Dragonfly Release Notes
Release date2019.01.16
Reference number TM021-A-05

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

Release Notes
Version 4.0
This document describes the new features, product enhancements, and otherimprovements implemented in the Dragonfly and Dragonfly Pro 4.0 software release.
You should read these release notes carefully before you install this new version.

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

Official Linux Release . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Dragonfly Organizer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Bone Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Image Stitching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Stitch 3D Datasets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Create 4D Datasets. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Macro Builder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Hyper‐Dimensional Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Plugin Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Feret Diameter Measurements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Feret Diameters Definition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Feret Diameter Measurements for ROIs and Meshes . . . . . . . . . . . . . . . . . . . . 18
Feret Diameter Measurements for Multi‐ROIs . . . . . . . . . . . . . . . . . . . . . . . . . 18

New Image Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Artifact Removal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Comprehensive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Segmentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Smoothing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Texture Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Thresholding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Additional Options for Image Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Add Gaussian Noise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Extract ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Overwrite Dataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

TM021-A-05

New Options for ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Graphing for ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Label Edges of Graph of ROI. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Statistical Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Volume Thickness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Interfacial Surface Computations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Selectable Connectivity for Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Remove Unwanted Objects (Process Islands) . . . . . . . . . . . . . . . . . . . . . . . . . 28
Create ROIs Using Neighbor Counts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Object Research Systems

4 Release Notes Version 4.0
Contents

Smoothing for Thickness Mesh Export . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Close Inner Holes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Geodesic Distance Maps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Export ROI as Binary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

New Options for Multi‐ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Graphing for Multi‐ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Statistical Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Previous Analyzes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Import Scalar Values. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Extract ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Split Non‐Connected Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Get Merged Label as Multi‐ROI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

New Options for ROIs and Multi‐ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Convex Hulls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Remove Touching Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Boolean Operators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

New Options for Meshes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Mesh Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Mesh Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Mesh Smoothing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Mesh Subdivider. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Get Non‐Manifold Edges Count . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
New Options for Scalar Meshes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Shape Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
New Options for Boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Take Box Shape from Feret Of. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Take Minimal Box Shape Of . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

New Options for Annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Extract Images from Visual Planes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Gamma Ramp for Window Leveling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Configurable Actions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Synchronize 3D Views. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Movie Maker. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
2D Animations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

Product Enhancements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .49

Deep Learning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Dataset Registration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Dataset Sampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Slice Alignment Outputs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Active Contour . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Connectivity Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Updates for the Dataset Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
List Items. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Undo for Applied Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Data Units . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

3D Presets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Dragonfly Release Notes

TM021-A-05

Fixed Mask . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Scaling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Refresh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Release Notes Version 4.0
Contents

Clip and Visual Effects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Legends. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Histograms and Graphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Slab Thickness Adjustments for 2D Views . . . . . . . . . . . . . . . . . . . . . . . . . 57
Text Annotations for 3D Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Support for RGB Images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
ROI Painter Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Measurement Inspector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
About Menu Items . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Developer Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

Menu Bar Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .62

File Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Tools Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Help Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

Changes to Contextual Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .63

Dataset Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Region of Interest Pop‐Up Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Multi‐ROI Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Mesh Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Shapes Pop‐Up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Preferences Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .66

Views Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
2D Settings Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
3D Settings Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Autosave Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

System Requirements Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67

Extending Dragonfly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67
Requesting New Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67
Getting Help. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .68

TM021-A-05

Learning Dragonfly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Reporting Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

Object Research Systems

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Dragonfly Release Notes

Release Notes Version 4.0
New Features ‐ Official Linux Release

New Features

The 4.0 software release for Dragonfly and Dragonfly Pro provides the following newfeatures. For information about deep learning enhancements — as well as
improvements for registering datasets, sampling, creating animations, and otherchanges — see Product Enhancements on page 49.

Official Linux Release
This software release marks the official release of the Linux versions for Dragonfly andDragonfly Pro.

Dragonfly Organizer
Dragonfly’s new Organizer provides an easy way to organize, manage, and share yourdata and analysis results. The Organizer is equipped with drag-and-drop features sothat you can readily add objects — such as image data, regions of interest, multi-ROIs,
meshes, screen captures, session files, and more — to a project.
Dragonfly Organizer dialog

With Dragonfly’s new Organizer you can:• Organize data in a variety of ways, add tags to a project and saved objects for easy
TM021-A-05

searching, as well as move, rename, merge, and delete projects.
• Create root folders that can hold multiple project folders.
• Search local drives and remote servers for matching tags and data types, or by date.
• Protect your private data while sharing your public projects with other users.

NOTE The Organizer is a separately licensed feature for Dragonfly. Contact Object Research
Systems to request pricing for this module and availability.

Object Research Systems

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8 Release Notes Version 4.0
New Features ‐ Bone Analysis

Bone Analysis
The Bone Analysis module for Dragonfly 4.0 lets you discover new productivity for yourbone image analysis needs. With the unique pairing of robust quantification with
options to map and analyze trabecular anisotropy by orientation, Dragonfly’s Bone
Analysis module lets you better understand complex metabolic bone diseases to help
develop new therapies and treatments. The benefits of Bone Analysis include thefollowing:• Computation of common bone morphometric measurements, as described byBouxsein et al. 2010. JBMR 25(7):1468-86, from segmented bone regions thatprovide quantitative descriptions of bone microarchitecture.
• Computation of anisotropy with surface orientation of trabecular bone.
• Mapping of orientation and value — from a mesh and from an ROI — colorizedaccording to the orientation of the vectors.

NOTE Bone Analysis is a separately licensed feature for Dragonfly 4.0. Contact Object
Research Systems to request pricing for this module and availability.

Bone Analysis results

Mapping of trabecular bone thickness

Mapping of surface normal anisotropy

analysis of high-resolution micro–computed tomography (micro-CT) images. You shouldnote that currently available micro-CT scanners can achieve an isotropic voxel size of as
low as a few micrometers, which should be sufficient for investigating structures such as
mouse trabeculae that have widths of approximately 30 to 50 micrometers. You should
also note that measurement error will decrease as the ratio of voxel size to object size
decreases, regardless of scale.

Dragonfly Release Notes

TM021-A-05

NOTE The Bone Analysis module is a pre-clinical research application designed to facilitate theRelease Notes Version 4.0
New Features ‐ Bone Analysis

Dragonfly's Bone Analysis module can separately segment and identify cortical andtrabecular bone in whole-bone specimens. The calculation of common bonemorphometric measurements from these segmented regions then provide quantitativedescriptions of bone microarchitecture.
To start an analysis, choose Bone Analysis in the Tools menu. Automated segmented

routines, cortical and trabecular measurements, as well as mappings of anisotropy, areavailable in the Bone Analysis dialog shown in the following screen capture.
Bone Analysis dialog

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Global measurements for segmented cortical and trabecular areas
Abbreviation

Measurement

Description

Ani.MIL

Anisotropy (MIL)*

A measurement of the orientation of trabecular architecture that uses the meanintercept length (MIL) method.
The MIL method (Whitehouse, 1974; Harrigan and Mann, 1984; Cowin, 1986) uses
the mean distance between material intersections (bone–marrow interfaces) along
linear traverses over a range of orientations. Because MIL traverses cross bothmaterials, the result is a combined measure that incorporates features of bothmaterials.

Object Research Systems

910 Release Notes Version 4.0
New Features ‐ Bone Analysis

Abbreviation

Measurement

Description

Ani.SVD

Anisotropy (SVD)*

A measurement of the orientation of trabecular architecture that uses the star
volume distribution (SVD) method (Cruz-Orive et al.,1992; Karlsson & Cruz-Orive,1993).
In this method, the distribution is determined by placing a series of points within thematerial of interest, and measuring the lengths of the lines emanating from them invarious directions until they encounter a boundary. These lines are consideredinfinitesimal cones, with their vertex at the origin and subtending a solid angle as
they approach the material interface.

TV

Total volume

Volume of the entire region of interest.

BV

Bone volume

Volume of the region segmented as bone, calculated in the same manner as TV.

BV/TV

Bone volume fraction

Ratio of the segmented bone volume to the total volume of the region of interest.

Ct.Th

Average cortical thickness**

Mean thickness of cortical bone.

Tb.Th

Average trabecular thickness**

Mean thickness of trabeculae.
Calculated by fitting maximal spheres within the trabecular structure. The diametersof the spheres within the bone and the marrow regions provide estimates of Tb.Th
and Tb.Sp.

Tb.Sp

Average trabecularseparation**

Mean distance between trabeculae.

Ct.Ar

Average cortical area

Cortical bone area, computed as:

Ma.Ar

Average marrow area

Medullary (or marrow) area.

Tt.Ar

Average total area
(cortical + marrow)

Total cross-sectional area inside the periosteal envelope.

Ct.Ar/Tt.Ar

Average cortical area fraction

Cortical area fraction.

Ps.S3D

Periosteal surface (3D)

Total surface area of the periosteum, which is the membrane that lines the outersurface of all bones, except at the joints of long bones.

