Characterization of spatial resolution

through Fourier ring correlation in digital

neutron radiography

PC Ramatlhatse
orcid.org/0000-0001-6457-428X

Mini-dissertation submitted in partial fulfilment of the

requirements for the degree Master of Science in Applied
Radiation Science and Technology at the North-West University

Supervisor: Prof V.M Tshivhase

Co-supervisor: Mr. M.J Radebe

Graduation ceremony: July 2020

Student number: 23029684
Declaration

I, Pelonomi Cynthia Ramatlhatse, herein declare that the work presented in this mini-dissertation:
“Characterization of spatial resolution through Fourier ring correlation in digital neutron
radiography” is my original work and has not been submitted to any other Institution for
examination. I further declare that all material used in this dissertation has been fully
acknowledged correctly in the references.

Signature:

Date: 21 November 2019

i
Acknowledgement

Firstly, I would like to give all the glory and thanks to the Almighty God for all He has enabled
and helped me to do and achieved thus far on my academic journey.

To my supervisor, Prof Victor Tshivhase and Co-supervisor, Mr Mabuti Radebe, thank you for the
enormous support you have shown and guidance throughout this study. I would also like to
acknowledge the assistance from Dr Thulani Dlamini for his insightful suggestions and guidance,
it was very helpful. The moral support of my fellow colleagues at the South African Nuclear
Energy Corporation (Necsa) and Center of Applied Radiation Science and Technology (CARST)
at the North West University is highly appreciated.

To my Parents (Mogorosi and Kelebogile Ramatlhatse), siblings and nephew; thank you for your
endless support and motivation to keep sane throughout my academic journey, I will forever be
grateful for the love, patience and guidance I have received thus far.

Lastly, I would like to thank the North West University, CARST for the exposure and opportunity
provided me to study radiation science. To the author of Fourier Ring Correlation MATLAB code,
Manuel Guizar-Sicairos, thank you for making the code available to use free of charge and Vila-
Comamala et al for the implementation of the code.

The financial assistance of the National Research Foundation (NRF) towards this research is
acknowledged. Opinions expressed and conclusions arrived at, are those of the author and are not
necessarily to be attributed to the NRF.

ii
Dedication

I would like to dedicate this work to everyone who believed in me, to everyone who think that
they cannot make it this far, it’s possible only if you put your mind and heart to it. Perseverance
and dedication is all that it takes.

iii
Abstract

Spatial resolution is a very important parameter in any imaging system, from medical to industrial
even in astronomy and it should be considered every time images are analysed or even before
processing. The aim of this work was to characterize spatial resolution in digital neutron
radiography using the proposed method of Fourier Ring Correlation (FRC), a method which was
mainly developed for cryo-microscopy imaging. This proposed method was adopted in this work
for determination of spatial resolution. The Modulation Transfer Function (MTF) also known as
Spatial Frequency Response (SFR) is the method used in digital neutron radiography to determine
the spatial resolution of an image. The reason for adopting the FRC method was to determine if
this proposed method is suitable to be applied in digital neutron radiography to find the spatial
resolution of images. The current method used in neutron radiography, which is the standard
method MTF/SFR, uses an edge analysis which has been observed to be a complex technique to
find the spatial resolution.

The results were achieved using MATLAB. Different MATLAB functions were used for FRC and
MTF/SFR. The FRC results were compared with that of the standard method in neutron
radiography MTF/SFR. This comparisons were made at different Object to Detector Distance
(ODD). The percentage differences of FRC and MTF/SFR at different ODD’s were 88.24%,
3.57%, 3.70% and 26.67%. The results yielded a higher percentage difference than expected,
especially the 88.24% is quite high. FRC can be applied in neutron radiography to determine the
spatial resolution as the results from different ODD’s have shown a percentage differences less
than 5%. The conclusion from this study is that FRC method can be used to determine spatial
resolution in neutron radiography but filtering needs to be done as part of image analysis. Although
it is recommended, in future studies, apodization and filtering methods should be taken into
consideration for better spatial resolution.

Keywords:

Fourier Ring Correlation (FRC), neutron radiography, spatial resolution, Modulated Transfer
Function (MTF), Spatial Frequency Response (SFR).

iv
Table of contents

DECLARATION ................................................................................................................... I

ACKNOWLEDGEMENT .................................................................................................... II

DEDICATION ..................................................................................................................... III

ABSTRACT ........................................................................................................................ IV

TABLE OF CONTENTS ...................................................................................................... V

LIST OF ABBREVIATIONS ........................................................................................... VIII

LIST OF TABLES ................................................................................................................ X

LIST OF FIGURES ............................................................................................................. XI

