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Introduction to X-ray microtomography

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 Introduction to X-ray microtomography
Georg Siroky

Institute for Surgical Technologies and Biomechanics University Bern

Introduction
Since the discovery of X-rays at the beginning of the 20th century, a vast
number of applications for non-destructive and non-invasive X-ray imag-
ing have emerged. Not only are X-rays widely used in material science
and physics, they are also used in computed tomography (CT) as the gold
standard for biomedical imaging. The fast improvement of digital data pro-
cessing made it possible to leap from simple two dimensional radiographic
images, to three-dimensional tomographic patient data within one century.
X-ray microtomography (microCT) is a special case of tomographic meth-
ods. Although it uses the same principle as clinical CT imaging, it offers
higher spatial resolution at the micrometer scale. MicroCT is a corner stone
of modern material science and provides a deeper understanding of structural
features and processes of organic and non-organic materials. This tutorial
will introduce the most important parameters available to optimize image
quality of X-ray microtomography scans. Furthermore, we will provide a
basic introduction to image processing and segmentation.

1
Contents
1 X-rays: Generation and Interaction 3
1.1 X-ray Tube . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.2 X-ray Spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.3 Interaction of X-rays with matter . . . . . . . . . . . . . . . . 8

2 MicroCT Parameters 12
2.1 Photon Energy . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.2 Intensity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.3 Beamhardening and Filters . . . . . . . . . . . . . . . . . . . 14
2.4 Voxel Size and Resolution . . . . . . . . . . . . . . . . . . . . 15

3 Image Processing and Image Analysis 17

3.1 Filtering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.2 Segmentation . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
3.3 Trabecular bone morphometry . . . . . . . . . . . . . . . . . 19
3.4 Anisotropy . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
3.5 Noise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

4 Tasks 22
4.1 Scanning parameters . . . . . . . . . . . . . . . . . . . . . . 23
4.2 Anisotropy and homogenized deformation . . . . . . . . . . . 23
4.3 Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

5 Pre-Lab Quiz 25

Aims and Targets

Students will learn about the basics of microCT imaging, the most important
scanning parameters and some basics of image processing. To facilitate a
general understanding of microCT imaging we will discuss the underlying
physical laws which involve:

ˆ Generation of X-rays

ˆ X-ray energy spectrum

ˆ Interaction of X-rays with matter

ˆ Linear attenuation of X-rays

2
Given the basic physical laws, the tutorial will continue introducing the tech-
nical aspects of microCT scanners. We will focus specifically on parameters
and adjustments regularly made by the operator. The following aspects will
be introduced:

ˆ Photon energy [kVp]

ˆ Intensity [µA]

ˆ Integration time [ms]

ˆ Voxel Size [µm]

ˆ Sample size [mm]

Finally, we will quantitatively analyze the obtained CT data of cancellous

bone using an open source visualization tool (ImageJ & BoneJ). This will
enable the students to quantify the image quality and morphological parame-
ters of the scanned bone samples. The following concepts will be introduced:

ˆ Signal to noise ratio (SNR)

ˆ Filtering

ˆ Segmentation

ˆ BV/TV

ˆ Anisotropy

Once the students have completed their practical session and obtained the
CT data, they are asked to write a summarizing report. This will introduce a
brief review of the fundamental theory, description of the experiments as well
as an analysis of the CT images. The following sections will introduce the
theoretical foundation to understand this laboratory session. The following
pages are a compendium of sources documented in the reference section.
The student is encouraged to consult the original material for deeper study
of the subject.

