D RAGONFLY R ELEASE N OTESV ERSION 3.6

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Title
Dragonfly Release Notes
Release date2018.06.08
Reference number TM021-A-04

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

Release Notes
Version 3.6
This document describes the new features, product enhancements, and otherimprovements implemented in the Dragonfly and Dragonfly Pro 3.6 software release.
You should read these release notes carefully before you install this new version.

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

Arrow Annotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
New Options for Active Contours . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Export Active Contour Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Generate Active Contour Paths . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Cut Selected Active Contour Paths . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Additional Image Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
New Options for Image Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
New Options for Regions of Interest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Selectable Color for Range Selections. . . . . . . . . . . . . . . . . . . . . . . . . . 8
Skeletonize ROI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
New Options for Multi‐ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Cyclical LUT Colors for Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Synchronize Scenes Views with Selection . . . . . . . . . . . . . . . . . . . . . . 10
Additional Visual Effects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
New Options for the Measurement Inspector . . . . . . . . . . . . . . . . . . . . . . . 11
2D Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3D Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
3D Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
New Options for Selected Objects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Additional Support for CZI Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

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Product Enhancements and Other Changes. . . . . . . . . . . . . . . . . . . . . . 15

Improved TXM File Import . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Switching Loaders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Updates for Exporting Multiple Screenshots . . . . . . . . . . . . . . . . . . . . . . . . 16
Additional Options for Managing Scalar Information . . . . . . . . . . . . . . . . . . 16
Point Set Export for JSON . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Animating Object Movements in the Movie Maker . . . . . . . . . . . . . . . . . . . . 17
Macro Player Updates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Developer Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

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Menu Item Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Preferences Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
System Requirements Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Extending Dragonfly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Getting Help. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

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Request a New Feature. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20

Dragonfly Release Notes

Release Notes Version 3.6
New Features

New Features

The 3.6 software release for Dragonfly and Dragonfly Pro provides the following newfeatures. For information about product enhancements and other changes, such as
improved TXM file import, additional options for exporting screenshots, and a list of
Macro player updates, see Product Enhancements and Other Changes on page 15.

Arrow Annotation
You can use the new Arrow annotation as a pointer to call attention to a certain
specimen feature or to indicate a particular area of interest on 2D and 3D views. Arrowannotations can be included in animated sequences and will appear in exported
screenshots. You should note that by default, captions are not added to arrow pointers.
However, you can add text manually after you create the annotation.
Arrow annotation

The Arrow annotation is available on the Annotate panel, shown below.
Annotate panel

The properties available on the Data Properties and Settings for modifying theTM021-A-04

appearance of an Arrow annotation include its thickness and the style of its control
points, as well as the text that will appear with the annotation. In 3D views, you canchoose to set the size of the annotation and its direction. If these options are not set,
then the size or orientation of the annotation will be adjusted automatically for the best
fit as the view is zoomed and rotated.

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56 Release Notes Version 3.6
New Features

The properties for a selected Arrow annotation are available in the Properties box, as
shown below.
Arrow properties

NOTE The color applied to an Arrow annotation is selectable in the object list. In addition, a popup menu is available for exporting and looking at the annotation.

New Options for Active Contours
A number of new options are available in Dragonfly 3.6 for working with Active Contour
paths and sets. You can now export Active Contour sets directly to an ROI or multi-ROI,
generate a new set of Active Contour paths from an ROI or multi-ROI, as well as limit acut to selected Active Contour paths.

Export Active Contour Sets

Active Contours sets can be exported directly to ROIs and multi-ROIs, either as outlinesthat are one pixel wide or as a completely filled object. In addition, the options in the
Generate from Selected Paths dialog, shown below, lets you assign a unique name,color, and shape to an generated ROI, multi-ROI, or mesh.
Generate from Selected Paths dialog

Generate Active Contour Paths

In previous editions of Dragonfly, you could cut a mesh in the current view orientation
to generate a new set of Active Contour paths. This functionality is updated to include
regions of interest and multi-ROI to the list of objects you can cut.

capture.

Dragonfly Release Notes

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You can choose the object to cut in the drop-down menu shown in the following screenRelease Notes Version 3.6
New Features

Object to cut options

Cut Selected Active Contour Paths

This new option lets you limit a cut to a set of the selected paths.

