Fiber Orientation in 3D

Individual Object Analysis

vs

Local Orientation

Method note
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1. Introduction

Fibrous structures are some of the most abundantly encountered features in both
natural and synthetic materials. XRM offers the possibility to analyse both individual
fiber properties e.g. diameter, orientation and the local orientation of fiber bundles in
composite materials (eg. CFRP).

This document will provide an overview of following topics related to fiber orientation
analysis

1) Types of analysis in CTAn:

a. Individual Object analysis

b. Local Orientation

2) Data Interpretation

3) 3D Visualization in CTVox

This document will not cover strategies for scanning and reconstructing, these topics
are well document in the relevant manuals and method notes.

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2. Segmentation and filtering

Before starting with the analysis, one of the first steps in the post-processing of
reconstructed data is typically filtering. CTAn offers several possibilities for smoothing,
noise reduction and unsharp masking. Especially edge preserving filters are of interest
in the case of loosely packed fibers (Figure 1).

Figure 1. Reconstruction slice before and after conditional mean filtering in 3D space using
CTAn (round kernel with radius 3 and threshold 10). The sample is a concrete sample
containing steel fibers scanned with the SKYSCAN 1173 at an image pixel size of 56µm.

Once the images have been binarized, morphological operations can help mitigate
problems such as touching fibers (e.g. opening, watershed operation) or artificial gaps
in fibers (e.g. closing). More information on image filters and the watershed operation
can be found in the method notes ‘MN077 - Image filtering in CTAn’ and ‘MN073_New
in CTAN_1.15’.

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3. Individual Object Analysis

This method is preferred where individual fibers can and need to be separable. The
algorithm will perform the orientation analysis of each individual fiber. This analysis is
illustrated below using scan data of individual metal fibers placed inside a plastic
container. It is important to note, when performing an Individual Object Analysis (IOA)
the calculation is performed on binarized images. First apply a Threshold on the fibers
of interest in Custom Processing to Binarize the fibers (Figure 2).

A B

Figure 2. A) Greyscale image of metals fibers, B) Binarized image of metal fibers

In 3D space the orientation is determined by the main eigenvalues of the second

moments of inertia of the fibers (Loebl, 1985, Marghitu and Dupac, 2012) When
selecting the IOA analysis option in the Internal Tab in Custom Processing the following
window will appear (Figure 3). Here you will select the analysis to be performed.
A B

Figure 3. A) Individual Object Analysis Orientation (Theta), B) Individual Object Analysis

Orientation (ID) – This gets activated when the Sphere Section Box is Ticked

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There are two options:

A) Orientation (Theta)
If “Orientation (Theta)” is selected, then by default the polar angle theta is
applied – an angle in 2D only – the equatorial or azimuthal angle is calculated
(using ISO 31-11, and ISO 80000-2:2009).
0°

A Theta: 0° - 90°

Theta

90°
90°

B) Orientation (Id) – Sphere Section

Sphere section outputs 3D angle as a limited number of 3D spherical segments
defined by an angle in Theta and Phi. A drop menu under the ‘Sphere section”
tick box allows you to choose between 4 angle options 90°, 45°, 30° and 15°. A
smaller angle such as 15° provides better resolved spatial orientation
information

The sphere sections are determined by:

90° − 𝜗 𝜑
𝐼𝑑 = 𝐼𝑁𝑇 ( ) + 𝐼𝑁𝑇( )
𝑥° 𝑥°

where 𝑥° = (90°or 45°or 30° or 15°, depending on your selection) which divides the
half sphere into sections, as illustrated in the figure below eg. Below 45° was selected
0°
B Theta: 0° - 90°

Theta
Phi: 0° - 360°
0° - 360°
90° Sphere section

Index 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
Theta (°) n/a 0-45 0-45 0-45 0-45 0-45 0-45 0-45 0-45 45-90 45-90 45-90 45-90 45-90 45-90 45-90 45-90
Phi (°) n/a 0-45 45-90 90-135 135-180 180-225 225-270 270-315 315-360 0-45 45-90 90-135 135-180 180-225 225-270 270-315 315-360

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The results of the analysis provides a detailed overview of each individual fiber.