CHAPTER 1: INTRODUCTION .......................................................................................... 1

1.1 Background .....................................................................................................1

1.1.1 Neutron interaction with matter ......................................................................2

1.1.2 Neutron radiography ....................................................................................... 3

1.1.3 Spatial resolution ............................................................................................ 6

1.1.4 Fourier ring/shell correlation ..........................................................................8

1.2 Problem statement and motivation .................................................................9

1.3 Research aim and objectives...........................................................................9

CHAPTER 2: LITERATURE REVIEW ............................................................................. 10

2.1 Introduction ..................................................................................................10

2.2 Resolution .....................................................................................................10

2.3 Spatial resolution .......................................................................................... 11

2.4 ISO 12233 .....................................................................................................12

v
2.5 Modulation transfer function ........................................................................12

2.5.1 Bar pattern method ....................................................................................... 13

2.5.2 Slit method ....................................................................................................13

2.5.3 Edge method .................................................................................................14

2.6 FRC/FSC theoretical behaviour....................................................................16

2.7 Filtering methods .......................................................................................... 18

2.7.1 Apodization ..................................................................................................20

2.7.1.1 Different types of apodizing functions ......................................................... 29

2.7.1.1.1 Hamming window ........................................................................................ 29

2.7.1.1.2 Hanning ........................................................................................................29

2.7.1.1.3 Blackman window ........................................................................................ 29

2.7.1.1.4 Triangular .....................................................................................................30

2.7.1.1.5 Cosine ...........................................................................................................30

2.7.1.1.6 Gaussian........................................................................................................30

2.7.2 Filtering using ImageJ .................................................................................. 31

2.7.2.1 Types of filtering in ImageJ ..........................................................................31

2.7.2.1.1 Mean ............................................................................................................. 31

2.7.2.1.2 Median ..........................................................................................................31

2.7.2.1.3 Gaussian blur ................................................................................................ 32

2.7.2.1.4 Minimum and maximum filter .....................................................................32

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2.7.2.1.5 Un-sharp Mask ............................................................................................. 33

CHAPTER 3: METHODOLOGY ....................................................................................... 34

3.1 Introduction ..................................................................................................34

3.2 Facilities – neutron sources ..........................................................................34

3.2.1 NEUTRA ......................................................................................................35

3.2.2 ICON ............................................................................................................ 37

3.3 Neutron radiography setup ...........................................................................39

3.4 Determination of spatial resolution .............................................................. 41

3.4.1 Matrix Laboratory (MATLAB) ....................................................................41

3.4.2 Fourier Ring Correlation method .................................................................42

3.4.3 Modulation Transfer Function (MTF) method ............................................. 45

CHAPTER 4: RESULTS AND DISCUSSION ...................................................................49

4.1 Introduction ..................................................................................................49

4.2 Fourier Ring Correlation results ...................................................................49

4.3 Modulation Transfer Function ......................................................................51

4.4 Comparisons of the FRC method with the standard method (MTF/SFR) ....52

4.4.1 FRC and MTF/SFR comparisons at different object-detector-distance. ......53

CHAPTER 5: CONCLUSION AND RECOMMENDATION ............................................ 58

5.1 Conclusion ....................................................................................................58

5.2 Recommendation .......................................................................................... 58

REFERENCES ..................................................................................................................... 60

vii
List of Abbreviations

CCD Coupled Charge Detector

Cryo-EM Cryo-Electron Microscopy

dpi dots per inch

ESF Edge Spread Function

FRC Fourier Ring Correlation

FWHM Full Width Half Maximum

GUI Graphical User Interface

ICON Imaging with Cold Neutrons

ISO International Organization for Standard

IMAT Imaging and Material Science

LSF Line Spread Function

MATLAB Matrix laboratory

MTF Modulation Transfer Function

NEUTRA Neutron Transmission Radiography

ODD Object-to-Detector-Distance

PSI Paul Scherrer Institute

SAR Synthetic Aperture Radar

SD Standard Deviation

SFR Spatial Frequency Response

SID Source-to-Image-Distance

SINQ Spallation Neutron Source

SNR Signal-to-Noise-Ratio

SwissFEL Swiss Free-Electron X-ray Laser

SµS Swiss Muon Source

viii
TOF Time of Flight

UWB Ultra-wideband

ix
List of Tables

Table 1-1: Summary of types of nuclear reactions ............................................................................ 2

Table 3-1: Properties of the NEUTRA (Lehmann et al., 2001)....................................................... 36

Table 3-2: Properties of NEUTRA imaging detector system (Lehmann et al., 2001). ................... 37

Table 3-3: Properties of camera system used at ICON (Kaestner et al., 2011). .............................. 38

Table 3-4: Resolution and scintillators accessible at ICON (Kaestner et al., 2011)........................ 38

Table 3-5: Resolution and scintillators accessible at ICON (Kaestner et al., 2011)........................ 39

Table 4-1: Summary of FRC and MTF/SFR results at different ODD ........................................... 57

x
List of Figures

Figure 1-1: Schematic sample of radiation attenuation by the material (Maher, 2016). ................... 4