1 X-rays: Generation and Interaction

The basis of both planar radiography and CT is the differential absorption
of X-rays by various tissues. For example, bone and small calcification’s
absorb X- rays much more effectively than soft tissue. X-rays generated

3
from a source are directed towards the patient, as shown in Figure 1. X-
rays which pass through the patient are detected using a solid-state flat panel
detector which is placed just below the patient. The detected X-ray energy
is first converted into light, then into a voltage and finally is digitized. The
digital image represents a two-dimensional projection of the tissues lying
between the X-ray source and the detector. [5]

Figure 1: Setup for planar radiography [5]

The basic principle of CT is shown in Figure 2, together with a photo-

graph of a modern multi-detector helical scanner. The X-ray source and a
bank of X-ray detectors are rotated in synchrony around the patient. The
rotation speed is high, with one revolution taking less than a second. A series
of one-dimensional projections is acquired during the rotation, and these are
then reconstructed to form a two-dimensional image. The third dimension
is acquired by moving the patient in a horizontal direction while the images
are being acquired, and also by having not just one but many detector rows
(currently up to 320) in the horizontal direction. Using this type of state-
of-the-art multi-detector helical CT scanner, very high resolution images of
large volume can be acquired very rapidly. [5]

4
 Figure 2: Helical CT Scanner [5]

1.1 X-ray Tube

For both planar radiography and CT the X-ray source is a specialized piece
of equipment known as an X-ray tube. A photograph of an X-ray tube and
a schematic diagram of its major components are shown in Figure 2.3. All of
the components of the X-ray system are contained within an evacuated ves-
sel. The evacuated vessel is surrounded by oil for both cooling and electrical
isolation. The whole assembly is surrounded by a lead shield with a glass
window, through which the X-ray beam is emitted. X-rays are produced by
a beam of high energy electrons striking the surface of a metal target. A
negatively-charged cathode acts as the source of these electrons, and consists
of a small helix of thin tungsten wire, through which an electric current is
passed. When the temperature of the wire reaches ˜2200 °C, electrons have
sufficient energy to leave the metal surface.[5]
A potential difference between the anode and cathode of between 25 and
140 kV (depending upon the particular type of clinical study) is applied,
such that the electrons produced at the cathode are attracted to the anode,
striking it at high velocities. This potential difference is known as the accel-
erating voltage, or kVp. When the high energy electrons strike the anode
surface, part of their kinetic energy is converted into X-rays. [5]

5
 Figure 3: Main components of a X-ray tube [5]

1.2 X-ray Spectrum

X-ray tubes produce X-rays with a wide range of energies, up to a maximum
value given by the kVp, as shown in Figure 4. The very low energies are
absorbed by the tube itself. Characteristic lines are seen as sharp lines,
superimposed upon a broad energy distribution from general radiation. The
spectrum represents a plot of the relative number of X-rays produced as a
function of their energy. When one refers to the energy of the X-ray beam,
this number represents the weighted average of all of the different energies,
and is typically about two-thirds of the kVp value. There are two separate
mechanisms by which X-rays are produced, one which results in a broad
spread of energies, and the other which produces distinct sharp lines, both
of which are evident in Figure 4. The first mechanism involves an electron
passing close to the nucleus of an atom of the metal forming the anode,
and being deflected from its original trajectory by the attractive forces from
the positively charged nucleus. This deflection results in a loss of electron
kinetic energy, and this energy loss is converted into an X-ray. The maximum
energy that an X-ray can have corresponds to the entire kinetic energy of
the electron being transferred to the X-ray, i.e. the kVp value. Given the
small size of the nucleus in relation to the entire atom, it is much more likely
that the electron will undergo only a partial loss of energy, and so a wide

6
spectrum of X-ray energies is produced: this is termed general radiation or
Bremsstrahlung (braking radiation in German). Although the distribution
decreases roughly linearly with energy, many of the very low energy X-rays
are absorbed by the housing of the X-ray tube itself, as evident on the left-
hand-side of Figure 4. Sharp peaks are also present in the X-ray energy
spectrum, and the energy at which these peaks occur is characteristic of the
particular metal used in the anode, hence the name ‘characteristic radiation’.
[5]

Figure 4: Energy Spectrum of X-ray tube [5]

Info Box: Lab sized microCT scanners use cone-beam sources with a
poly-chromatic energy spectrum. This implies that both effects:

ˆ Characteristic Radiation

ˆ Bremsstrahlung

contribute to the total energy spectrum. By using filters, e.g. Aluminum or

Copper, one can change the shape of the spectrum towards higher energy
peaks.