Ec.S3D

Endocortical surface (3D)

Total surface area of the endocortex, which lines the inner surface of all bones.

Ps.Pm

Periosteal perimeter

Total perimeter of the periosteum.

Ec.Pm

Endocortical perimeter

Total perimeter of the endocortex.

cortical volume (Ct.V) / (number of slices x slice thickness).

* The orientation of trabecular architecture can affect mechanical behavior and is often associated with disease and aging.

TM021-A-05** Assessed using direct 3D methods.

Dragonfly Release Notes

Release Notes Version 4.0
New Features ‐ Bone Analysis

In addition to the global parameters available in the Bone Analysis dialog for volumes,
areas, and perimeters, per slice measurements in any oblique for segmented corticaland trabecular areas are available in the Slice Analysis panel, as shown below.
Slice Analysis panel

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Per slice measurements for segmented cortical and trabecular areas
Abbreviation

Measurement

Voxel Count

Number of voxels contained in the selected region of interest.

lXX

Moment of inertia (XX).

lYY

Moment of inertia (YY)lmax

Maximum moment of inertia.

lmin

Minimum moment of inertia.

J

Polar moment of inertia.

Th

Mean thickness.

Pm

Perimeter.

ROI Area

Area of the labeled voxels contained in the selected region of interest.

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12 Release Notes Version 4.0

New Features ‐ Image Stitching

Image Stitching
Dragonfly’s powerful new Image Stitcher provides automated and manual alignments toprecisely combine, or stitch, overlapping 2D or 3D image tiles to create a single highresolution image. The coordinates of the tiles in a dataset can be taken directly from a
configuration file or a grid layout can be selected in the Layout Editor to position thetiles in the Stitching workspace. However, the real advantage of Dragonfly's Image
Stitcher can be found in the automated alignment methods that can correct both
systematic and non-systematic collection errors.

NOTE The Image Stitcher is a separately licensed feature for Dragonfly and is currently

available as beta for evaluation purposes. Contact Object Research Systems to request
pricing for this module and availability.

Right-click the dataset with the image files that you need to stitch in the Data
Properties and Settings panel and then choose Image Stitching in the pop-up menu to
open the Stitching contextual window, shown below.
Stitching window

The workspace contains a view of the image tiles arranged in the selected grid layout.
You can apply different LUTs to your Reference and To Stitch selections, as well as

Stitcher panel… Options and controls for automatically and manually aligning

overlapping 2D and 3D tiled images and stitching the result into a single high-resolution
image are available in the Stitcher panel. Additional options let you blend overlapping
regions to create a seamless result, as well as to save a configuration file of thecoordinates of each image tile in the stitched result.

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outline the images that are contained within the mosaic.

Release Notes Version 4.0
New Features ‐ Image Stitching

Stitcher panel

NOTE You can also translate and rotate the currently selected image tile(s) with the Translate
and Rotate tools to position image tiles within a mosaic.

Preview windows… Preview windows are available for evaluating the Feature Base andTemplate Matching methods. You can pan, zoom, and customize the window, as well assave the figure. The example below illustrates how the best matches within two
overlapping images are mapped to each other in the Feature Base preview window.

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Feature Base preview window

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14 Release Notes Version 4.0

New Features ‐ Stitch 3D Datasets

Stitch 3D Datasets
The new Stitch 3D Datasets feature lets you combine, or stitch, multiple volumetric
datasets into a single 3D dataset. Select one or more of the datasets you plan to stitch
in the Data Properties and Settings panel, right-click, and then choose Stitch 3D

Datasets in the pop-up menu to open the Stitch 3D Datasets dialog, shown below.

Stitch 3D Datasets dialog

The options for stitching let you assign data values to voxels that are out-of-bounds, aswell as choose a blending method, interpolation type, and resolution for the output. The
dimensions of the stitched dataset can be constrained to the referenced box.

Create 4D Datasets
You can create a 4D, or time-enabled, dataset from multiple volumetric datasets with
the new Create 4D Dataset feature. Select one or more of the datasets you plan toinclude in your new 4D dataset, right-click, and then choose Create 4D Dataset in the
pop-up menu to open the Create 4D Dataset dialog, shown below.

The options in the Create 4D Dataset dialog let you assign data values to voxels thatare out-of-bounds, as well as to choose a target resolution for the output. The
dimensions of the 4D dataset can be constrained to the referenced box.

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Create 4D Dataset dialog

Release Notes Version 4.0
New Features ‐ Macro Builder

Macro Builder
This Dragonfly release adds a new Macro Builder that provides an intuitive, visual way
to build and edit complex macros or to combine multiple macros for batching. Based on
Google’s Blockly, which uses interlocking, graphical blocks to represent code concepts
like variables, logical expressions, iterations, and more, the Macro Builder lets you
apply programming principles without having to worry about syntax or the intimidationof a blinking cursor on the command line.

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Macro Builder

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16 Release Notes Version 4.0

New Features ‐ Hyper‐Dimensional Imaging

Hyper‐Dimensional Imaging
This release introduces a beta version of Dragonfly’s Hyper-Dimensional Imaging
module that facilitates the interactive visualization, manipulation, and data analysis ofmulti-dimensional datasets. You can exploit the multi-dimensionality of a dataset —with the goal of finding objects, identifying materials, and detecting processes — by
applying dedicated analytical tools that operate on individual signals.
Choose Tools > HyperChannel Manager on the menu bar to open the Hyper Channel
tab on the left sidebar.

Visualization of multi‐dimensional image

Plugin Toolbar
The new Plugin Toolbar, shown below, lets you quickly access any of the available
Dragonfly plugins — such as the Organizer, Bone Analysis, Deep Learning, and Active
Contour modules, as well as the Infinite Toolbox. The Plugin Toolbar is available byPlugin Toolbar panel

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default on the left sidebar.

Release Notes Version 4.0
New Features ‐ Feret Diameter Measurements

Feret Diameter Measurements
This software release includes Feret diameter measurements for regions of interest,
multi-ROIs, and meshes. The measurements of the minimum, mean, and maximum
Feret diameters are available in the Statistical properties and Information boxes on the
Data Properties and Settings panel for regions of interest and meshes and in the Object
Analysis dialog for multi-ROIs.

Feret Diameters Definition
The Feret diameter, or Feret's diameter, is a measure of an object’s size in an arbitrary
direction. This measurement, which can be defined as the distance between the twoparallel planes restricting the object perpendicular to that direction, is also sometimes
called the caliper diameter as it can refer to the measurement of object size with acaliper. This measure is often used in the analysis of particle sizes in microscopy, where
the minimum Feret diameter can be used as the equivalent diameter in a sieve analysis.
Feret diameters computed for a multi‐ROI and filtered in the Measurement Inspector

Min Feret diameter… The shortest distance between any two points along the object

boundary at an arbitrary angle, also known as minimum caliper diameter.

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Mean Feret diameter… The mean value of the Feret diameters over a sufficient numberof orientations. In Dragonfly, measurements for the mean Feret diameter are taken
every 5 degrees.

Max Feret diameter… The longest distance between any two points along the object
boundary at an arbitrary angle, also known as maximum caliper diameter.

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18 Release Notes Version 4.0

New Features ‐ Feret Diameter Measurements

Feret Diameter Measurements for ROIs and Meshes
Feret diameter measurements for ROIs and meshes are available in the Statisticalproperties and Information boxes on the Data Properties and Settings panel,
respectively. Click the Compute Feret Diameter button in the Statistical properties box

to compute Feret lengths for a selected region of interest. For meshes, check the Feretdiameter option in the Information box and then click the Refresh button.
Feret diameter measurements for ROIs and meshes

Information for meshes
Statistical properties for ROIs

Feret Diameter Measurements for Multi‐ROIs
Feret diameter measurements for all connected components in a multi-ROI, which can
examined in table and histogram views, are available as a selectable statistical property(see Statistical Properties on page 34).

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Feret diameter measurements for multi‐ROIs

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Release Notes Version 4.0
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.

Artifact Removal
Vertical, horizontal, and arbitrary angle destriping filters are available in Dragonfly 4.0
for cases in which striped artifacts appear on images. The destriping filters work byadding a pattern that interferes with the image to remove stripes, as shown in theexample below for vertical destriping.
Original data (left) and preview after vertical destriping (right)

NOTE Striping can be caused by opaque or scattering parts of a sample that block part of theillumination beam during acquisition.

Comprehensive
This software release features the option to process image data directly in the Image
Processing toolbox with deep learning models trained for tasks such as denoising,segmentation, and image enhancement. You should note that a selection of trained anduntrained deep learning models are available for download in the Infinite Toolbox(https://infinitetoolbox.theobjects.com/). You will need to download at least one model
before you can access the comprehensive filters.