Figure 1-2: Simple set-up of neutron radiography. ........................................................................... 5

Figure 1-3: Geometric un-sharpness (Molina, 2016). ....................................................................... 7

Figure 2-1: Alignment steps for the edge test method (Samei and Flynn, 1997) ........................... 15

Figure 2-2: Non-apodized real SAR image (Akhter, 2012). ........................................................... 23

Figure 2-3: Apodized real SAR image by implementing the proposed weighting function (Akhter,
2012). ................................................................................................................. 24

Figure 2-4: SAR non-apodized image with different (10-110) integration angle (Akhter, 2012). . 24

Figure 2-5: Apodized image using Rectangular weighting function (Akhter, 2012). ..................... 25

Figure 2-6: Apodized image using Hanning weighting function (Akhter, 2012). .......................... 25

Figure 2-7: Apodized image using Hanning weighting function in the angular direction (Akhter,
2012). ................................................................................................................. 26

Figure 2-8: Apodized image by Hanning weighting function (Akhter, 2012). ............................... 27

Figure 2-9: Apodized image by Hamming weighting function in the angular direction (Akhter,
2012). ................................................................................................................. 27

Figure 2-10: SAR apodized image after applying proposed new linear weighting function (Akhter,
2012). ................................................................................................................. 28

Figure 3-1: PSI campus (Paul-Scherrer-Institute, 2019) ................................................................. 35

Figure 3-2: Graphic layout of the NEUTRA facility at PSI thermal beam line of SINQ (Lehmann
et al., 2003). ....................................................................................................... 36

Figure 3-3: Neutron radiography setup. .......................................................................................... 40

Figure 3-4: Gadolinium knife edge test object (Radebe, 2017). ..................................................... 41

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Figure 3-5: Computational steps on how to compute FSC/FRC. Fig 3-5e is the FRC/Resolution
curve (Radebe, 2017)......................................................................................... 44

Figure 3-6: Region of interest selection on Gadolinium edge with 50% Gadolinium edge selection
and 50% air selection......................................................................................... 45

Figure 3-7: Cropped Gadolinium knife edge image to display ROI with 50% selection on
Gadolinium edge and 50% air selection. ........................................................... 46

Figure 3-8: Edge Spread Function (ESF) curve of Gadolinium knife edge test object. .................. 47

Figure 3-9: Line Spread Function which is the ESF derivative. ..................................................... 48

Figure 3-10: MTF/SFR curve with sampling efficiency of 17%. ................................................... 48

Figure 4-1: FRC and spatial frequency curve. ................................................................................ 50

Figure 4-2: FRC curve and spatial resolution solutions at approximately 0 mm ODD. ................. 50

Figure 4-3: MTF/SFR curve with the threshold curve to determine the spatial resolution. ............ 51

Figure 4-4: FRC curve at 12 mm ODD. .......................................................................................... 53

Figure 4-5: MTF/SFR curve at 12 mm ODD. ................................................................................. 54

Figure 4-6: FRC curve at 32 mm ODD. .......................................................................................... 55

Figure 4-7: MTF/SFR curve at 32 mm ODD. ................................................................................. 55

Figure 4-8: FRC curve at 104 mm ODD. ........................................................................................ 56

Figure 4-9: MTF/SFR curve at 104 mm ODD ................................................................................ 56

xii
Chapter 1: Introduction

1.1 Background

In the late 1920’s, Rutherford and Chadwick were working on atomic disintegration, when they
noticed that a proton is not the only particle in the nucleus, they found that the atomic number was
less than the atomic mass (meaning that the number of protons is equivalent to the positive charge
of the atom) in the nucleus (Chadwick, 1932). Rutherford made a postulate that there could be an
unknown particle without a charge; he named the unknown particle “neutron”. Chadwick did not
rest his mind about the unknown particle. In the early 1930’s, two German physicists, Walther
Bothe and Herbert Becker performed an experiment that showed that beryllium, fluorine, lithium
and boron atoms have a great penetrating power when bombarded with an alpha particle from
polonium and they assumed that it was gamma (γ) rays because at that time, previous research had
shown that γ-rays have the greatest radiation penetrating power. Not so long after the findings of
the two German physicists, Irene Curie conducted a research on the absorption of secondary
radiation of Be and Li and showed that Be and Li have the ability to penetrate through a material
easier that the γ-rays could not. Chadwick was working on the same experiment Curie performed
but he was examining the properties of radiation in Be when he discovered that the γ-rays
hypothesis is not correct. He concluded that the unknown particle consists of a mass slightly
greater than the mass of a proton and has no electrical charge and is more penetrative than γ-rays.
He named the particle neutron just as Rutherford had named it (Nesvizhevsky and Villain, 2017)
and he published his findings before more research followed on neutrons.