7
1.3 Interaction of X-rays with matter
In order to produce images with high signal to noise ratio (SNR) and high
contrast to noise ratio (CNR), three basic criteria should be satisfied: (i)
sufficient X-rays must be transmitted through the body for a high SNR,
(ii) X-ray absorption must be sufficiently different between different tissue-
types in order to produce high contrast, and (iii) there must be a method
for removing X-rays which are scattered through unknown angles as they
pass through the body. For the energies used in diagnostic X-ray imaging,
there are two major mechanisms by which X-rays interact with tissue. The
first mechanism is the photoelectric interaction with differential attenu-
ation between, in particular, bone and soft tissue. The second mechanism,
Compton scattering, involves the X-ray being deflected from its original
trajectory. The X-ray energy is reduced, but the scattered X-ray may still
have enough energy to reach the detector. Compton scattered X-rays give a
random background signal, and so their contribution to the image should be
minimized to improve the CNR. Coherent scattering won´t be considered
as an additional form of X-ray interaction, due to its minor importance in
clinical CT imaging. [5]

Info Box: The three basic criteria for CT imaging are:

1. Sufficient photon flux through the specimen for high SNR

2. High difference in absorption of tissue of interest to obtain high con-

trast

3. Filtering scattered X-rays

Photoelectric attenuation
The first mechanism, in which tissue absorbs X-rays, provides the contrast
in X- ray images. These ‘photoelectric interactions’ are very similar to the
phenomenon of characteristic radiation. The first step is that the energy
of the incident X-ray is absorbed by tissue, with a tightly bound electron
being emitted from either the K- or L-shell, as shown in Figure 5. This
ejected electron has an energy equal to the difference between the energy
of the incident X-ray and the binding energy of the electron. The second
step is that an electron from a higher energy level fills the ‘hole’ with the
emission of a ‘characteristic’ X-ray, with an energy equal to the difference
in the binding energies of the two electrons. This characteristic X-ray has
a very low energy, a few keV at most, and is absorbed by the tissue. The

8
net result of the photoelectric effect in tissue, therefore, is that the incident
X-ray is completely absorbed and does not reach the detector. [5]

Figure 5: Photoelectric effect illustrated on the orbital model [5]

The probability of a photoelectric interaction occurring depends on the

energy (E) of the incident X-ray, the effective atomic number (Zeff) of the
tissue, and the tissue density:
3
Zef f
PP epp ∼ ρ · (1)
E3
Equation 1 indicates that, at low X-ray energies, the photo- electric effect
produces high contrast between bone (high attenuation) and soft tissue (low
attenuation), but that the contrast decreases with increasing X-ray energy.

Compton Scattering
Compton scattering refers to the interaction between an incident X-ray and
a loosely bound electron in an outer shell of an atom in tissue. In Compton
scattering a small fraction of the incident X-ray energy is transferred to this
loosely-bound electron. With the additional energy, the electron is ejected,
and the X-ray is deflected from its original path by an angle h, as shown in
Figure 6. The energy of the scattered X-ray can be calculated by applying
the laws of conservation of momentum and energy. [5]

9
 Figure 6: Principle of Compton scattering [5]

Attenuation Coefficient
The attenuation of X-rays through the body has been experimentally deter-
mined to be an exponential process with respect to distance traveled. The
exponential function can be characterized in terms of a tissue linear attenu-
ation coefficient (µ). The value of µ depends upon the energy of the incident
X-rays. One can therefore express the number (N ) of X-rays transmitted
through a certain thickness (x) of tissue as:

N = N0 · e−µ(E)x (2)
where No is of the number of incident X-rays. The value of l is the sum
of the individual contributions from photoelectric absorption and Compton
scattering:

µtot (E) = µComp (E) + µP hoto (E) (3)

X-ray attenuation in tissue is most often characterized in terms of a mass
2
attenuation coefficient (µ/ρ), measured in units of cmg . Figure 7 left the in-
dividual contributions from photoelectric attenuation and Compton scatter
add together to give a net tissue linear attenuation coefficient (the specific