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Original data (left) and after denoising with comprehensive filtering

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20 Release Notes Version 4.0

New Features ‐ New Image Filters

Original data (left) and after membrane detection with comprehensive filtering

Original data (left) and after segmentation with comprehensive filtering

You should note that downloaded models, as well as models that you created andtrained for processing image data, are available in the Options box of the Image
Processing panel, circled below, when you choose either Deep Learning or Deep

Learning Denoiser as a comprehensive filter.

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Options for Deep Learning filters

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Release Notes Version 4.0
New Features ‐ New Image Filters

NOTE Deep Learning Denoising requires two inputs — the original data that you need toprocess and a variation of the original data that was processed with a comparable
smoothing filter, such as a Gaussian or mean filter.

You should also note that the second input must be the same shape as the first.

Segmentation
A number of new image segmentation filters — K-Means and Mini-Batch K-Means — areavailable in this software release to partition images into meaningful regions.
Original data (left) and preview after K‐Means clustering (right)

K‐Means… The K-Means algorithm clusters data by trying to separate samples in ngroups of equal variance, minimizing a criterion known as the inertia or within-cluster
sum-of-squares. This algorithm requires the number of clusters to be specified and has
been used across a large range of application areas. Refer to https://scikit-learn.org/
stable/modules/clustering.html for more information about K-Means clustering.

Mini‐Batch K‐Means… The Mini-Batch K-Means option is a variant of the K-Meansalgorithm which uses mini-batches to reduce computation times, while still attempting
to optimize the same objective function. Mini-batches are subsets of the input data,
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randomly sampled in each training iteration. In contrast to other algorithms that reducethe convergence time of K-Means, Mini-Batch K-Means produces results that are
generally only slightly inferior to the standard algorithm. Refer to https://scikitlearn.org/stable/modules/clustering.html for more information about this variation of
the K-Means clustering.

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22 Release Notes Version 4.0

New Features ‐ New Image Filters

Smoothing
Additional filters to help reduce the amount of noise in an image include Anisotropic
Diffusion, Kuwahara, and Lipschitz.

Anisotropic Diffusion… Is a technique aimed at reducing image noise without removing

significant parts of the image content, typically edges, lines or other details that areimportant for the interpretation of the image. Anisotropic diffusion is a generalization ofthis diffusion process as it produces a family of parameterized images, but eachresulting image is a combination between the original image and a filter that depends
on the local content of the original image. As a consequence, anisotropic diffusion is a
non-linear and space-variant transformation of the original image. Anisotropic diffusion
generally preserves the sharpness of edges better than Gaussian blurring.
Original data (left) and after anisotropic diffusion filtering (right)

Kuwahara… Provides non-linear smoothing for adaptive noise reduction. Most filtersthat are used for smoothing are linear low-pass filters that effectively reduce noise, but
can also blur out the edges. However, the Kuwahara filter is usually able to applysmoothing on the image while preserving its edges.

Lipschitz… Implements a Lipschitz cover of an image that is equivalent to a grayscale

opening by a cone. The Lipschitz cover can eliminate slowly varying image backgrounds
by subtraction of the lower Lipschitz cover, which is a top-hat procedure.

Texture Analysis
New texture analysis filters that can characterize the texture of a region by quantifying
spatial variation in pixel intensities include the following:

Membrane Projections… Enhances membrane-like structures of an image throughThresholding
Additional thresholding filters, which output an image composed of basic classes andcan be used as masks for segmentation purposes or other image processing tasks,
include the following:

Adaptive Gaussian… The threshold value is the weighted sum of neighbourhood values
where weights are a Gaussian window.

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directional filtering.

Release Notes Version 4.0
New Features ‐ Additional Options for Image Data

Additional Options for Image Data
This software release includes additional options for working with image data, as
described below. See Image Stitching on page 12, Stitch 3D Datasets on page 14, andCreate 4D Datasets on page 14 for information about Dragonfly’s new comprehensive
image processing plugins.

Add Gaussian Noise
This Dragonfly release provides the option to artificially add Gaussian noise to an
image. Deliberately corrupting an image with noise may be useful in cases in which youneed to test the resistance of an image processing operator to noise or to assess theperformance of various noise filters.
To add Gaussian noise to an image, right-click the required dataset and then choose
Add Gaussian Noise in the pop-up menu. You can select the level of noise required in
the Standard Deviation dialog.

Extract ROIs
Available from the Data Properties and Settings pop-up menu, the Extract ROIs item

automatically creates a new region of interest for each intensity value in the selected
dataset.

Overwrite Dataset
If required, you can overwrite the values of a dataset with the intersecting values of areference dataset. To overwrite dataset values, right-click the reference dataset andthen choose Overwrite Dataset in the pop-up menu. The dataset that will beoverwritten is selectable in the Choose a Dataset to Overwrite dialog, shown below.
Choose a Dataset to Overwrite dialog

NOTE The reference dataset and the dataset to overwrite must be of the same data type —TM021-A-05

UBYTE, SHORT, UINT, or FLOAT. For best results, the datasets should also be within thesame value range. If required, you can convert or normalize data within a selected range
with the Dataset Tools.

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24 Release Notes Version 4.0

New Features ‐ New Options for ROIs

New Options for ROIs
A number of new features and options are available in Dragonfly 4.0 for working with
regions of interest — including graphing, computing volume thicknesses, removing
unwanted objects, and creating geodesic distance maps. These new features andoptions are described in the following topics.

Graphing for ROIs
The graphing option for regions of interest can provide a ready-made framework for
performing a wide range of pore network simulations to better understand how porous
materials behave and how to improve them. For example, to create a graph of a regionof interest that describes a void space, right-click the ROI in the Data Properties andSettings and then choose Create Graph from ROI in the pop-up menu. Graphs ofregions of interest can be examined in 3D views, as shown below.
Graph of connected and non‐connected porosity

Graph settings, as well as information about the graphed objects, are available on the
Data Properties and Settings panel and in the Measurement Inspector, as shown in theTM021-A-05

following screen captures.

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Release Notes Version 4.0
New Features ‐ New Options for ROIs

Data Properties and Settings panel and Measurement Inspector

You can do the following in the Data Properties and Settings panel and in the
Measurement Inspector:• Adjust the radius of spheres representing pores or nodes, as well as their connectors.
• Apply different LUTs to ports and adjust measurement ranges by filtering minimum

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and maximum values in the Measurement Inspector.

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26 Release Notes Version 4.0

New Features ‐ New Options for ROIs•

Plot histograms of selected measurements, as shown below.

• Export results to a CSV file for additional analysis.

Label Edges of Graph of ROIThis option lets you automatically create a multi-ROI in which the segments contained
within the selected region of interest are labeled as separate connected components.
You should note that segments are determined by first skeletonizing the region ofinterest, applying a watershed, and then expanding the ROI and assigning a label toeach branch.
To label the edges of a selected region of interest, right-click, and then choose Label

Edges of Graph of ROI in the pop-up menu. The computed multi-ROI will appear as a

new item in the Data Properties and Settings panel.

Statistical Properties
This software release provides additional statistical properties for selected regions ofinterest.

Interpolated Surface… Provides a more robust method — known as Fast Marching — forcalculating the surface of a selected region of interest than what was available
previously with the pixel-wise computation.

Feret diameters… Provides measurements of the minimum, mean, and maximum Feretdiameters contained in the selected region of interest (see Feret Diameter

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Measurements for ROIs and Meshes on page 18).

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Release Notes Version 4.0
New Features ‐ New Options for ROIs

Volume Thickness
Measurements of volume thickness that are based on the sphere-fitting method areavailable in this software release for evaluating structures fully described by a region ofinterest. You should note that one of the key advantages of local thickness
measurements is that the bias from the 3D orientation of the structure is kept to aminimum.
To create a volume thickness map, as shown below, right-click a region of interest andthen choose Create Volume Thickness Map in the pop-up menu. The new dataset willappear in the Data Properties and Settings panel.
Volume thickness of a bone segmentation

You should note that local thickness for a point in solid is defined as the diameter of thelargest sphere which fulfils two conditions:• The sphere encloses the point, but the point is not necessarily in the center of thesphere.
• The sphere is entirely bounded within the solid surfaces.

Interfacial Surface Computations
This software release offers the opportunity to compute the interfacial surface between
two regions of interest. For example, between regions of interest describing oil droplets
and water. You should note that computations are performed in 3D with interpolated

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surfaces that are not limited by pixel-wise methods.

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28 Release Notes Version 4.0

New Features ‐ New Options for ROIs

Selectable Connectivity for Processing
This software release lets you choose the level of connectivity — 6-connected or 26connected — that determines how voxels in a region of interest are labeled as separate
components in generated multi-ROIs and when removing unwanted objects. You shouldnote that a set of voxels in an image which are connected to each other is called aconnected component. Finding all connected components in an image and marking eachof them with a distinctive label is usually referred to as connected component labeling.
Connectivity is selectable for creating multi-ROIs, and processing islands, as shown in
the following illustration and explained below. You should note that 18-connected is notavailable as an option in Dragonfly and is included here for reference purposes only.
6‐connected versus 26‐connected

6‐connected… Propagation is done by strictly using the 6 faces adjacent to the current

seed. This was the default mode in previous Dragonfly versions, and will result in the
maximum number of labeled objects.

