BRUKER MICRO-CT ACADEMY

Volume 2, Issue 6, June 2015

In this issue:

New features in CT-Analyzer 1.15

Bruker microCT news

Upcoming events

Image of the month

Bruker microCT

Kartuizersweg 3B

B-2550 Kontich, Belgium

Tel: +32 (0)3 877 5705

Fax: +32 (0)3 877 5769

applications.BmCT@bruker.com

www.bruker-microCT.com

Welcome

Just a month ago we had our annual user meeting in Bruges, Belgium. During this meeting we announced and

presented details of important updates and new capabilities in our flagship 3D analysis program CT-Analyzer (“CTAn”).

This June newsletter highlights some of these new features.

New features in CT-Analyzer 1.15:

Major acceleration of 3D thickness measurement

3D thickness and separation calculation is now 5-8

times faster than the previous versions. An

innovative new algorithm adds multi-threading while

not compromising accuracy by subdividing the

analyzed volume. In fact, accuracy is slightly

improved with the result that Tb.Th and Tb.Sp

results will be 1-2% different than in previous

versions – so please follow our normal advice in

staying with a single CTAn version for the whole of

any single study.

Figure 1. Mapping of spatially resolved local thickness in

3D, illustrated by this thickness-color image, is now 5-8

times faster in CTAn.

ROI drawing: multiple and subtractive shapes

CTAn now allows drawing of multiple ROI shapes

using keyboard SHIFT plus right-mouse-button

drawing. Also, you can make subtractive shapes

using keyboard CTRL plus right-mouse-button

drawing, to allow both ROI correction and creation of

hollow shapes. These are both illustrated below in

figure 2 by the twin ROI shapes for two molar tooth

root canals, and the hollow cortical bone ROI.

Figure 2. Multiple ROI shapes allow both molar tooth root

canals to be delineated (above), and subtractive ROI

shape drawing allows a hollow ROI for cortical bone to be

drawn (below).

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BRUKER MICRO-CT ACADEMY

Volume 2, Issue 6, June 2015

Figure 4. A binarised cross-section through scanned

straight hair (above) shows several neighboring strands

fused by pixel connections; these are separated by the

watershedding process (below) so that most hair strands

become discreet binarised objects for accurate analysis.

Conditional mean filtering

A goal of smoothing reconstructed images is

sometimes to clarify boundaries between regions of

different density. Ideally this should be done without

compromising spatial resolution of object boundaries

and internal porous spaces. An efficient way to

achieve this is the conditional mean filter –

neighboring voxels are smoothed if their greyscale

difference is less than a certain value (“threshold“).

At object boundaries, sharp greyscale gradients

exempt them from smoothing, thus preserving

detailed architecture of structures while allowing

substantial smoothing of less abrupt material

gradations within objects (see figure 3).

Watershedding

This is the name of a technique of separating

objects that are connected by bridges a few pixels

wide in binarised images but which represent

discreet elongated objects with approximately

circular cross-section. In the example below,

watershedding is shown to separate individual

human hairs in a binarised cross-section image.

ROI reference level: up or down?

The reference level function in CTAn assists with

positioning the selected range relative to a

landmark, such as an anatomical location in a

biological structure.

Figure 3. An unsmoothed image of Haversian cortical

bone (above), the results of Gaussian smoothing (middle)

and conditional mean filtering (below) both with a 5 voxel

radius.

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BRUKER MICRO-CT ACADEMY

Volume 2, Issue 6, June 2015

Figure 5. Clicking “Upside-Down” in the Selection /

Analytic tab moves the selected vertical range to below,

rather than above the reference level.

The button “Upside-Down” has been added in order

to simplify use of the reference level where the

landmark location is above, not below, the selected

range of cross-sections in the “Z” (height) axis. This

is illustrated above in figure 5, where a VOI for a

region of a rat distal femur for trabecular bone

analysis, and bone around a metal implant, are

selected relative to reference points above the

analyzed region (the clear, non-colored band).

Live update in BatMan

Operations carried out in the Custom Processing

page of CTAn, and also in the corresponding Batch

Manager (“BatMan”) module, are now updated live –

in real time – in the image display window. This

means you no longer have to wait for the end of a

task list to see the outcome of the operations – you

can see the outcomes of each individual plugin as

soon as it is completed.

A new COLLECTIONS tab in custom processing

The new, fifth tab is added at the new first tab in the

custom processing page. It is titled “collections” and

its purpose is to allow the user to keep a list of

frequently used task lists on hand for quick and easy

call-up. Right-click “edit” on a task list in the

collections tab to load it to the Task list tab – which

now moves to second place just to the right of the

collections tab (see figure 6 below).

Figure 6. The collections tab allows often-used task lists

(e.g. “root canal”) to be available for quick access.

Peripheral object area (exclude VOI boundaries)

In some analyses you need to measure object

surface area but exclude surfaces that are artificially

cut in the crossectional plane by the top and bottom

VOI boundaries. An example is the analysis of bone

implant contact (BIC) around an orthopedic implant

surface (see figure 7). The 2D slice-by-slice analysis

not allows both intersection surface (BIC) and object

surface to be measured while excluding these

artificial cut surfaces.

Figure 7. Measurement of “peripheral area” of objects and

of intersection surface, excludes artificial cut surfaces

(right, shown in red).”

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BRUKER MICRO-CT ACADEMY

Volume 2, Issue 6, June 2015

DIR Jun. 22-25 Ghent, Belgium

ICTMS Jun.29-Jul.03 Québec, Canada

TCES Jul. 17-21 Southampton, UK

SCA Aug. 16-20 Newfoundland and Labrador, Canada

ESB Aug.30-Sep.03 Krakow, Poland

Metfoam Aug.31-Sep.02 Barcelona, Spain

WMIC Sep. 02-05 Honolulu, USA

XNPIG Sep. 08-11 Bethesda, USA

Other enhancements

‒ Standard deviation of thickness and separation

measurements added to summary table reports

(indicated homogeneity of architecture)

‒ Color palette adjustment: in addition to altering the

cross-section image appearance, you can choose

whether or not to apply the same color change to the

projection window (spr image) and the volume

rendered image window

‒ Bone Mineral Density calibration: at the “histogram”

tab in preferences, the date and time of the last

applied BMD calibration is displayed

‒ Reset CTAn window layout: have you got in trouble

with rearranging the CTAn window and can’t get a

pane back to the right place? Now you can “Reset

Window Layout” from the View Menu, or just click

F12

‒ Batman: tickboxes added to listed datasets, allowing

selection or deselection

‒ Thresholding: The Ridler-Calvard method of auto-

threshold is added, complementing the Otsu

thresholding already present

For more information, we’d like to refer you to the

MN073_New in CTAN_1.15.

Bruker microCT News

The release of CT-Analyzer version 1.15.4.0 on the

Bruker microCT website.

A training course for users of SkyScan microCT

systems was held at Bruker Kontich during June 1-5,

and was attended by 9 scientists from Poland,

Spain, Italy and France.

MicroCT workshop at the Tissue Engineering

Centre, National University of Malaysia Medical

Centre 15-16 June. This was a 2-day workshop with

presentations from users as well as hands-on

training on new features in hard and software.

Upcoming Events

Bruker microCT will participate with an exhibit in the

forthcoming conferences. Please click the link below for

more information. We hope to see you there!

Image of the Month

Seven second scan of a mouse in the new

SkyScan1278 high-speed low-dose in-vivo microCT

scanner. Contrast in the kidneys is from injected contrast

agent Iomeron400. Leading edge camera technology

provides remarkable image quality with such a short

scan. Voxel size is 200um.

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