Additional Image Filters
The following new filters are available in this software release for processing image data
and for creating classifiers for trainable segmentation.

Denoising Filters… The newly added Tv_bregman filter performs total-variation

denoising using split-Bregman optimization, while the newly added Tv_chambolle

performs total-variation denoising on n-dimensional images.

The principle of total-variation denoising is to minimize the total variation of the image,which can be roughly described as the integral of the norm of the image gradient. Total
variation denoising tends to produce “cartoon-like” images, that is, piecewise-constantimages. Refer to http://en.wikipedia.org/wiki/Total_variation_denoising for more
information about the principle of total-variation denoising.

NOTE The code for the Tv_chambolle filter is an implementation of the algorithm of Rudin,
Fatemi and Osher that was proposed by Chambolle in An algorithm for total variation
minimization and applications, Journal of Mathematical Imaging and Vision, Springer,
2004, 20, 89-97.

Hessian Filter… This software release adds a Hessian filter for finding continuous edges

in an image. Almost equal to Frangi filter, this filter is implemented with an alternative
method for smoothing.

Thresholding Filters… Available for thresholding operations, the Niblack, Sauvola, andTriangle filters are designed to output an image composed of two basic classes —foreground and background. The Niblack filter applies a Niblack local threshold to anarray, while the Sauvola filter uses a modification of the Niblack technique. The

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Triangle filter returns a threshold value based on the triangle algorithm.

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8 Release Notes Version 3.6
New Features

New Options for Image Data
This software release includes an Export button on the Explosion panel for exporting theimage bricks of an exploded dataset as individual datasets.
Explosion panel

The selectable parameters include the number of bricks in the X, Y, and/or Z direction.
You should note that the position in space of each exported brick will be calculated sothat the constituent parts can be reassembled coherently. In the example below, theoriginal image data that was exploded into four bricks was reassembled in a 3D and 2D
view.
Datasets exported from the Explosion panel and then displayed in the same views

New Options for Regions of Interest
A number of new options are available in Dragonfly 3.6 for working with regions ofinterest.

Selectable Color for Range Selections

In previous versions of Dragonfly, intensity range selections made in the Range box on
the ROI Tools panel were highlighted a constant red. In this software release, thehighlight color denoting the selected intensity range is selectable in the Colors
Preferences dialog.

Dragonfly Release Notes

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preferences. This preference is circled on the following screen capture of theRelease Notes Version 3.6
New Features

Colors preferences

You should note that a defined intensity domain of image data values can be used tocreate new regions of interest and are also applicable to the ROI Painter tools,
morphological operators, and clipping tools. In this context, only voxels that correspondto a value within the range will be affected by any applied operation.

Skeletonize ROIThis new feature for Dragonfly 3.6 lets you reduce each connected component in aregion of interest to a single-voxel wide skeleton. Right-click an ROI and then choose

Get Skeleton of ROI to create a skeleton of the selected region of interest, as shown
below.

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Original ROI (green) and skeletonized ROI (red)NOTE Refer to http://scikit-image.org/docs/dev/api/skimage.morphology.html?
highlight=skeleton%203d#skimage.morphology.skeletonize_3d for information about
the implementation of this feature.

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New Features

New Options for Multi‐ROIs
A number of new options are available in Dragonfly 3.6 for working with multi-ROIs.
These new features are described in the following topics.

Cyclical LUT Colors for Labels

Whenever “Label” is displayed as the scalar measurement for a multi-ROI, the selected
LUT will now be applied as a periodic or cyclical color map. This means that when labels
are mapped to a color map of k discrete colors, labels 1 through k are be mapped tothose colors. Labels k+1 through 2*k are mapped to the same colors, while labels
2*k+1 through 3*k are mapped to those same colors and so on.
This periodic (or cyclical) color map should make it easier to visually resolve different
labels in a multi-ROI.

Synchronize Scenes Views with Selection

In order to let you quickly find objects in a multi-ROI, you can now synchronize
selections made in the Object Analysis dialog with the MPR views shown in theworkspace. This setting, circled below, is available on the lower right corner of the
Object Analysis dialog.
Object Analysis dialog

This default synchronization option does the following:•

When a row in the Object Analysis table is selected, the MPR views are recentered on the unweighted center-of-mass of the selected item.