18‐connected… Propagation is done using the 6 faces and 12 edges adjacent to thecurrent seed. Will result in fewer connected components than 6-connected. You shouldnote that this option is currently not available in Dragonfly.

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

corners adjacent to the current seed. Will result in the fewest connected components,

Remove Unwanted Objects (Process Islands)
In cases in which you need to refine thresholded segmentation results or isolate objectsof a certain size, this Dragonfly release provides options to remove small objects from a
region of interest, as well as to isolate larger objects.

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but computation times may increase.

Release Notes Version 4.0
New Features ‐ New Options for ROIs

Right-click a region of interest in the Data Properties and Settings panel and thenchoose Process Islands in the pop-up menu. You can then choose to remove or keep
objects as described in the following table.
Process Islands options

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Description
Remove (6-connected)

Removes all objects, as determined by the 6-connected* method, that have a voxel count lower than aselected threshold. Voxel counts can be selected in the Minimal Voxel Count dialog, shown below.

Isolate (6-connected)

Keeps all objects, as determined by the 6-connected* method, that have a voxel count higher than aselected threshold. Voxel counts can be selected in the Maximal Voxel Count dialog, shown below.

Remove (26-connected)

Removes all objects, as determined by the 26-connected* method, that have a voxel count lower than aselected threshold. Voxel counts can be selected in the Minimal Voxel Count dialog.

Isolate (26-connected)

Keeps all objects, as determined by the 26-connected* method, that have a voxel count higher than aselected threshold. Voxel counts can be selected in the Maximal Voxel Count dialog.

Remove (6-connected)
nth First Biggest

Removes a selected number of the largest connected components, as determined by the 6-connected*
method and as ranked by voxel count**. For example, if 5 is selected as the threshold, then the largest 5
connected components will be removed from the selected region of interest. The number of components
to remove can be selected in the Remove Biggest Count dialog, shown below.

Isolate (6-connected)
nth First Biggest

Keeps a selected number of the largest connected components, as determined by the 6-connected*
method and as ranked by voxel count**. For example, if 12 is selected as the threshold, then all
connected components except for the 12 largest will be removed from the selected region of interest. The
number of components to retain can be selected in the Isolate Biggest Count dialog, shown below.

Remove (26-connected)
nth First Biggest

Removes a selected number of the largest connected components, as determined by the 26-connected
method* and as ranked by voxel count**. The number of components to remove can be selected in the
Remove Biggest Count dialog.

Isolate (26-connected)
nth First Biggest

Keeps a selected number of the largest connected components, as determined by the 26-connected*
method and as ranked by voxel count**. The number of components to retain can be selected in the
Isolate Biggest Count dialog.

* See Selectable Connectivity for Processing on page 28 for information about how connected components are computed.
** Objects with an identical voxel count will be considered as unique objects when ranked.

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30 Release Notes Version 4.0

New Features ‐ New Options for ROIs

Create ROIs Using Neighbor Counts
This new option for regions of interest lets you create a new ROI that contains only
voxels with an original neighbor count greater than or equal to a selected threshold.
Thresholds are selectable in the Neighbor Count dialog, shown below. To open the
dialog, select the required region of interest, right-click, and then choose Create ROI

Using Neighbor Count in the pop-up menu.
Neighbor Count dialog

NOTE This option can be applied to facilitate the topological analysis of skeletons, for example.

Smoothing for Thickness Mesh Export
In this software release, smoothing is selectable when regions of interest are exported tonormal and sampled thickness meshes from the ROI Tools panel on the Segment tab.
Export options for regions of interest

Two methods — Laplacian Smoothing and Hamming Windowed Smoothing — areavailable for smoothing in the Export as Thickness Mesh dialog, shown below. The

number of iterations is also selectable.
Export as Thickness Mesh dialog

Close Inner Holes
This software release includes an additional morphological operation for regions ofinterest that lets you close holes smaller than a thresholded distance.

region of interest and then choose Close Holes Smaller Than in the pop-up menu. The
threshold distance is selectable in the Threshold dialog.

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To close inner holes, as shown in the following illustration, right-click the requiredRelease Notes Version 4.0
New Features ‐ New Options for ROIs

Original region of interest (left, in red) and results of closing holes (right, in blue)

Geodesic Distance Maps
For flow analysis and other applications, this Dragonfly offers the option to create
geodesic distance maps that compute the shortest path from a seed point that joins all
points inside a region of interest. As shown in the example below, LUTs can be applied
to geodesic distance maps, which can be examined in 2D and 3D views and arecomputed using the Fast Marching method.

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Geodesic distance map of a pore network

To create a geodesic distance, right-click the region of interest that you need to map
and then choose Create Geodesic Distance Map in the pop-up menu. You can thenselect the seed point in the Choose a Seed ROI dialog.

NOTE The geodesic distance is the shortest path fully contained within a region that joins twopoints, while the Euclidean distance is the straight line distance.

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32 Release Notes Version 4.0

New Features ‐ New Options for Multi‐ROIs

Export ROI as Binary
Lets you export a region of interest as a binary file, in which labeled voxels are assigned
a value of 1 and all other voxels 0.

New Options for Multi‐ROIs
A number of new options are available in Dragonfly 4.0 for working with multi-ROIs.
These new features are described in the following topics.

Graphing for Multi‐ROIs
The graphing option for multi-ROIs provides an opportunity to investigate the interrelationship between connected components. To create a graph of a multi-ROI, rightclick the item in the Data Properties and Settings and then choose Create Graph from
Connectivity in the pop-up menu. Graphs of multi-ROIs, in which the centroid ofadjacent objects are linked, can be examined in 3D views as shown below.

NOTE You can automatically create a multi-ROI of the segments within a region of interest (seeLabel Edges of Graph of ROI on page 26).

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Graph of segments

Release Notes Version 4.0
New Features ‐ New Options for Multi‐ROIs

Graph settings, as well as information about the graphed objects, are available on the
Data Properties and Settings panel and in the Measurement Inspector, as shown in thefollowing screen captures.
Data Properties and Settings panel and Measurement Inspector

You can do the following in the Data Properties and Settings panel and in the
Measurement Inspector:• Adjust the radius of spheres representing the centroid of each connected component,
as well as their connectors.
• Apply different LUTs to ports and adjust measurement ranges by filtering minimum
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and maximum values in the Measurement Inspector.

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34 Release Notes Version 4.0

New Features ‐ New Options for Multi‐ROIs• Plot histograms of selected measurements, as shown below.

• Export results to a CSV file for additional analysis.

Statistical Properties
This software release includes a number of new statistical properties for analyzing
multi-ROIs. These properties are available in the Statistical Properties dialog.

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Statistical Properties dialog

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Release Notes Version 4.0
New Features ‐ New Options for Multi‐ROIs

New statistical properties for multi‐ROIs
Description
Voxel Count

Indicates the total number of voxels contained in each connected component.

Surface Area (interpolated)

Provides a more robust method for calculating the surface of the connected components in a multi-ROI
than was available previously with the pixel-wise method.

Volume/Surface Area
(interpolated)

Provides a more robust method for calculating the ratio of volume to surface area, as described above.

Surface Area (pixel-wise)

Pixel-based method implemented in previous Dragonfly versions for calculating the surface of theconnected components in a multi-ROI.

Volume/Surface Area
(pixel-wise)

Pixel-based method implemented in previous Dragonfly versions for calculating the ratio of volume tosurface area, as described above.

Min Feret diameter

The shortest distance between any two points along the object boundary at an arbitrary angle, also known
as the minimum caliper diameter.

Mean Feret diameter

The mean value of the Feret diameters over a sufficient number of orientations.

Max Feret diameter

The longest distance between any two points along the object boundary at an arbitrary angle, also known
as the maximum caliper diameter.

Min ortho Feret diameter

The shortest distance between any two points along the object boundary that are orthogonal to the
maximum Feret diameter.

Min ortho/Max Feretdiameter

The ratio of the minimum orthogonal Feret diameter to the maximum Feret diameter. This measure canprovide a good indication for the elongation of a particle.

Previous Analyzes
Whenever you need to re-analyze a multi-ROI, you now have the option to include
previously computed properties in your current analysis. These scalar values areavailable in the Statistical Properties dialog, as shown below. Click Scalar values toview and select the properties previously calculated that you want to appear with yourcurrent analysis.

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Statistical Properties dialog

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36 Release Notes Version 4.0

New Features ‐ New Options for Multi‐ROIs

Import Scalar Values
In some cases, you may want to import the scalar values of a multi-ROI or mesh thatwere exported to a CSV file. As a new feature for Dragonfly 4.0, you can import scalarvalues from either an ORS-formatted CSV file or from a generic CSV file that contains
the required IDs and corresponding values.
Scalar Value Slots Importer dialog

Extract ROIs
This new feature for Dragonfly 4.0 lets you extract a new region of interest from eachconnected component in the selected multi-ROI. For example, if there are 100
connected components in the selected multi-ROI, then selecting the Extract ROIs itemin the Data Properties and Settings panel will result in 100 new regions of interest —one for each connected component.