10
data are shown for water). The contribution from the photoelectric effect
dominates at low X-ray energies, but Compton scatter is the more impor-
tant term at high energies. Figure 7 right illustrates the mass attenuation
coefficient of lipid, muscle and bone as a function of X-ray energy. [5]

Figure 7: Mass attenuation coefficient as a function of energy [5]

Figure 7 also shows the mass attenuation coefficients of bone, soft tissue
and lipid as a function of the incident X-ray energy. At low incident X-ray
energies bone has by far the highest mass attenuation coefficient, due to the
prevalence of photoelectric interactions and the high effective atomic number
of bone compared to tissue and lipid. As the X-ray energy increases, the
values of the mass attenuation coefficient become much lower for all tissues.
At X-ray energies greater than about 80 keV, the difference in the mass
attenuation coefficients of bone and soft-tissue is less than a factor of 2.
There is also relatively little difference between the attenuation coefficients
for soft tissue and fat due to their closeness in effective atomic number. An
important feature in Figure 7 is the sharp discontinuities in the absorption

11
coefficient of bone at two distinct energies, a phenomenon is known as a K-
edge.

2 MicroCT Parameters
The previous chapter introduced the fundamental physical laws that lead to
contrast in a X-ray radiograph or in a CT image. Due to the broad variety of
specimen constitution, that can range from low density polymers to metals,
the operator is required to select scanning parameters to optimize image
contrast based on SNR and CNR. The following paragraphs will introduce
the main parameters to be choosen, while a deeper understanding of their
influence will be facilitated in the exercises.

2.1 Photon Energy

An X-ray is a electromagnetic waveform, and the energy of each X-ray pho-
ton is inversely proportional to its wavelength, see Equation 4. In other
words, X-ray photons with longer wavelengths have lower energies than
photons of shorter wavelengths. The energy of an X-ray photon, which
is produced by accelerated electrons striking the X-ray tube target (e.g.,
tungsten), is expressed as units of electronvolts (eV). Desktop microCT
systems produce a poly-chromatic beam, meaning that the X-ray tube pro-
duces a spectrum of photon energies. The highest possible photon energy
in that spectrum is equal to the applied electrical potential of the X-ray
tube. Therefore, the mean photon energy of the beam is always lower. For
an X-ray tube operating at 45 keV, the average photon energy of the poly-
chromatic beam is typically about 25 keV. It is acceptable to report the mean
photon energy (keV) of the spectrum, but it is usually more convenient to
report the applied electrical potential across the X-ray tube (kilovolts or
kVp, where p stands for peak voltage). Typically, microCT systems operate
in the range of 20 to 100 kVp and the attenuation of the X-ray photons as
they pass through material can be caused by either absorption or scattering
depending on their energy. The interaction of lower- energy X-rays (<50
keV) is dominated by the photoelectric effect and depends on the atomic
number of the materials. The ability to differentiate bone and marrow is
best at low energies; however, because the total attenuation of the X-rays
increases, only small objects can be measured at low energies because other-
wise noise becomes too large to allow quantitative analysis. The interaction
of higher-energy X-rays (>90 keV) is dominated by Compton scattering,
where the attenuation is approximately proportional to the density of the

12
material. In the medium range of X-ray energy (50 to 90 keV), both the
photoelectric effect and Compton scattering contribute to attenuation. [2]

~·c
EP hoton = =~·ν (4)
λ

Figure 8: X-ray spectrum with respect to peak energy[4]

2.2 Intensity
The information content of a voxel depends on the SNR. The tube current
is measured in microamperes (mA). The total number of photons for each
projection during a tomographic scan depends on the tube current (mA)
and the integration time for each projection (ms), as well as the number of
times each projection is repeated (frame averaging). The integration time
and number of frames per projection directly influence the duration of the
scan. Whereas SNR can be imp- roved by increasing the integration time
and frame averaging, this comes at the tradeoff of a longer scan time with
higher radiation exposure. The radiation dose is proportional to the tube
current and duration of X-ray exposure; therefore, frequently the product
of these parameters is reported (mAs). Alternatively, tube current (mA),
integration time (ms), and frame averaging can be reported independently.
[2]