Neutrons are part of the nucleus and are usually characterised as fast, epithermal, thermal and cold
neutrons. Their energies and scattering characters determines their characteristics or classification
(Hawkesworth and Walker, 1981, Bayon et al., 1992). Neutrons are nuclear particles and are more
penetrating as compared to electrons and protons, because they have no charge (Van Rooyen,
2006). Neutrons are electrically neutral particles and indirectly ionising, they interact directly with
the nucleus and usually interact with the nuclei in reactions such as (n, p), (n, α), (n, np).

1
1.1.1 Neutron interaction with matter

The elastic scattering (n, n) reaction produces a low energy neutrons from fast emitted neutron
source. Neutrons collide with a nucleus and transfer its energy to the nucleus by means of losing
kinetic energy (𝐸𝐾 ). The fraction of its initial energy depends on the angle it hits the nucleus. When
neutrons collides with a light nucleus, they loses more kinetic energy compared to when they
collides with a heavy nucleus.

Inelastic scattering (n, n) or (n, n, γ) reaction is more like elastic scattering but when the neutrons
collide with the nucleus, they have enough kinetic energy to stimulate the nucleus into its excited
state. When neutrons are absorbed by the nucleus, gamma-photons are usually emitted when the
excited product nucleus returns to its ground energy state. At high incident energies, neutrons are
capable of producing charged particles such as protons and alphas by nuclear reaction that happens
with nuclei (Alaa Eldin, 2011, Van Rooyen, 2006).

Neutron capture, (n, γ) reaction, is another type of nuclear reaction which occurs when an atomic
nucleus collides with one or more neutrons and combine to form a heavier nucleus. The multiple
or compound nucleus decays by release of gamma ray (Stacey, 2001).

Charged particle emission (n, p) and (n, α) reactions, neutrons may be absorbed or scattered
depending on which reaction took place. The reactions are either exothermic (release) or
endothermic (absorb) (Lamarsh and Baratta, 2001).

Fission reaction (n, f) happens when a heavy nucleus splits into two unequal parts, each with a
different mass. Fission reaction usually takes place in nuclear research reactors or nuclear power
plants. Uranium (235U) and Plutonium (239Pu) undergoes fission after absorption of neutrons.

Table 1-1: Summary of types of nuclear reactions

Type of reaction Formula Example

𝐴
(n, n) 𝑍𝑋 + 10𝑛 → 𝐴
𝑍𝑋 + 10𝑛 59
27𝐶𝑜 + 10𝑛 → 59
27𝐶𝑜 + 10𝑛
(n, γ) 𝐴
𝑍𝑋 + 10𝑛 → 𝐴+1
𝑍𝑋 + 00𝛾 59
27𝐶𝑜 + 10𝑛 → 60
27𝐶𝑜 + 00𝛾

𝐴
(n, p) 𝑍𝑋 + 10𝑛 → 𝐴
𝑍−1𝑋 + 11𝛽 59
27𝐶𝑜 + 10𝑛 → 59
26𝐹𝑒 + 11𝛽
(n, α) 𝐴
𝑍𝑋 + 10𝑛 →
(𝐴+1)−4
+ 42𝐻𝑒
59
27𝐶𝑜 + 10𝑛 → 56
25𝑀𝑛 + 42𝐻𝑒
𝑍−2𝑋

2
 𝐴
(n, f) 𝑍𝑋 + 10𝑛 → 𝐴
𝑍𝑋 + 10𝑛 235
92𝑈 + 10𝑛 → 141
56𝐵𝑎
92
+ 36𝐾𝑟 + 3( 10𝑛)

1.1.2 Neutron radiography

After the discovery of neutrons between the years 1935 to 1938, two German scientists started
working with neutrons in a laboratory from a small neutron generator to produce neutron
radiographs. Research reactors then became available in the 1950’s; Thewlis and Derbyshire made
a demonstration that neutron radiographs can be produced by utilising thermal neutrons beam from
the nuclear research reactors. The application of neutron radiography started expanding rapidly
since then (Chankow, 2012).

Neutron radiography is a process of imaging using neutrons. It is a non-destructive imaging

technique (Lehmann et al., 2014), where neutrons are used to produce radiographs. It is the process
whereby neutrons are passed through an object to produce visible image of the material making
up its internal contents. The neutron radiography digital imaging technique is similar to the X-ray
radiography principle. Unlike X-rays, neutrons do not interact with electrons, their interaction is
not determined or dependent on the atomic number (Z) of the sample material (Koerner et al.,
2000) but the size of the nucleus. Neutrons interact with the material by absorption, scattering or
transmission (Lehmann et al., 2010). Both neutrons and X-rays are determined by their respective
attenuation cross-section as described by the Beer-Lambert law in Eq.1.