Split Non‐Connected Labels
In cases in which you create a multi-ROI and objects with the same label are notconnected, you can choose to split those non-connected labels. This can be necessary incases in which you create a multi-ROI from the greylevel values of a dataset. Right-click
the required multi-ROI and then choose Split Non‐Connected Labels in the pop-up
menu to split not connected labels.

In the following example, the original multi-ROI with six labeled objects extracted fromthe data values of dataset (using the option New Greylevel Multi‐ROI ) is on the left.

After splitting the non-connected labels of the greylevel multi-ROI, there are 165
labeled objects, as shown on the right.

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Results of splitting non‐connected labels

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Release Notes Version 4.0
New Features ‐ New Options for ROIs and Multi‐ROIs

Get Merged Label as Multi‐ROI
Lets you create a new multi-ROI with one labeled connected component from a multiROI that contains a number of labels that were merged. For example, through a
Boolean operation.

New Options for ROIs and Multi‐ROIs
The following new options — Convex Hulls, Remove Touching Objects, and Boolean
operators for removing and keeping intersecting labels — are available in this software
release for regions of interest and multi-ROIs.

Convex Hulls
This new option for Dragonfly 4.0 lets you generate convex hulls as filled or outlined
regions of interest or multi-ROIs, or as meshes. Convex hulls are calculated from theminimum set of points that define a polygon containing all of the labeled voxels of aregion of interest or all of the labeled voxels of each connected component in a multiROI. If you imagine the points as pegs on a board, you can find the convex hull bysurrounding the pegs by a loop of string and then tightening the string until there is no
more slack.
In the illustration below, a convex hull as a mesh (in blue) was generated from a regionof interest describing the outline of a mechanical part.
Convex hull as a mesh

Convex Hull as a Filled ROI or Multi‐ROI… Lets you generate a convex hull as a filled

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region of interest for a selected ROI, or as a series of filled convex hulls for eachconnected component in a selected multi-ROI.

Convex Hull as an Outer Shell ROI or Multi‐ROI)… Lets you generate a convex hull as an

outlined region of interest for a selected ROI, or as a series of outlined convex hulls foreach connected component in a selected multi-ROI.

Convex Hull as a Mesh… Lets you generate a convex hull as a mesh for a selected ROI,
or as a series of convex hulls for each connected component in a selected multi-ROI.

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38 Release Notes Version 4.0

New Features ‐ New Options for ROIs and Multi‐ROIs

You should note that in this case, each connected component in the multi-ROI will be
generated as an unstructured grid.

Remove Touching Objects
You can automatically remove objects from a selected region of interest or multi-ROI
that touch another region of interest or multi-ROI by selecting the Remove Objects That
Touch Another ROI or Multi‐ROI in the Data Properties and Settings pop-up menu item.

You should note that objects can be defined as groups of labeled voxels that areconnected.

Boolean Operators
This software release includes two new Boolean operators — Remove Intersected andKeep Intersected — for modifying and refining regions of interest and multi-ROIs.
These options are available in the Boolean operations panel, as shown below.
Boolean operations

Remove Intersected… Automatically removes all labeled components of the initiallyselected item that intersect with the other regions of interest or multi-ROIs selected forthe operation.

Keep Intersected… Automatically keeps only the labeled components of the initiallyselected item that do not intersect with the other regions of interest or multi-ROIs

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selected for the operation.

Dragonfly Release Notes

Release Notes Version 4.0
New Features ‐ New Options for Meshes

New Options for Meshes
A number of new options, including new mesh settings, smoothing, and a meshsubdivider, are available in this Dragonfly release for working with meshes.

Mesh Information
This software release provides additional statistical properties, circled below, forselected meshes.
Information for meshes

Feret diameters… Provides measurements for the minimum, mean, and maximum Feretdiameters contained in the selected mesh (see Feret Diameter Measurements for ROIs

and Meshes on page 18). Check the Feret diameters option and then click the Refresh

button to compute the Feret diameters.

Mesh Settings
A new Fill mode — Outlined — is available for rendering meshes in 3D views. In thismode, meshes are rendered simultaneously as a solid outline and in wireframe, as
shown below.

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Outlined mesh

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40 Release Notes Version 4.0

New Features ‐ New Options for Meshes

This setting is available on the Data Properties and Settings panel, as shown below.
Mesh settings

Mesh Smoothing
After generating a mesh, it is sometimes necessary to modify that mesh before further
processing or analysis can begin. In particular, meshes extracted from volumetric image
data obtained by CT or MRI devices often contain significant amounts of noise.
Removing noise while preserving the shape of a mesh, as shown in the example below,
is now an option for Dragonfly 4.0.
Original mesh (left) and smoothed mesh (right)

The options for smoothing a selected mesh are available in the Mesh Smoothing dialog,
shown below.

The Mesh Smoothing panel offers two filters for smoothing meshes — Laplacian
Smoothing and Hamming Windowed Smoothing. Outputs of the smoothing operation
can be a new mesh, so that the original remains unmodified, or a modified mesh.

Dragonfly Release Notes

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Mesh Smoothing panel

Release Notes Version 4.0
New Features ‐ New Options for Meshes

Mesh Subdivider
Adding subdivisions to a polygon mesh can useful when you need to add detail in a
global manner or to create smoother surfaces. Subdividing adds resolution to a mesh byincreasing the number of its cells. You should note that for each subdivision level
increase, the number of triangles will increase by approximately a factor of 4. For
example, if n=2, the number of triangles in the resulting mesh will be 16x the numberof triangles in the original mesh.
Original and subdivided mesh

The options for subdividing meshes are available in the Mesh Subdivider dialog, shown
below.
Mesh Subdivider panel

The methods available for subdividing meshes include Linear Subdivision, Loop
Subdivision, and Butterfly Subdivision filtering. In addition, the number of subdivisions
requested can be selected. Outputs of the subdivision operation can be a new mesh, so

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that the original remains unmodified, or a modified mesh.

NOTE Refer to https://cmake.org/Wiki/VTK/Examples/CSharp/Meshes/Subdivision for
information about the implementation of Dragonfly’s Mesh Subdivider.

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42 Release Notes Version 4.0

New Features ‐ New Options for Meshes

Get Non‐Manifold Edges CountYou can now compute non-manifold edge counts to verify that a mesh does not containany edges with more than two faces attached to it. You can use this option to evaluate
the integrity of a mesh that will be used for 3D printing.
As shown in the example below, non-manifold topology polygons have a configurationthat cannot be unfolded into a continuous flat piece. This condition, in which more than
two faces share an edge, is known as multiply connected geometry.
Non‐manifold edge (in red)

Right-click the mesh you need to analyze and then choose Get Non Manifold Edges

Count in the pop-up menu. Results are available in the Mesh Information dialog, shown
below. You should note that a value of 0 indicates that the mesh does not contain any
non-manifold edges.
Mesh Information dialog

New Options for Scalar Meshes
Histograms, as well as export and import functions, are now available in the Scalar
information box on the Data Properties and Setting panel, shown below, for selectedscalar meshes.
Scalar information for meshes

The new options for scalar meshes are described in the following table.
Description

HistogramLets you plot selected scalar values on a histogram. For information about the new
options available for histograms, such as saving figures and customizing captions, seeHistograms and Graphs on page 56.

ExportLets you export the scalar values contained in the selected mesh to a CSV file.

ImportLets you import scalar values from a CSV file.
NOTE You can also import scalar values from the Data Properties and Settings panel
pop-up menu item Import Scalar Values From a CSV File.

Dragonfly Release Notes

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FunctionRelease Notes Version 4.0
New Features ‐ Shape Properties

Shape Properties
The basic properties of a selected shape — such as the height, radius, surface, andvolume of a capsule — are now available in the Data Properties and Settings panel. The
Basic properties panel is circled below on the following screen capture.
Basic properties for shapes

NOTE Some shapes have additional functions, such as masking for dataset registration (seeDataset Registration on page 49).

This software release also provides an Align Centroid With option for shapes. This popup menu item automatically aligns the centroid of a selected shape with the centroid of
another object. Applicable objects include volumetric image data, regions of interest,
multi-ROIs, and meshes. Reference objects can be selected in Choose the Object toTM021-A-05

Align With dialog.

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44 Release Notes Version 4.0

New Features ‐ New Options for Boxes

New Options for Boxes
In this software release, boxes can be automatically reduced to the smallest encasing
rectangle — based on either the maximum Feret diameter of a region of interest or
mesh or on the minimal box shape. The results of resizing boxes to segmented ROIs is
illustrated below.
Resized boxes
Box shape from Feret of aregion of interest

Minimal box shape

Take Box Shape from Feret Of
Reduces the selected box to the smallest encasing rectangle — based on the maximum
Feret diameter and minimum orthogonal Feret diameter of the labeled voxels of aregion of interest or of an unstructured grid, such as a mesh. You can select therequired object in the Choose an Object dialog, as shown below.
Choose an Object dialog

Take Minimal Box Shape Of
Reduces the selected box to the smallest or minimal encasing rectangle of a region ofChoose an Object dialog.