13
2.3 Beamhardening and Filters
A fundamental assumption in most mCT systems is that the incident X-
ray energy spectrum is equivalent to the X-ray energy spectrum that exits
the specimen. However, a consequence of the energy dependence of absorp-
tion is that the spectrum of a poly-chromatic X-ray beam, as is used in
desktop mCT systems, changes as it passes through a given sample: The
lower-energy portion of the beam is preferentially stopped, whereas the high-
energy portion passes through more easily. This differential absorption of
low- and high-energy photons leads to so-called beam hardening, whereby
the average energy of the X-ray beam is increased owing to filtering of lower-
energy photons. Beam- hardening effects can be reduced by placing a filter
(e.g., a thin aluminum foil, see Figure 9) or beam-flattening filter in the
X-ray path to narrow the energy spectrum. Mathematical methods can re-
duce beam hardening further, but these are only approximate because the
correction depends on the path length of the beam and material composi-
tion of the sample. In general, a rule of thumb for selecting X-ray energy is
that a higher energy is needed for thicker and denser samples. Optimizing
the absorption contrast can be achieved by experimenting with varying X-
ray energies and beam-hardening reduction methods (e.g., filters, software).
However, it is important to note that the settings must be adjusted to match
the object diameter and density, implying that optimal settings for a single
bone may not be suitable for scanning multiple bones simultaneously or for
scanning an object of greater size and/or density. [2]

14
 Figure 9: X-ray spectrum with respect to different filters[3]

2.4 Voxel Size and Resolution

A voxel is the discrete unit of the scan volume that is the result of the to-
mographic reconstruction. It is a 3D volume representing two dimensions
within the slice and the slice thickness. Typically, voxels from microCT im-
ages have all three dimensions equal and therefore are described as isotropic
voxels. Ideally, the smallest voxel size (i.e., highest scan resolution) available
would be used for all scans; however, higher-resolution scans require longer
acquisition times because they must collect more projections and generate
large data sets. Therefore, the tradeoff between voxel size and scan time
should be carefully considered. Differences in voxel size (e.g., 10 to 20 mm)
have little effect on the evaluation of structures with relatively high thickness
(i.e., 100 to 200 mm), such as cortical bone or trabeculae in humans or large
animal models. However, when analyzing smaller structures such as mouse
or rat trabeculae with approximate dimensions of 20 to 60 mm, voxel size can
have significant effects on the results. Scanning with low resolution (large

15
voxel size, >100 mm) relative to the size of the structure of interest can
cause an underestimation of bone mineral density owing to partial-volume
effects and overestimation of object thickness. Generally, as the ratio of
voxel size to object size decreases, so does the measurement error regardless
of scale. it should be made clear that voxel size is not equivalent to spatial
resolution of the mCT image. In radiologic physics, CT spatial resolution
typically is reported from measurement of the modulation transfer function
(MTF). Nevertheless, no standardized approach has been accepted by mCT
device manufacturers in reporting spatial resolution. The relationship be-
tween spatial resolution and voxel size depends on several factors (i.e., mean
absorption of sample, detector noise, reconstruction algorithm, X-ray focal
spot size and shape, detector aperture, and scanner geometry), and thus
it is more appropriate to report voxel size directly. Therefore, one should
report the nominal isotropic resolution or isotropic voxel size to reflect that
it is not true spatial resolution. [2]

Figure 10: Comparison of imagequality under varying voxel size [2]

16
Info Box: The most important imaging parameters of a microCT scanner
are:

ˆ Energy [kVp]: given in terms of maximum energy of the spectrum

(p ... peak). Determines contrast, as rule of thumb: “lower energies
lead to higher contrast”

ˆ Intensity [µAs]: is product of integration time Ii [ms] times tube

current It [mA]. Higher intensity leads to lower noise but also lower
contrast.

ˆ Filter: aluminum or copper filters can be used to reduce artifacts,

such as beamhardening. The higher the attenuation of the filter
(heavy materials, high thickness), the bigger is the energy peak shift
towards higher energies.