•

When an object is selected in an MPR view, the list is focused on the selected item.

Additional Visual Effects
In this Dragonfly release, the options for the visual effects that can be applied toshapes, regions of interest, and clipped regions now include a cyclical lookup table(LUT) function. This option is circled below.

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Visual effects options

Dragonfly Release Notes

Release Notes Version 3.6
New Features

New Options for the Measurement Inspector
Whenever you work with selected measurement ranges, you can now choose to show or
hide measurements that fall outside the In window rendering range. This new option for
the Measurement Inspector is circled below.
Measurement Inspector

2D Settings
This Dragonfly release includes the option to apply tricubic interpolation to image datathat is shown in 2D views. As shown below, the 2D interpolation options — Nearest,
Linear, and Cubic — are available in the 2D settings box on the Data Properties andSettings panel.

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Interpolation options for 2D views

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12 Release Notes Version 3.6
New Features

3D Settings
This Dragonfly release adds the option to adjust the hard gradient setting that isavailable for image data shown in 3D views. As shown below, adjustments with theslider can help you clean-up visualizations that are affected by noise.
Progressive hard gradient adjustments

As shown below, the Hard gradient setting and adjustment slider are available in the 3D
settings box on the Data Properties and Settings panel.
Slider for Hard gradient setting

3D Views
You can now choose to apply an image as the background of 3D views. This option isavailable in the 3D Views Background Color dialog, as shown below.

NOTE A background image for 3D views can be set as a preference or changed temporarily in
the Scene’s Views Properties panel.

Dragonfly Release Notes

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3D View Background Color dialog

Release Notes Version 3.6
New Features

New Options for Selected Objects
The following new options — Create a Box from Current Bounding Box and Create a

Box from Current Box — are available for image data, regions of interest, multi-ROIs,

and meshes in the Data Properties and Settings panel pop-up menus. These new
options can help maintain consistency between different objects.

Additional Support for CZI FilesFor Dragonfly Pro users, this software release provides the option to export image datain the CZI file format from the Data Properties and Settings panel. CZI is a proprietary
format used by ZEISS microscopes to save data, such as image stacks and time lapse
series. Contact Object Research Systems for information about the availability of

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Dragonfly Pro.

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Dragonfly Release Notes

Release Notes Version 3.6
Product Enhancements and Other Changes

Product Enhancements and Other Changes

This release provides the following product enhancements for Dragonfly and Dragonfly
Pro. For information about new features, such as the Arrow annotation, additional filters
for image processing and the Segmentation Trainer, as well newly implemented options
for image data, regions of interest, and multi-ROIs, see New Features on page 5.

Improved TXM File Import
TXM files are encoded with the ZEISS Xradia stage coordinates and they use a XZYmatrix encoding. In order insure that TXM files automatically appear in the orientationconsistent with the ZEISS Xradia stage, Dragonfly Pro users can now choose Scout andZoom mode (XZY) during a file import operation. This option is available in the TXM axis
transformation box, circled below.
Import Datasets dialog

Other options in the TXM axis transformation box include the following:

Legacy Mode (XYZ)… Will import your TXM file with standard XYZ matrix decoding. This

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was the default behavior for all releases of Dragonfly Pro prior to version 3.6.

Other Transform… If selected, then a ZYX axis transformation will be applied. You shouldnote that you can also make your adjustments in the Axis transformation dropdown
menu in the Transform box that is available for all file formats.

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

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16 Release Notes Version 3.6

Product Enhancements and Other Changes

Switching LoadersThis software release adds the option to choose a different loader — DICOM Loader,
Mesh Loader, or Session Loader — in the Import Datasets dialog.
Import Datasets dialog

Updates for Exporting Multiple Screenshots
The Dragonfly 3.6 release includes the option to select different resolutions forexporting images captured from 2D views and from 3D views.
Multiple Screenshots panel

Additional Options for Managing Scalar Information
Whenever you need to manage the scalar information contained in a multi-ROI or
mesh, you can now select multiple scalar value slots whenever you need to delete slots,
map scalar values from another object, or copy scalar values.