Dragonfly Release Notes

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interest or unstructured grid, such as a mesh. You can select the required object in theRelease Notes Version 4.0
New Features ‐ New Options for Annotations

New Options for Annotations
As a new option for annotations — such as Rulers, Angles, and Regions — you canchoose to show or hide associated captions in 2D or 3D views. This option is available in
the Properties box and is circled below.
Annotation properties

Extract Images from Visual Planes
As a new option for Dragonfly 4.0, you can extract a 2D image that corresponds to theoblique or double-oblique angle of a selected visual plane.
As shown in the screen captures below, a single-slice 2D image (on right) was extracted
from the visual plane displaying the data of the corresponding MPR plane (on left).

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Visual plane and extracted dataset

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46 Release Notes Version 4.0

New Features ‐ Gamma Ramp for Window Leveling

Gamma Ramp for Window Leveling
Gamma correction, or often simply gamma, is a nonlinear operation used to optimize
the contrast and brightness in the midtones of an image. The option to control the
gamma curve, which is a new feature for Dragonfly 4.0, can help you better visualize
the dynamic range of selected window leveling values as shown in the comparative
images below.
Original image (left) and the same image with gamma corrected (right)

The gamma curve, as well as adjustment controls, are available in the Window Levelingpanel, shown below.
Window Leveling panel
Gamma curve… The gamma curve determines how
tones are displayed by defining the relationshipbetween input values and the resulting image
luminance. The curve is adjustable with the Gamma
slider.

Gamma slider… Lets you adjust the applied gamma
curve. You should note that the local gamma typicallyrises from 1.0 to about 2.0.

Configurable Actions
Additional configurable actions are available for adjusting the window leveling gamma
value.

Adjust window leveling gamma in any mode… Lets you adjust the gamma curve in any
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mode. For example, when zooming.

Dragonfly Release Notes

Release Notes Version 4.0
New Features ‐ Synchronize 3D Views

Synchronize 3D Views
This software release lets you synchronize the 3D views available in multiple scenes in
the workspace with the orientation and zoom applied to a reference 3D view. Select the

Position option in the Scenes Views Synchronizer panel, as shown below, to set the

selected 3D view as the reference for all other 3D views in the Dragonfly workspace.
Scenes Views Synchronizer for 3D views

Movie Maker
A number of new options for creating animated sequences in the Movie Maker panel, as
well as other improvements, are available in this software release.
New controls for working on the timeline include the following:• Set keyframe position… Lets you manually set an exact keyframe position on thetimeline. To open the Keyframe Time dialog, right-click the required keyframe andthen choose Set Keyframe Position in the pop-up menu. The keyframe position can

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be selected in the Keyframe Time dialog, shown below.

• Update keyframe without camera… Lets you update all changes made to a keyframe,
except for those related to the camera — such as zooms or rotations. This option lets

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48 Release Notes Version 4.0
New Features ‐ 2D Animations

you maintain the original position of an object, regardless of any applied camera
manipulation. For example, after rotating a view to adjust a clip box.

• Loop playback… If selected, lets you preview your animated sequence in acontinuous loop.

In addition, the following improvements have also been implemented for the Movie
Maker:• Easier manipulation of mesh frames.
• When new objects are added to the timeline, they will appear at the relevant
keyframe and onwards only.
• Better interpolation for regions of interest and multi-ROIs, as well as improved
performance for animating scalar values.

2D Animations
For 2D animations, this software release provides the option to export 2D animations as
images to a number of different file formats. Click the Export button on the 2D

Animation panel, shown below, to export the selected sequence to a series of BMP, GIF,
JPEG, and TIFF image files or in the EPS file format.

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2D Animation panel

Dragonfly Release Notes

Release Notes Version 4.0
Product Enhancements ‐ Deep Learning

Product Enhancements

This release provides the following product enhancements for Dragonfly 4.0. For
information about new features, such as the Organizer, Image Stitcher, and the Bone
Analysis modules, as well newly implemented options for image data, regions ofinterest, and multi-ROIs, see New Features on page 7.

Deep LearningThis software release features a number of enhancements for the initial version of the
Deep Learning tool that was first introduced in Dragonfly 3.6. These enhancements
include the following:• The segment dataset with classifier feature can now use deep learning models.
• Multiple channel inputs, such as RBG, are now supported.
• Implementation of options to check and uncheck parameters such as zoom, range,
and rotation for data augmentation.
• Elastic deformation on patches with the option to add Gaussian noise.
• Training data statistics are shown for segmentation.
• You can download trained and untrained neural networks from the Infinite Toolbox, as
well as publish your own neural networks to the Infinite Toolbox.

Dataset Registration
This software release provides additional options for Dragonfly's feature-based
registration workflows, which can automatically register datasets by applying thetransformations required to match features between two datasets. These new options,circled below, include using masks and scaling.

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Dataset Registration dialog

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50 Release Notes Version 4.0

Product Enhancements ‐ Dataset Sampler

Fixed Mask
If a fixed mask is selected, calculations for the required transformations will be
constrained to the 3D region defined by the selected mask. In other words, voxels
outside the mask will not be considered when the required transformations arecomputed. Fixed masks can be a region of interest or any shape, such as a box or
sphere, and must overlap with the selected Fixed dataset.

Scaling
The registration options now include independent scaling in the X, Y, and Z dimensions
in the lattice coordinate system of the selected mobile dataset. The Initial step andSmallest step for scaling is selectable, and, in Advanced Mode, you can select the initialand smallest steps for each axis.

RefreshLets you update the registration score estimate after a change to the registration
method, fixed mask, or mobile dataset.

Dataset Sampler
This software release adds the option to upsample or downsample data by a selectedfactor. These additional options are circled below on a screen capture of the Dataset
Sampler panel.

Upsample by a factor… Lets you select an upsampling factor that will be applied

uniformly to the spacing values of the input dataset. For an input spacing size of 3.02
nm and an upsample factor of 2, the resulting spacing size will be 1.51 nm. Likewise,
for an input matrix size of 512 x 512 x 256 and an upsample factor of 2, the resulting
matrix will be 1024 x 1024 x 512.

Downsample by a factor… Lets you select a downsampling factor that will be applied

uniformly to the spacing values of the input dataset. For an input spacing size of 3.02

Dragonfly Release Notes

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Dataset Sampler panel

Release Notes Version 4.0
Product Enhancements ‐ Slice Alignment Outputs

nm and a downsample factor of 2, the resulting spacing size will be 6.04 nm. Likewise,
for an input matrix size of 512 x 512 x 256 and a downsample factor of 2, the resulting
matrix will be 256 x 256 x 128.

Slice Alignment Outputs
In this software release, you can choose to crop the output of an alignment to thedimensions of the registration selection box or to the dimensions of a user-defined box.
This option, circled below, is available in the Output options box at the bottom of the
Slice Registration dialog
Slice Registration panel

Active Contour
For users who use the Active Contour for segmentation tasks, this software releaseadds the option to set the direction of the path normals to inward or outward. For
example, in cases in which you need to define a tube-like structure with a hollow center.
The Normals Inward option is circled on the following capture of the Active Contour
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panel.

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52 Release Notes Version 4.0

Product Enhancements ‐ Connectivity Analysis

Active Contour panel

Connectivity Analysis
This software release features an accelerated connected component analysis comparedwith what was available in previous Dragonfly versions. Connectivity is also selectable(see Selectable Connectivity for Processing on page 28).

Updates for the Dataset Properties
A number of changes and updates are available in this software release for the Dataset
Properties and Settings panel and for modifying dataset properties.

List Items
Two new items have been added the Dataset Properties and Settings panel as the resultof major new features for Dragonfly 4.0. These are Graphs and Vector Fields .

Graphs… Lets you filter the Data Properties and Settings panel list to show only graphs(see Graphing for ROIs on page 24 and Graphing for Multi-ROIs on page 32 for
information about graph objects).

Vector Fields… Lets you filter the list to show only vector fields (see Bone Analysis on

page 8 for information about vector fields).

Dragonfly Release Notes

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Dataset Properties and Settings panel

Release Notes Version 4.0
Product Enhancements ‐ 3D Presets

Undo for Applied Changes
In this software release, changes to the position in space or orientation applied to adataset in the Advanced Dataset Properties panel can be undone by clicking the Undo

button in the Move panel, shown below.
Move panel

Data Units
The data units selected during file import, circled below, are now displayed in theDataset Properties panel and can be edited, if required.
Dataset Properties panel

3D Presets
Applying a 3D preset to selected image data lets you quickly apply grouped 3D settings,
scene's views properties, and lighting effects to improve the visualization of 3D
renderings. In this software release, the default 3D presets available in the new dropdown menu are categorized for specific materials, such as biological samples, concrete,
plastics, and metals. In addition, you can also create your own 3D presets for particularmaterials or data samples. You should note that you can edit and save user-defined 3D
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presets, but not the default presets.