ˆ Voxel Size [µm]: defines the amount of details visible in the CT

image. The voxel size shall not be confused with the resolution of
the CT scanner. To estimate the true resolution one has to consider
other factors such as mean absorption of sample, detector noise, re-
construction algorithm, X-ray focal spot size and shape, detector
aperture, and scanner geometry.

3 Image Processing and Image Analysis

Image processing and analysis are terms that refer to optimizing the im-
age quality of an acquired dataset (processing) with subsequent generation
of quantitative information (analysis). Given that the imaging parameters
are correct, one can optimize the image quality by image post-processing.
Image analysis provides tools to obtain quantitative information from the
image data. This tutorial will introduce the most important morphometric
measures used to quantify cancellous bone samples.

3.1 Filtering
Filtration Reconstructed microCT data inherently include signal noise that
should be reduced by filtering while maintaining sharp contrast between
bone and marrow. Removal of image noise is best accomplished by a low-
pass filter, but this essentially blurs the image. Edge enhancement requires
a high-pass filter, yet this may result in increased noise, see Figure 11. Gen-
erally, a Gaussian filter does well at balancing these competing objectives,

17
is easy to implement, and is fast, even for large data sets. It is perhaps
the most commonly used filter, but other options such as median filtering
also provide good results. Alternatively, examples of edge-preserving filters
include the anisotropic diffusion filter and the Laplace-Hamming filter. The
rule of thumb is to apply a minimum amount of filtering to avoid degrading
the microCT data. For example, too much Gaussian filtration will result in
a blurred image that limits the ability to extract bone microarchitecture. A
filter always should be applied prior to structural extraction, and it is impor-
tant that all parameters used to define the filter be reported. For a Gaussian
filter a standard deviation of between 0.5 to 2.0 will suffice depending on
noise and voxel size, but each application will have different requirements.
[2]

Figure 11: Applying a Gaussian filter with different parameters[2]

3.2 Segmentation
The segmentation process is a critical step in the analysis and generally in-
volves separating the mineralized and nonmineralized structures for subse-
quent quantitative analysis. A mistake at this stage of the microCT analysis
will have a systematically impact on all subsequent results. It is essential to
compare 2D images from the original and segmented images for some (if not
all) mCT scans to ensure that the extracted bone is a good representation
of the actual structure. Once the region to be analyzed has been identified
(or contoured), there are several options for segmentation, all of which have
the general goal of extracting a “physiologically and anatomically accurate”
representation of the bone tissue (i.e., similar to histology). The simplest
approach is to use a global threshold that extracts all voxels from the mCT

18
data exceeding a given CT value (density). The advantage of using a global
threshold is that it is efficient and requires setting only one parameter. In
practice, the threshold is often set using either a fixed CT value or a percent
of the CT-value range. Yet there is no consensus on a threshold that should
be used for all studies, and extreme care must be taken when selecting a
threshold (see Figure 12) in studies where bone mineralization may not be
constant for all groups (i.e., during growth and development or fracture
healing) or when there are extreme ranges of bone volume fraction among
groups in which case a single global threshold may not be adequate. [2]

Figure 12: Different treshold values and their impact on segmented bone
volume[2]

3.3 Trabecular bone morphometry

The standard method of quantitatively describing bone architecture is the
calculation of morphometric indices, also referred to as quantitative mor-
phometry. In the past, the microarchitectural characteristics of trabec-

19
ular and cortical bone have been investigated by examining 2D sections
of bone biopsies, combined with calculation of morphometric parameters
using stereologic methods. Whereas some measurements such as BV/TV
and bone-surface-to-volume ratio (BS/TV) can be obtained directly from
2D images, several key parameters, including trabecular thickness (Tb.Th),
trabecular separation (Tb.Sp), and trabecular number (Tb.N), are derived
indirectly after assuming a fixed-structure model such as a rodlike or plate-
like structure. The basic morphometric indices include the measurement
of bone volume (BV) and the total volume of interest (TV). These indices
can be derived from either a simple voxel-counting method or a more ad-
vanced volume-rendering method, also referred to as volumetric marching
cubes (VOMACs), where the latter method may be more accurate for small
or very complex structures. The ratio of these two measures is termed bone
volume fraction (BV/TV). Another basic measure is the bone surface (BS),
which is conventionally computed by triangulation of the object surface us-
ing a marching-cubes algorithm. The bone surface density (BS/TV) and
specific bone surface (BS/BV) then can be derived easily by dividing the
total volume or bone volume, respectively. [2]