𝑰 = 𝑰𝒐 𝝀𝒆−𝝁𝝀𝒅 Eq.1
where, 𝐼0 and I are the incident and transmitted beam intensities for a given wavelength 𝜆, 𝜇 is the
attenuation coefficient and d is the thickness of the absorber (Sun et al., 2017). The Beer-Lambert
law describes the absorbance and transmission of photons through a material. The law describes
the primary photons, photons which have not yet interacted with any material. When photons pass
through a material, they may interact via absorption or scattering. The attenuation coefficient also
known as the linear attenuation coefficient 𝜇 is dependent on the density of the material (Dance et
al., 2014). Figure 1-1 schematically shows the attenuation principle (absorption or scattering).

3
Figure 1-1: Schematic sample of radiation attenuation by the material (Maher, 2016).

The attenuation coefficient for each element is different for neutrons and for X-rays (Van Rooyen,
2006). The reason for this is that the X-ray attenuation increases with atomic number of each
element while the neutrons attenuation is randomly as a function of the atomic number because
neutrons interact directly with the nucleus. All radiographic techniques are based on the same
general principle that radiation is attenuated as it passes through matter, whether making use of X-
rays, gamma-rays or neutrons, the basic principle is still the same (Koerner et al., 2000).

4
Figure 1-2: Simple set-up of neutron radiography.

A simple experimental setup, Figure 1-2 of a neutron radiography system consisting of a neutron
source, a collimator that contains a small pinhole “D” that allow neutrons to pass through an object
and a detector (Koerner et al., 2000). An object is placed between the collimator exit and a detector
that records a two dimensional image and contains information about the composition and
structure of an object being analysed. The neutrons from the neutron source pass through the small
pinhole of a collimator guided by the beam to hit an object being analysed. Neutrons penetrate an
object to different degrees, which are dependent on the elements making up the sample. After
attenuation, the neutrons which are transmitted, are detected by the detector system that captures
and forms images of the object that are displayed on the computer for analysis.

Neutrons are either scattered or absorbed by the atomic nuclei (Alam et al., 2006). They have the
greatest penetrating ability of the four types (alphas, betas, gammas and neutrons) of radiation and
the most difficult to shield (Alaa Eldin, 2011, Van Rooyen, 2006). Different neutron sources
available worldwide for neutron radiography include nuclear reactors, particle accelerators and
radioisotopes. Their source intensity, properties and energies (fast, thermal and cold) differs
accordingly. In neutron radiography, neutron beam characteristics are of great importance and
include: collimation, which is generally expressed as the beam tube length to diameter ratio (L/D)
and it is the main factor influencing the image quality; the beam intensity, which is the controlling
factor for exposure time and beam quality, is important for non-neutron background in
radiographs. In all the three categories of neutron sources, the nuclear research reactor is the best

5
source of neutrons because of the higher neutron flux profile, and they give better radiographs
(Hawkesworth and Walker, 1981).

Image quality is a concern in neutron radiography, and in order to obtain a high quality
radiographs, neutron beam and detector must have certain characteristics. Characteristics of digital
images include resolution, spatial resolution, pixel size, voxels, contrast, and sharpness.

1.1.3 Spatial resolution

Spatial resolution determines how close two features of an object are and how proximate lines can
be to each other and still be visibly resolved in an image. Resolution is measured in different ways
and its units are described by their physical size (expressed as pixels per unit distance, dots per
inch (dpi), lines per mm and lines per inches) to their over-all sizes. The common units in spatial
resolution are pixels per unit distance and dpi (Ball and Price, 1995). A two-dimensional image
has a three-dimension, namely the width, height and a gray-scale. The height and the width are
classified as spatial hence the word spatial resolution (Bushberg et al., 2002). However, in some
texts they omit the word spatial and refer just to resolution. Spatial resolution also refers to the
number of independent pixel per unit length. The higher the resolution, the more detailed the image
is. In most cases, spatial resolution is lost when two objects becomes close together and appear as
one, then the image is not visible enough for interpretation. In digital imaging, the resolution
depends on characteristics of the system creating the image not just the number of pixels in an
image. The optical pixel size and image resolution are not equivalent in reality even though they
are often used interchangeably. For instance, the image with a small pixel size does not literally
mean that the image has high resolution or vice versa. The resolution of the system is understood
in order to know how the edges in an image are blurred. Resolution limit explains exactly how
much information makes up an image.