# Orientation theta° Orientation phi°

1 21.22 42.87
In this example there were 36 fibers
2 11.27 326.71 in total. The analysis provides the
3 15.04 33.78
angle and orientation of each fiber
4 86.52 189.56
5 33.60 134.13 in both Theta and Phi (Table on left).
6 24.34 278.54
Depending on the analysis selected,
7 36.66 111.46
8 34.32 287.03 the visualization can be performed
9 29.08 243.25 for either the Theta angle or the
10 14.81 306.47
11
Sphere section. The Theta
59.42 260.97
12 11.96 348.86 visualization uses the Theta angle as
13 64.18 175.23
indicated here in the table on the
14 61.55 114.95
15 25.83 83.96 left. Theta angle is the angle with
16 83.80 150.85 respect to the Z-axis. The Sphere
17 36.03 223.46
18 15.23 172.13
Section visualization groups the
19 11.74 203.63 fibers into sections depending on
20 27.31 183.42
both the Theta and Phi angle as
21 7.68 237.33
22 38.22 228.21 indicated in Figure B on the previous
23 15.04 291.99
page.
24 52.34 189.43
25 48.54 182.72
26 74.08 264.96
27 47.51 133.10
28 51.15 331.03
29 89.13 320.25
30 49.92 316.56
31 69.08 177.01
32 69.21 178.69
33 53.45 195.83
34 59.42 204.36
35 12.63 326.13
36 87.28 144.51

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After the analysis is performed the images will be stored in the Clipboard section of
Custom Processing. Save the new images by selecting Save Bitmaps -> Apply to
Clipboard and save the images in a new folder.

To visualize the data, open CTVox -> Load Volume. Navigate to the new folder where
the images were saved, select 1 of the images, before clicking Open, tick the box in
the bottom corner “Mark as discrete data” (Figure 4)

Tick box before clicking open

Figure 4. When loading up the IOA data, it is beneficial to tick the “Mark as discrete data box”
before loading. This improves the overall look and colour of the fibers.

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After the data is loaded adjust the width of the opacity window to only include the
histogram of the data. A rainbow colour scheme can be applied to highlight the change
in angle of the different fibers.

IOA Orientation (Theta) (Figure 5)

The theta angle range is between 0° and 90°, this is highlighted with the rainbow
colour scheme, Blue is almost vertical (0° - 30°), Green has a slight angle (30° - 60°)
and Red is almost horizontal (60° - 90°).

Histogram adjust

0° - 90°

Figure 5. Rainbow colour scheme applied to the IOA Orientation Theta results. The histogram
is adjusted to only show the 0° - 90° range.

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IOA Orientation in Sphere Section (Figure 6)

In the example of the sphere section set to 45°, the sphere sections range from 1 - 8,
this is highlighted with the rainbow colour scheme, Blue sphere section (1 - 2), Green
sphere section (3 - 4), Orange (5 – 6) and Red sphere section (7 - 8). The sphere
sections refer to the description indicated at the start of the Method Note.

Histogram adjust

1-8

Figure 6. Rainbow colour scheme applied to the IOA Orientation Sphere Section. The
histogram is adjusted to only show the 1 - 8 range.

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4. Local Orientation

The local orientation analysis is based on the calculation of grey scale gradients within
a certain radius. Local orientation is calculated using the method of Straumit et al.
(2013, 2015) to determine local anisotropy tensors in microCT image data. The input
for this plugin is a grey scale image. The output is an image intensity map based on
these grey-scale gradients either by Theta angle or Sphere section. While the
anisotropic diffusion filter assesses anisotropy to smooth while preserving edges, the
local orientation function measures and maps in 3D the local orientation of structures,
where there is anisotropy.

In the Local Orientation dialog window when 3D space is selected the “Output” option
appears with a drop-menu with two choices, Theta angle or Sphere section similar to
the IOA options. The radius value is adjusted according to the fiber thickness, this can
be optimized by selecting the 2D mode and performing a preview.

Tick Inside VOI Select 2D for Preview

Option

Fiber Bundles

Below is an analysis example of a carbon fiber reinforced polymer (CFRP), scanned at

300 nm with SKYSCAN 2214 (Figure 7). The Local Orientation analysis is used to
determine the main orientation of the fiber bundles relative to each other.

Something to note is that the plugin operates on the entire image, every voxel is taken
into consideration. Due to the large number of voxels in a dataset this analysis can be

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very time consuming to perform. However, it is possible to reduce the overall analysis
by selecting the Inside VOI tick box in the dialog windows, restricting the calculations
to the voxels that are inside a VOI. Even if the fibers cannot be segmented due to
limited contrast or limited resolution, having a rough VOI will significantly speed up
the analysis. Threshold the fibers and apply to Region of Interest. (Figure 7).
A B

Figure 7. Carbon Fiber Reinforced Polymer scanned at 300 nm on the SKYSCAN 2214 with
CCD2. A) Greyscale image, B) VOI of fibers

Please note the following 2 important considerations.

- Local orientation analysis is a time-consuming algorithm. Make sure that you

generate a VOI of the fibers of interest and select the Inside VOI option in the
dialog box.
- Radius should be set appropriately. The example below shows the original
image (left) and the VOI image (right) of the CFRP scanned at 300 nm.

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The local orientation analysis with a very small radius is shown below. There is range
of orientations within one fiber and the measurement relates to intra-fiber
orientation.