3.4 Anisotropy
The degree of anisotropy (ie, a description of how the structural elements are
oriented), tog- ether with bone volume fraction, may explain a significant
part of the mechanical properties of a 3D structure. Therefore, several
methods to estimate the anisotropy of trabecular bone have been proposed,
including those based on mean intercept length (MIL), volume orientation
(VO), star volume distribution (SVD), and star length distribution (SLD).
These and other measures of architectural anisotropy are reviewed in detail
elsewhere. [2]

3.5 Noise
Yet in practice raw CT images are not smooth. They are always, to a greater
or lesser extent, corrupted by noise. This appears as a random ‘graininess’
throughout the image, which is often so strong as to obscure details. This
paragraph considers the nature of the noisiness, where it comes from and
what can be done about it. Before starting, it may be helpful to know the
one major lesson of this chapter for the CT operator is simply [1]:

Info Box: To reduce noise, more photons need to be detected

20
In general, we can assume that noise in CT images has the following three
characteristics:

1. Noise is random – For any pixel, the noise is a random positive or

negative number added to the ‘true value’ the pixel should have.

2. Noise is independent at each pixel – The value of the noise at any pixel
does not depend upon where the pixel is, or what the noise is at any
other pixel.

3. Noise follows a particular distribution – Each noise value can be seen

as a random variable drawn from a particular distribution. If we have
enough noise values, their histogram would resemble a plot of the
distribution.

There are many different possible noise distributions, but we only need to
consider the Poisson and Gaussian cases. No matter which of these we have,
the most interesting distribution parameter for us is the standard deviation,
see Figure 13. Assuming everything else stays the same, if the standard
deviation of the noise is higher then the image looks worse. The reason we
will consider two distributions is that there are two main types of noise for
us to worry about [1]:

1. Photon noise, from the emission (and detection) of the light itself.
This follows a Poisson distribution, for which the standard deviation
changes with the local image brightness.

2. Read noise, arising from inaccuracies in quantifying numbers of de-

tected photons. This follows a Gaussian distribution, for which the
standard deviation stays the same throughout the image.

21
Figure 13: Noise values added to an otherwise noise-free image, along with
the resulting histograms. Noise with a higher standard deviation has a worse
effect when added to an image. [1]

Note that there are many norms to calculate the SNR. A simple estimate
for the SNR is given by:

M ean(Signal)
SN R [dB] = (5)
StdDev(N oise)

4 Tasks
The students will learn how to obtain CT images, perform image post-
processing and obtain morphological parameters from the image data. The
final report should include all given tasks and students are asked to write
a brief description and discussion of the results. Groups will get a bovine
trabecular bone sample to perform the tasks.

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 No. Energy [kVp] Current [mA] Integration Time [ms]
1 45 88 100
2 45 88 500
3 45 200 100
4 45 200 500
5 90 88 100
6 90 88 477
7 90 200 100
8 90 200 500
Filter settings for all Datasets: Cu=0.1mm and Al=0.1mm

Table 1: Scanning Parameters

4.1 Scanning parameters

Description
Different scanning parameters can be defined by the CT operator. Your task
is to determine the optimal scanning parameters for the given sample and
quantify the time effort for the given scanning parameters. Besides scanning
time, the signal to noise ration (SNR) should be determined to quantify the
image quality. The questions to be answered are:

1. How does integration time influence the total scanning time?

2. What are the best/ worst parameter-sets for the Bone Samples based
on SNR?

3. Explain how each parameter influences the SNR positively (how to

obtain high SNR).