Point Set Export for JSON
You should note that in this software release, the length units of Points annotation data
(Scout and Zoom tags) that are exported in the JSON file format are automaticallyencoded in micrometers with a precision of two decimal points. You should note that
this will be applied regardless of the Preferences settings for the default unit orsignificant digits for measurements.

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Choose Scalar Value Slots to Delete dialog

Release Notes Version 3.6
Product Enhancements and Other Changes

In this scheme, a measurement of 5.2 mm will be exported as 5200.00 µm, 3.762834
mm as 3762.83 µm, 3.762837 mm as 3762,84 µm, and so on.

Animating Object Movements in the Movie Maker
In this software release, Movie Maker keyframes now encode the position andorientation of objects such as image data, regions of interest, multi-ROIs, and shapes.
If values are different between sequential keyframes, then that object will be translatedor rotated during that keyframe interval.
With this additional information, it is possible rotate an object regardless of whether thecamera is stationary or being animated.

NOTE You should note that support for meshes will be available in a future software release.

Macro Player Updates
A number of updates for the Macro Player are available in this 3.6 product release.
These updates include the following:•

The current step being executed is highlighted.

•

Steps are fully selectable when playing/editing a macro.

•

The progress of the macro is shown during execution.

•

The macro path specification was added as the argument of the filename in thecompile call instead of 'string'.

Developer Documentation
The developer documentation for Dragonfly has been updated for version 3.6. Choose

Help > Dragonfly Developer Documentation on the menu bar to open theTM021-A-04

documentation system.

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18 Release Notes Version 3.6
Menu Item Changes

Menu Item Changes

The following changes and new menu items are implemented for Dragonfly 3.6.

Dataset Pop‐Up Menu

A number of new items, listed below, and other changes have been implemented for thedataset pop-up menu. These are listed below.
Dataset pop‐up menu changes
Description
Export as CZILets Dragonfly Pro users export image in the CZI file format. See Additional Support for CZI Files on
page 13.

Create a Box from Current
Bounding Box

Lets you create a box that corresponds to the dimensions of the current bounding box.

Create a Box from Current
Box

Lets you create a box that corresponds to the dimensions of the current box.

Region of Interest Menu

A number of new items, listed below, and other changes have been implemented for theregion of interest pop-up menu. These are listed below.
Region of interest pop‐up menu changes
Description
Get Skeleton of ROI

Lets you reduce each connected component in a region of interest to a single-voxel wide skeleton. See
Skeletonize ROI on page 9.

Create a Box from Current
Bounding Box

Lets you create a box that corresponds to the dimensions of the current bounding box.

Create a Box from Current
Box

Lets you create a box that corresponds to the dimensions of the current box.

Multi‐ROI Menu

A number of new items, listed below, and other changes have been implemented for themulti-ROI pop-up menu. These are listed below.
Multi‐ROI pop‐up menu changes
Description
Create a Box from Current
Bounding Box

Lets you create a box that corresponds to the dimensions of the current bounding box.

Create a Box from Current
Box

Lets you create a box that corresponds to the dimensions of the current box.

Mesh Pop‐Up Menu

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

Mesh pop‐up menu changes
Description
Create a Box from Current
Bounding Box

Dragonfly Release Notes

Lets you create a box that corresponds to the dimensions of the current bounding box.

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pop-up menu for meshes. These are listed below.

Release Notes Version 3.6
Preferences Changes

Preferences Changes

Colors Preferences

Changes for the Colors preferences are indicated in the following table.
Colors preferences
Description
Background3D views. Lets you select a bitmap as the background for 3D views.

General colors

Range selection. Lets you select the highlight color for a selected intensity range.

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.

Extending Dragonfly

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

Getting Help

Learning Dragonfly
Just by taking a quick look around www.theobjects.com/dragonfly, you’ll find somegreat free resources, such as our latest instructional videos, recorded webinars, andTM021-A-04

user 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.

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20 Release Notes Version 3.6
Request a New Feature

Send Report to ORS dialog

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

Request a New Feature

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

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to an existing workflow.

Dragonfly Release Notes