Below the radius for the local orientation analysis is gradually increased. When the
fibers are not too densely packed, one can choose the radius in the range of the fiber
thickness for a characterisation of local fiber orientation (left). When the radius is
bigger, the information is spread across several fibers and in this example more
representative of fiber bundles (right).

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In summary:

The algorithm assigns every voxel inside a window of voxels in the sample with a local
orientation (theta angle) calculated inside a certain radius around this voxel (eg. radius
15 means the 31x31x31 voxels window) and counts the number of voxels with the
same orientation within the full dataset. Theta angle measurement is the angle with
respect to the Z-axis (Illustrated at the start of the Method Note).

After the analysis is performed the images will be stored in the Clipboard section of
Custom Processing. Save the new images by selecting Save Bitmaps -> Apply to Image
inside ROI and save the images in a new folder.

To make it easier to visualize the Local orientation data it is advised to load both the
Greyscale and the Local Orientation images together. The first step is to load up the
Greyscale images into CTVox. After the Greys scale images are loaded click on Load
Volume again and navigate to the folder containing your Local Orientation images. In
this folder select one image, tick the box “Mark as discrete data” and click Add. This
will load the Local Orientation Data alongside the Greyscale data (Figure 8)

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Mark as discrete

Click Add

Figure 8. Load the Local Orientation data alongside the Greyscale data. Click on Mark as
Discrete data and click Add.

After the Local Orientation data is loaded adjust the width of the opacity window of
the Local Orientation data to only include the histogram on the data. In contrast to
the IOA results a rainbow colour scheme will not be the best option in this specific
case. In the case of this CFRP the fibers are perpendicular to each other. To provide a
clearer image only two colours are assigned to the histogram.

What we can see is that the histogram for these results indicates two distinctive peaks.
The first peak is at 0° and the second peak is at 90°, this highlights the two major
orientations in Theta for the fiber bundles. By maximizing the opacity curve all the
data represented by the histogram becomes visible, adding only green to the left peak
and red the right peak provides a clear distinction between the two orientations. What
we see is that the vertical fibers (0°) are green and the horizontal (90°) are red. This
matches perfectly with our previous statement that Theta angle is calculated with
respect to the Z-axis.

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Figure 9. Both the Greyscale images and the Local orientation data was loaded in CTVox to
visualize the fibers more clearly

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Individual Fibers

This analysis can also be applied on individual fibers. Like the fiber bundles the analysis
is performed on the Greyscale images. First an VOI is generated for the individual and
fibres before the analysis is performed (Figure 10).

A B

Figure 10. A) Greyscale image, B) VOI image

Next the Local Orientation plugin is opened and a radius value of 20 was chosen in this
case (Figure 11)
A B

Figure 11. A) Local plugin, radius 20, Output Theta angle, B) Output image has homogenous
greys scale over the fibre indicating the entire fibre is selected and not only small sections
inside the fiber

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The results of the analysis highlights how the direction of a fiber changes along its
length (Figure 12).

After the analysis is performed the images will be stored in the Clipboard section of
Custom Processing. Save the new images by selecting Save Bitmaps -> Apply to Image
inside ROI and save the images in a new folder

Load the new Data into CTVox and apply a similar histogram adjustment and rainbow
colouring as in the previous analysis. The image below highlights this by changing the
colour as the angle in Theta changes. The vertical fibers (0° - 30°) are blue, the fibers
at a slight angle are green (30° - 60°) and the horizontal fibers are red (60° – 90°).

Figure 12. The vertical fibers (0° - 30°) are blue, the fibers at a slight angle are green (30° - 60°)
and the horizontal fibers are red (60° – 90°).

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5. Individual Object Analysis vs Local Orientation

Individual Object Analysis Local Orientation

Preferable Types of Fibers Single fibers that are not Fiber bundles like CFRP of
connected fabric and individual fibers

Analysis Binarized Images Greyscale Images

Visualization Mark as Discrete Data Load Both Greyscale and

Local Orientation Data

Mark as Discrete Data

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6. Refences

Loebl J (ed.) Image analysis principles and practice p159 – p161 (Gateshead, UK: Loebl )
(1985)

Marghitu, DB. and Dupac, M. Advanced Dynamics: Analytical and Mumerical Calculations
with MATLAB, Chapter 2, p73 – p141. (2012)

Straumit I, Lomov SV, Verpoest I, Wevers M. Determination of local fibers orientation

in composite material from micro-CT data. In: Proceedings of the 11th International
Conference on Textile Composites (TexComp-11) 2013 Sep 19.

Straumit I, Lomov SV, Wevers M. Quantification of the internal structure and

automatic generation of voxel models of textile composites from X-ray computed
tomography data. Composites Part A: Applied Science and Manufacturing. 2015 Feb
1;69:150-8.

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