4. What kind of artefacts do you identify the scans?

Table 1 contains the scanning parameters available:

4.2 Anisotropy and homogenized deformation

You are asked to predict the deformation of your bone sample using and
adequate modeling strategy. Therefore, you will quantify the anisotropy by
computing the fabric tensor. BoneJ offers a plugin to obtain this informa-
tion. The fabric tensor will allow you to compute the engineering constants

23
of your sample (essential equations are given below). The engineering con-
stants are then compared with results from a FE model of your sample. The
solution of the FE analysis allows you to compare experimental and theo-
retical deformations and identify potential uncertainties of the experiment.
You need to complete the following tasks:

1. Load the optimal CT data-set of the Bone-Sample in ImageJ.

2. Apply an appropriate Gaussian filter and use the optimal threshold to

segment the bone.

3. Compute the fabric eigenvectors and eigenvalues using BoneJ.

4. Assemble the fabric tensor using equation 6.

5. Compute the engineering constants using equations 7, 8 and 9 with

the given material constants in Table 2.

6. Compare the longitudinal stiffness computed from the fabric tensor

with the stiffness obtained from the experiment.

7. Perform a sensitivity analysis of the longitudinal and transverse stiff-

ness by altering the volume fraction in equation 7.
3
X 3
X
M= mi (mi ⊗ mi ) = mi Mi (6)
i=1 i=1

i = 0 ρk m2l
i (7)

mli
vij = v0 (8)
mlj

µij = µ0 ρk mli mlj (9)

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 Par. Value
0 16546 MPa
ν0 0.180
µ0 5594 MPa
k 1.84
l 1.72

Table 2: Constants

Par. Value Par. Value Par. Value

1 v12 µ12
2 v13 µ13
3 v23 µ23

Table 3: Engineering Constants

4.3 Report
Write a report that includes all results from previous task. Introduce gen-
eral theoretical background if necessary. The following sections should be
included:

1. Abstract

2. Materials and Methods

3. Task description

4. Results

5. Discussion

5 Pre-Lab Quiz
The following questions should be prepared by the students prior to the lab.
This will ensure that all students will have a general understanding of the
topics covered in this course.

1. What is the difference between X-ray radiography and computed to-

mography?

2. What property of a specimen provides contrast in a CT image?

25
 3. Write the general Beer-Lambert´s law for attenuation.

4. How can you determine in an energy spectrum between Characteristic

Radiation and Bremsstrahlung?

5. What is an k-Edege?

6. Name the five main parameters (and their units) to be chosen by the
CT operator.

7. Describe which parameters are needed to determine the Intensity?

8. Draw an energy spectrum for two different filters (Filter 1=0.1 Alu-
minum, Filter 2= 0.4 Copper). Consider the source energy to be the
same in both cases.

9. Draw a histogram for the following 8-bit picture: Total number of pix-
els 100. 20 pixels Value=245, 60 pixels Value=125, 10 pixels Value=75,
10 pixels Value=45.

10. Describe what isotropic and anisotropic material properties means.

11. Give an simple equation for the Signal to Noise Ratio (SNR).

12. What does BV/TV stand for?

13. Name three morphometric measures.

14. What is the mean intercept length (MIL) method used for?

26
 References
[1] Peter Bankhead. Analyzing fluorescence microscopy images with ImageJ.
QueenÂŽs University Belfast, 2014.

[2] S.K. Boyd; B.A. Christiansen; R.E. Guldberg; K.J. Jepsen; R. Mueller
M.L. Bouxsein. Guidlines for assessment of bone microstructure in ro-
dents using micro-computed tomography. Journal of Bone and Mineral
Research, 2010.

[3] W. Zhao; L. Xing; Q. Zhang; Q. Xie; T. Niu. Segmentation-free x-ray

energy spectrum estimation for computed tomography using dual-energy
material decomposition. Journal of Medical Imaging, 2017.

[4] D.R. Osborne; S. Yan; A. Stuckey; L. Pryer; R. Richey; J.S. Wall. Char-
acterization of x-ray dose in murine animals using microct, a new low-
dose detector and nanodot dosimeters. Plos one, 2012.

[5] N. B. Smith; A. Webb. Introduction to Medical Imaging. Cambridge

University Press, 2011.

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