Factors affecting image quality include spatial resolution, noise and contrast. Noise in radiography
is defined as any uncertainties that do not correspond to similarities in the radiation attenuation of
an object to be imaged whereas contrast is defined as the differences in radiographic density and
is the ratio of radiation intensities transmitted in different areas of a radiograph (Alaa Eldin, 2011).
Factors affecting spatial resolution include detector blur, geometric un-sharpness and pixel size.
Detector blur is produced when neutrons are converted into light on the scintillator screen; when

6
neutrons enter the scintillator screen guided by the beam line they are converted into light (to
enable the camera to interpret them). The light gets divergent and blurriness gets formed.
Geometric un-sharpness or penumbra refers to the loss of detail in an image caused by the
increasing size of the focal spot of the radiographic equipment, object-film distance and object-
focal spot distance are the main factors controlling geometric un-sharpness (Fitzgerald and
Francisco, 1947). This occurs because the radiation does originate over an area and not from a
single point (Smith, 1999). The maximum un-sharpness or penumbra may be calculated using
Eq.2, where the f is the source focal spot size, b is the distance from the object to the detector and
a is the distance from the source focal spot to the object,

𝑼𝒈 = 𝒇 × 𝒃⁄𝒂 . Eq.2

Figure 1-3: Geometric un-sharpness (Molina, 2016).

Figure 1-3 with a point source, an object and a film. The path of the radiation from each edge of
the source to each edge of the feature of the focal spot, the locations where this radiation will
expose the film and the density profile across the film. The radiation hitting the film originates
from the source focal spot and hence a geometric un-sharpness is produced in the image at the
edges where the film is located, because as the size of a source focal spot increases, the amount of

7
geometric un-sharpness also increases. Therefore, to avoid such increase in blurriness of an image,
one must consider the use of small source focal spot as possible. Geometric un-sharpness is
controlled by the source size, source to object distance and object to detector distance (Smith,
1999). Application of spatial resolution is widely used in the printing industry; for instance, the
newspaper company will use about 75 dpi to print their paper. The higher the dpi, the more quality
the printout will be. In general, the size of an object does not matter in spatial resolution (Gonzalez
and Woods, 2002). Unser defines resolution as the spatial frequency at which ring-shaped
samplings of the two Fourier transforms register negligible cross-correlation (Unser et al., 1987).

1.1.4 Fourier ring/shell correlation

Fourier Shell Correlation (FSC) was introduced in 1982 by van Heel; however, its metrics was
only introduced in 1986 by van Heel. FSC was originally applied to cryo-electron microscopy
(cryo-EM) and electron microscopy (EM) of structural biology. FSC is a mathematical method
used for calculating resolution of an image. It measures the cross correlation between two, three
dimensions (3-D) whereas Fourier Ring Correlation (FRC) measures cross correlation between
two, two dimensions (2-D). FSC is also known as the spatial frequency correlation. FRC assesses
resemblance of two independent reconstruction of the same object to regulate threshold resolution
in frequency space. It measures the standardized cross correlation to estimate the resolution of an
image in Fourier domain over the corresponding rings and varies in thickness and radii (Saxton
and Baumeister, 1982). The FRC curve is plotted as a function of spatial frequency in Fourier
space, which is computed from two images having the same data set (Nieuwenhuizen et al., 2013).
The resolution (limiting resolution) is estimated at the intersection of threshold and FRC curve. It
has been shown that FRC may be applied to microscopy and nanoscopy data and supplies a
software tool that is easy to use, which interprets positional information in description films tested
to their actual resolution (Saxton and Baumeister, 1982).

FSC/FRC has now made its way in other fields, such as X-ray tomography, X-ray crystallography,
planetary science and super resolution microscopy. Basically, FSC/FRC metrics are applicable to
all 3-D and/or 2-D data (Van Heel and Schatz, 2017).

8
1.2 Problem statement and motivation

Fourier Ring Correlation (FRC) has been applied in microscopy and nanoscopy (Nieuwenhuizen
et al., 2013, van Heel and Schatz, 2005) to analyse the threshold criterion that is suitable for
determining spatial resolution limit. Nieuwenhuizen et al., 2013 have worked with FRC to measure
resolution limit in super resolution microscopy and different nanoscopy methods. In neutron
radiography, the method used to determine the spatial resolution of images is the Modulated
Transfer Function (MTF) or Spatial Frequency Response (SFR) (Cao and Biegalski, 2007), which
uses Fourier analysis of an edge image. The edge analysis is a complex method to determine the
spatial resolution of an image hence this study seek to adapt FRC as a method to characterize
spatial resolution in digital neutron radiography. The FRC method has not been applied to neutron
radiography to determine the spatial resolution. Since digital neutron imaging is developing
towards imaging in the micron and submicron range, there is a need to develop tools to assess
spatial resolution in this range.

1.3 Research aim and objectives

The aim of this study was to establish the suitability of the FRC to characterise spatial resolution
in digital neutron radiography, especially in the micron and submicron range of digital neutron
radiography. The research objectives were to:

 Formulate the experimental protocol to analyse digital neutron radiographs on which

FRC assessment can be conducted.
 Assess the algorithm and mathematics of FRC in assessing spatial resolution in digital
neutron radiography.
 Adapt and apply FRC to evaluate spatial resolution in digital neutron radiography.
 Apply the MTF/SFR standard method to evaluate the spatial resolution.
 Compare FRC results to the standard method, MTF/SFR.