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54 Release Notes Version 4.0

Product Enhancements ‐ 3D Settings

3D presets

NOTE User-defined 3D presets can be published to the Infinite Toolbox and shared with the
Dragonfly user community.

3D Settings
In cases in which a leveled object’s boundaries are indistinct, the new Edge detectsetting can help visualizations by adding a delineated edge computed from voxel depth
to a rendering, as shown below.
Edge detect

This new option is available in the 3D settings panel, as shown below.

NOTE The Gamma boost option has been removed from the 3D settings panel. However, you

should note that full gamma adjustments are available in the Window Leveling panel (seeGamma Ramp for Window Leveling on page 46).

Dragonfly Release Notes

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3D settings

Release Notes Version 4.0
Product Enhancements ‐ Clip and Visual Effects

Clip and Visual Effects
In Dragonfly 4.0, selected visual effects for clips and shapes now appear in a new 3D
live effects box, circled below. You can select the properties of a visual effect, as well as
re-order effects, as previously.
Visual effects

Legends
In this software release, legends can be positioned vertically or horizontally in 2D and
3D views and their height or width can be adjusted.

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Legends in 3D view• To change the orientation of a legend, right-click the legend and then choose Verticalor Horizontal in the pop-up menu. You should note that you can choose a default

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56 Release Notes Version 4.0

Product Enhancements ‐ Histograms and Graphsorientation for legends in the 2D Settings preferences (see 2D Settings Preferenceson page 66).
• To change the width or height, drag from the start or end point of the legend, as
shown below.

Histograms and Graphs
A number of additional options are now available for histograms plotted from regions,regions of interest, and meshes with scalar information. You can save an image of the
figure, as well as edit captions and the plotted data range. In addition, you should notethat these options are also available for intensity profiles and for the results of a slice
analysis.
Histogram dialog

The new options for histograms and graphs are described in the following table.
New options for histograms and graphs
Description

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Save… Saves the figure as a bitmap image, vector graphic, or in the PDF file format. The figure can also
be saved as raw data or PGF code for LaTeX.

Dragonfly Release Notes

Release Notes Version 4.0
Product Enhancements ‐ Slab Thickness Adjustments for 2D Views

Description
Settings… Lets you edit the captions on the histogram or graph, apply scaling, and set a data range.
These options are available in the Figure options dialog, shown below.

Slab Thickness Adjustments for 2D Views
In previous Dragonfly versions, the slab thickness of MIPs, mIP, and average intensity
projections could only be adjusted in the corresponding MPR views of the dataset. This
software version includes a Slab Thickness dialog, in which a thickness value can beentered directly from the view in Slab mode.
Right-click inside the view in Slab mode and then choose Set Slab Thickness in the

pop-up menu. You can then enter the required slab thickness in the Enter a New SlabThickness dialog, as shown below.

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New Slice Thickness dialog

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58 Release Notes Version 4.0

Product Enhancements ‐ Text Annotations for 3D Views

NOTE Selected slab thickness values are also now displayed in the associated MPR views, as
shown below.

Text Annotations for 3D Views
You should note that a new interactive text annotation — that indicates the size of the3D view when you are in Orthographic view mode or the distance to the camera pivot
point (PD) for perspective views — is available in this software release for 3D views. You
can drag up or down from the text annotation to adjust the zoom factor.
Text annotations for 3D views

Orthographic projection

Perspective viewSupport for RGB Images
This software release offers additional options for importing RBG images. RGB outputs
are available in the File Import dialog, as shown below.
RGB output options

Output options for RGB images

As three separate channels

If selected, all three channels — Red, Green, and Blue — will be loaded
and each separate channel will be identified as to its originating channel
in the Data Properties and Settings panel. For example, Blue Imported
Data.

As one luminance channel

If selected, the RGB image will be converted into a single-channel
luminance representation. In Dragonfly, the conversion of an RGB image
to a luminance channel is computed as follows:
Luminance = 0.2126*R + 0.7152*B + 0.0722*GNOTE Refer to https://en.wikipedia.org/wiki/Grayscale for more
information about luminance conversions.

Dragonfly Release Notes

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Description

Release Notes Version 4.0
Product Enhancements ‐ ROI Painter Tools

Description
As one grayscale channel(RBG channels are identical)

If selected, one channel will be loaded. You should note that if the Image
Loader determines that all three channels are not identical after theloading, a message box will appear.

NOTE The above options are not available for RGBA images. For these images, all fourchannels — Alpha, Red, Green, and Blue — will be imported and added automatically to
the Data Properties and Settings panel.

If required, you can export RGB channels in the BMP, JPEG, PNG, and TIFF file formats.
Select the three separate channels on the Data Properties and Settings panel — Red,
Green, and Blue — right-click, and then choose the Export as RGB item in the pop-up

menu. You can drag channels up and down to match them to a specific output in the
Export as RGB dialog, as well as replace channels.
Export as RGB dialog

ROI Painter Tools
A number of performance related issues were addressed in this software release. These
include the following:• Acceleration of adding and subtracting with the Circular Brush tool when painting onvery large regions of interest — with or without a defined range.
• Acceleration of adding and subtracting with the Square Brush tool when painting onvery large regions of interest — with or without a defined range.

Measurement Inspector
A number of issues related to the performance of the Measurement Inspector wereaddressed in this software release. These include the following:• Quicker response when making range selections.
• Updates for new graph requirements (see Graphing for ROIs on page 24 and Graphing

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for Multi-ROIs on page 32).

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60 Release Notes Version 4.0

Product Enhancements ‐ About Menu Items

About Menu Items
Information in the Help > About menu item has been categorized by type — Actions,
Image Filters, Macros, Menu Items, Object Analysis Statistics, and so on.
About submenu items

In addition, information about each item is available in a separate dialog. Double-click
an item in the About Plugins dialog to view the information available for the selected
item, as shown below.

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About Plugins dialog

Dragonfly Release Notes

Release Notes Version 4.0
Product Enhancements ‐ Developer Documentation

Developer Documentation
The developer documentation for Dragonfly has been updated for version 4.0. Choose

Help > Dragonfly Developer Documentation on the menu bar to open the

documentation system.

IMPORTANT NOTE Some architectural changes were implemented in Dragonfly 4.0.

You may need to update development work in progress accordingly. You should also

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note that citations are now added automatically to user-created plugins and extensions.

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62 Release Notes Version 4.0

Menu Bar Changes ‐ File Menu

Menu Bar Changes

The following changes and new items for the menu bar are implemented for Dragonfly
4.0.

File Menu
New items, listed below, and other changes are available for the File menu.
File menu changes
Description
Open the Organizer

Opens the Organizer, which provides an easy way to organize, manage, and share your data (seeDragonfly Organizer on page 7).

Tools Menu
A number of new items, listed below, and other changes have been implemented for the
Tools menu.
Tools menu changes
Description
Bone Analysis

Opens the Bone Analysis dialog, which helps you better understand complex metabolic bone diseases(see Bone Analysis on page 8).

HyperChannel Manager

Opens the Hyper Dimensional tab on the left sidebar (see Hyper-Dimensional Imaging on page 16).

Macro Builder

Opens the Macro Builder, which provides an easy way to combine macros for batching (see Macro
Builder on page 15).

Open All Users Folder in FileBrowser

Automatically opens the Dragonfly directory with the Python All Users Extensions folder in your installedfile manager. The Python All Users Extensions folder can otherwise be found in ProgramData > ORS >Dragonfly.

Open Current User Folder inFile Browser

Automatically opens the Dragonfly directory with the Python Users Extensions folder in your installed file
manager. The Python Users Extensions folder can otherwise be found in AppData > Local > ORS >Dragonfly.

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

Dragonfly Release Notes

Submenu items — Actions, Image Filters, Macros, Menu Items, Object Analysis Statistics, Plugins,
Property Panels, and Slice Analysis Measurements — have been added to the About item to help you findinformation about Dragonfly plugins easier. In addition, the available information has been augmented
with attributions, contact information, and versioning (see About Menu Items on page 60).

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Description
AboutRelease Notes Version 4.0
Changes to Contextual Menus ‐ Dataset Pop‐Up Menu

Changes to Contextual Menus

The following changes and new items for the contextual menus are implemented for
Dragonfly 4.0.

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
Image StitchingLets you precisely combine, or stitch, overlapping 2D or 3D image tiles to create a single high-resolution
image that is beyond the normal aspect ratio and resolution of a microscope's field of view (see Image
Stitching on page 12).

Add Gaussian NoiseLets you artificially add Gaussian noise to an image (see Add Gaussian Noise on page 23).

Extract ROIs

Automatically creates a new region of interest for each intensity value in the selected dataset (see Extract
ROIs on page 23).

Overwrite Dataset

Overwrites the intersecting values of a selected dataset with the corresponding values of another dataset(see Overwrite Dataset on page 23).

Create 4D Dataset

Lets you can create a 4D, or time-enabled, dataset from multiple volumetric datasets (see Create 4D
Datasets on page 14).

Export as RGB*

Lets you export selected red, green, and blue channels as image files (see Support for RGB Images on
page 58).

Stitch 3D Datasets

Lets you combine, or merge, multiple volumetric datasets into a single 3D dataset (see Stitch 3D Datasetson page 14).

* Available for multiple selections only.

Region of Interest Pop‐Up Menu
A number of new items, listed below, and other changes have been implemented for theregion of interest pop-up menu in this software release.
Region of interest pop‐up menu changes
Description
Create Graph from ROI

Lets you map pore networks by showing pore throats and porosity connections (see Graphing for ROIs on
page 24).

Label Edges of Graph of ROI

Lets you automatically create a multi-ROI in which the segments contained within the selected region ofinterest are labeled as separate connected components (see Label Edges of Graph of ROI on page 26).

Export ROI as Binary

Lets you export a region of interest as a binary file (see Export ROI as Binary on page 32).

New Multi-ROI(6-connected)

Creates a new multi-ROI in which connectivity is determined strictly using the 6 faces adjacent to thecurrent seed (see Selectable Connectivity for Processing on page 28).

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NOTE This item was previously named New Connectivity Multi-ROI.
New Multi-ROI(26-connected)

Creates a new multi-ROI in which connectivity is determined in all directions, using the 6 faces, 12 edges
and 8 corners adjacent to the current seed (see Selectable Connectivity for Processing on page 28).

Multi-ROI Analysis

Replaces the item previously named New Connectivity Multi-ROI Analysis, which was based on 6connected propagation.

Process Islands

Lets you remove unwanted objects or isolate objects in a region of interest (see Remove Unwanted
Objects (Process Islands) on page 28).

Close Holes Smaller Than

Lets you close holes smaller than a thresholded distance (see Close Inner Holes on page 30).

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64 Release Notes Version 4.0

Changes to Contextual Menus ‐ Multi‐ROI Pop‐Up Menu

Description
Create Volume Thickness
Map

Lets you measure the thickness volume of a region of interest (see Volume Thickness on page 27).

Create Geodesic Distance
Map

Lets you generate a geodesic distance map that shows the shortest curve between two points along thesurface of a region of interest (see Geodesic Distance Maps on page 31).

Convex Hull (as a Filled
ROI)

Lets you generate convex hulls as filled regions of interest (see Convex Hulls on page 37).

Convex Hull (as an Outer
Shell ROI)

Lets you generate convex hulls as outlined regions of interest (see Convex Hulls on page 37).

Convex Hull (as a Mesh)

Lets you generate convex hulls as meshes (see Convex Hulls on page 37).

Remove Objects That Touch
Another ROI or Multi-ROI

Automatically removes objects from the selected region of interest that touch another ROI or multi-ROI(see Remove Touching Objects on page 38). You should note that objects can be defined as groups oflabeled voxels that are connected.

Create ROI Using Neighbor
Count

Creates a new region of interest that only contains voxels with an original neighbor count greater than orequal to a selected threshold. See Create ROIs Using Neighbor Counts on page 30

Compute Interfacial Surface

Available for multiple ROI selections, automatically computes the interfacial surface between two regionsof interest (see Interfacial Surface Computations on page 27).

Multi‐ROI Pop‐Up Menu
A number of new items, listed below, and other changes have been implemented for themulti-ROI pop-up menu.
Multi‐ROI pop‐up menu changes
Description
Import Scalar Values from a
CSV File

Lets you import scalar values contained in a selected CSV file (see Import Scalar Values on page 36).

New Multi-ROI(6-connected)

Creates a new multi-ROI in which connectivity is determined strictly using the 6 faces adjacent to thecurrent seed (see Selectable Connectivity for Processing on page 28).

New Multi-ROI(26-connected)

Creates a new multi-ROI in which connectivity is determined in all directions, using the 6 faces, 12 edges
and 8 corners adjacent to the current seed (see Selectable Connectivity for Processing on page 28).

Create Graph from
Connectivity

Lets you graph the inter-relationship between connected components (see Graphing for Multi-ROIs on
page 32).

Convex Hull (as a Multi-ROI,
Each Label Being Filled)

Lets you generate filled convex hulls for each connected component in a multi-ROI, as a multi-ROI (seeConvex Hulls ON PAGE 37).

Convex Hull (as a Multi-ROI,
Each Label as an Outer
Shell

Lets you generate outlined convex hulls for each connected component in a multi-ROI, as a multi-ROI(see Convex Hulls on page 37).

Convex Hull (Each Multi-ROI
Label as a Mesh

Lets you generate convex hulls as meshes for each connected component in a multi-ROI, as a mesh (seeConvex Hulls on page 37).

Extract ROIs

Lets you extract a region of interest from each connected component in the selected multi-ROI (seeExtract ROIs on page 36).

Get Merged Label as MultiROI

Lets you create a new multi-ROI with one labeled connected component from a multi-ROI that contains a
number of labels that were previously merged (see Get Merged Label as Multi-ROI on page 37).

Remove Objects That Touch
Another ROI or Multi-ROI

Automatically removes objects from the selected multi-ROI that touch another region of interest or multiROI (see Remove Touching Objects on page 38). You should note that objects can be defined as groupsof labeled voxels that are connected.

Split Non-Connected Labels

Lets you a create a multi-ROI in which objects with the same label that are not connected are split (seeSplit Non-Connected Labels on page 36).

Dragonfly Release Notes

TM021-A-05

NOTE This item was previously named New Connectivity Multi-ROI.

Release Notes Version 4.0
Changes to Contextual Menus ‐ Mesh Pop‐Up Menu

Mesh Pop‐Up Menu
A number of new items, listed below, and other changes have been implemented for the
pop-up menu for meshes.
Mesh pop‐up menu changes
Description
Mesh Smoothing

Opens the Mesh Smoothing panel, in which you can smooth meshes with a selected method and numberof iterations (see Mesh Smoothing on page 40).

Mesh Subdivider

Opens the Mesh Subdivider panel, in which you can increase the resolution of the selected mesh bydividing its cells into smaller units (see Mesh Subdivider on page 41).

Get Non Manifold Edges
Count

Lets you compute the number of non-manifold edges in a selected mesh (see Get Non-Manifold Edges
Count on page 42).

Import Scalar Values from a
CSV File

Lets you import scalar values contained in a selected CSV file (see New Options for Scalar Meshes on
page 42).

Shapes Pop‐Up Menu
A number of new items, listed below, are available for the Shapes pop-up menu.
Shapes pop‐up menu changes
Description
Extract a One Slice Dataset
from Visual Plane*

Extracts a 2D image that corresponds to the oblique or double-oblique angle of a selected visual plane(see Extract Images from Visual Planes on page 45).

Align with Centroid

Lets you automatically align the centroid of a selected shape with the centroid of another object.

Mask ROI

Removes all labeled voxels from the selected region of interest that are outside of the shape.

Take Box Shape from FeretOf**

Reduces a box to the smallest encasing rectangle based on the maximum Feret diameter of the labeledvoxels of a selected region of interest or mesh (see Take Box Shape from Feret Of on page 44).

Take Minimal Box ShapeOf**

Reduces a box to the minimal encasing rectangle based on the labeled voxels of a selected region ofinterest or on the bounding box of a mesh (see Take Minimal Box Shape Of on page 44).

* Available for Plane shapes only.

TM021-A-05** Available for Box shapes only.

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66 Release Notes Version 4.0

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
Axis indicator size

Lets you choose the size of the Axis indicator that appears onscreen.

2D Settings Preferences
Changes for the 2D Settings preferences are indicated in the following table.
2D Settings preferences changes
Description
Legend initial orientation

Lets you choose a default orientation for the legend(s) that appear in the scene views.
Horizontal… If selected, legends will appear horizontally by default.
Vertical… If selected, legends will appear vertically by default.

3D Settings Preferences
Changes for the 3D Settings preferences are indicated in the following table.
3D Settings preferences changes
Description
Cubic interpolation

If selected, cubic interpolation will be applied by default to the objects rendered in 3D views.

Autosave Preferences
Changes for the Autosave preferences are indicated in the following table.
Autosave preferences changes
Description
New objects introduced in this Dragonfly release — Vector fields and Graphs — have been added to theobjects list.

TM021-A-05

Objects to include inautosave file

Dragonfly Release Notes

Release Notes Version 4.0
System Requirements Changes ‐ Autosave Preferences

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.

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

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

TM021-A-05

to an existing workflow.

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68 Release Notes Version 4.0

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.

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-05

Report an Issue on the menu bar.

Dragonfly Release Notes