9
Chapter 2: Literature review

2.1 Introduction

In this chapter, literature relevant to FRC techniques and spatial resolution are discussed. The
methods and techniques of finding the image resolution in digital neutron radiography are also
discussed. The Edge Spread Function (ESF), Line Spread Function (LSF), Modulation Transfer
Function (MTF) and ISO 12233 standards are discussed on how to determine the spatial resolution,
as well as filtering methods used in neutron radiography.

2.2 Resolution

Resolution estimation methods are not all based on data consistency in Fourier space using the
quantitative measure (Liao and Frank, 2010). These methods have been applied in data images and
diffraction patterns from electron microscopy, X-ray diffraction, optical microscopy, single
particle reconstructions and nanoscopy (Radebe, 2017). These methods can also be used in digital
neutron radiography and tomography. But should be slightly modified in order to characterize the
output data.

Resolution criteria have been limited to a value of λ/NA, where λ is the wavelength of light and
NA is the numerical aperture of image lens. This resolution was captured by Rayleigh and Sparrow
on the conventional law of optical imaging science. Abbe and Nyquist (1984) have placed these
criteria on solid foundations and they defined resolution as “the inverse of spatial bandwidth of
the imaging system". To produce super-resolution images, the resolution depends on numerous
factors including the fundamental spatial structure of the sample and the wide-ranging data
processing necessary to produce a final super-resolution image (Nieuwenhuizen, 2016).

In resolution test, data consistency is needed, usually, this is done by splitting the full data set into
two half datasets and comparing the resulting average data by calculating two reconstructions of
the same object independently (Liao and Frank, 2010, van Heel and Schatz, 2005). The
consistency of the resulting data set is compared as a function of frequency space (van Heel and
Schatz, 2005) over rings or shells ( reconstruction assessment is 3D) with a cumulative radius in
Fourier domain (Liao and Frank, 2010) to determine the resolution threshold (Banterle et al.,

10
2013). Another method, is by calculating the cross-correlation between nearby voxels in Fourier
space (Liao and Frank, 2010).

In cryo-electron microscopy (cryo-EM), FRC is usually used to evaluate single-particle

reconstructions of macromolecular multiplexes (Nieuwenhuizen et al., 2013). To compute FRC
resolution in cryo-EM, Nieuwenhuizen, 2016, divided the set of super-resolution images into two
equally independent subsets that constitute of single-emitter localizations and produced two sub-
images. Nieuwenhuizen et al. 2016 analysed different threshold criteria in cryo-EM and the
findings resulted in fixed threshold value approximated to 0.143 which was found to be appropriate
for microscopy images (Nieuwenhuizen, 2016). In cryo-EM, the single particle reconstruction is
usually measured in FSC (3D of FRC) and that is, the resolution is measured over shells in Fourier
Space as a function of spatial frequency (Diebolder et al., 2015).

2.3 Spatial resolution

Velo et.al, 2017, determined the spatial resolution of Gamma cameras used in medical imaging for
acquiring medical images with precise quantitative figures. They defined the spatial resolution of
gamma camera as the capacity of the overall camera system to precisely determine the location of
a gamma-ray on the X-Y plane with and without the scatter. Spatial resolution can be defined as
the ability to differentiate between two points, the higher the spatial resolution, the smaller the
distance between the two points. In the gamma cameras, it is believed that the spatial resolution
is related to the effectiveness and linearity of the collimator and its photomultiplier tube. In order
to quantify the spatial resolution, they determined the Full-width at half maximum (FWHM) of
the LSF from the acquired line source images and MTF was calculated. MTF was calculated by
Fourier transformation of the LSF. To determine the spatial resolution after data acquisition and
processing, a MATLAB program was used to analyse the data and the same data was analysed
using the standard processing system. The Graphical User Interface (GUI) as a MATLAB program
was developed to evaluate the spatial resolution of the gamma camera. The FWHM results from
the standard method (data processing system) and the GUI program were assessed and compared.
It was determined that the spatial resolution calculated from the MATLAB was lower than the one
from the standard method by 1.24 % (Velo and Zakaria, 2017).

11
The differences between the two programs were analysed and it was found that the standard
program was not installed with software that could determine the MTF. So the GUI results were
considered to be relevant for the spatial resolution. In their work to determine the spatial resolution
they strongly believed that the GUI program was reliable to use because it required less time for
data analysis, minimises human interface error in analysis because of the fact that the calculations
are performed automatically by the software. The benefits of using the GUI program are that the
line source images can either be obtained from actual or simulated gamma camera, the program is
faster, reliable, and cost-effective and not to forget that it is easier to use to analyse the spatial
resolution of the line source image in gamma cameras (Velo and Zakaria, 2017).

2.4 ISO 12233

The International Organisation for Standard (ISO) 12233 is the standard method created to
evaluate electronic still images. This standard describes the test charts, terminologies and test
methods for performing resolution measurements for both digital and analogue electronic still
images (ISO12233, 2014). The standard introduced the Spatial Frequency Response (SFR) and it
was the first to address the performance of the digital camera (Burns and Williams, 2008). The
SFR can be derived from the edge analysis or periodic signals; however, ISO introduces SFR based
on the edge analysis in a digital image. ISO 12233 defines SFR as a "multi-value metric that
measures contrast loss as a function of spatial frequency." SFR is measured based on the analysis
of an edge device and this analysis is done on digital images containing high-quality edge features.
The ESF is determined from the data set of an edge profile, and the LSF is calculated from the
first derivation of the estimated ESF (Burns and Williams, 2008) (ISO 12233). SFR is, in other
words, the normalised signal modulation function of spatial frequency and basically the MTF. The
following subsection discusses the MTF using different test methods. The Edge is the common
method used to find MTF/SFR.

2.5 Modulation transfer function

Modulation Transfer Function (MTF), also known as Spatial Frequency Response (SFR) is a well-
established factor to determine the estimation and evaluation of imaging system resolution (Cao
and Biegalski, 2007). It's a standard method used in the radiography imaging system (X-ray) to

12
determine the spatial resolution of an imaging system. MTF is defined as a simple measure of an
imaging system able to reproduce an image contrast and describe the signal transfer of the system
with varying spatial frequencies (Buhr et al., 2003, Cao and Biegalski, 2007, Samei and Flynn,
1997). Spatial frequency is similar to frequency of sound and it is measured in cycles per unit
length (millimetres or inches) instead of cycles per unit time (seconds) also known as Hertz which
is the measure of frequency of sound. MTF is useful when it comes to evaluating the quality of
an image in different imaging systems (Velo and Zakaria, 2017). It is measured in line pairs per
millimetre (lp/mm) and cycles per millimetre (cy/mm).

There are three methods which have been proposed to calculate MTF which are slit, edge or bar
pattern (Buhr et al., 2003). The methods that are commonly used in the radiographic system are
the edge and the slit method because of their benefits. The bar pattern method has been considered
to be challenging due to difficulties in determining the modulations in digital bar pattern images
(Buhr et al., 2003).

2.5.1 Bar pattern method

The bar pattern method uses a bar pattern test object, made with high atomic number metal
available in different frequency ranges and multiple thicknesses. The bar pattern test object is
placed on the detector to get the radiographs. After image acquisition, the radiographs of the bar
pattern are processed to attain the square-wave response function at each of the spatial frequencies
of the pattern. This is done by averaging the data of the related bar patterns. To obtain MTF using
this method, it is mathematically deduced from the square-wave response function of the averaged
bar pattern data. The advantages of this method include absolute ease, quick implementation and
conceptual simplicity. The disadvantages of the method are low accuracy, noise and course
sampling curve of the MTF (Samei, 2003).

2.5.2 Slit method

The slit test method has been used for many years as the traditional method to measure the MTF.
Usually, the slit test is performed with an object made with two thick lead metal pieces. This two
lead metal pieces are placed at a distance from each other in a way that they form an opening with
a width of about ten microns (Samei, 2003). When using the slit method, there are a few things to
13
keep in mind in order to acquire radiographs. Precise fabrication and alignment of the system in
the radiation beam is needed, high radiation exposure in order to allow sufficient transmission
through the narrow slit and correct slit width are required (Samei and Flynn, 1997). Even though
high radiation exposure is needed, it is often the main resolution limiting factor (Diebolder et al.,
2012). The image data is averaged to form an LSF. Using the obtained LSF, Fourier transform is
applied to the averaged data to deduce the MTF. The benefits of this method include high precision
at high spatial frequencies and the major disadvantage is correct alignment and manufacturing of
the slit device, which is time-consuming and complicated to take precise measurements.

2.5.3 Edge method

The edge method as mentioned, is commonly used in digital radiographic systems (Samei, 2003).
In this method, the edge test device and an opaque object with a straight edge are used to measure
the ESF of the radiographic system (Samei and Flynn, 1997). The edge device is made of a thin
metal foil, preferably a high atomic number material like lead, tungsten and platinum-iridium
alloys (Samei, 2003). In the Samei et al. 1997 experiment, an edge test was performed with a 5 ×
10 cm2, 250 µm lead foil. The lead foil was used as the attenuating material on a 115 kV
polychromatic X-ray beam. The lead foil was laminated between two acrylic thick slabs of about
1 mm, this was placed in a holder in order to station and align the edge in the X-ray beam. The
holder was made of two 6.35 mm lucite frames and had adjustable screws to easily tilt the edge
device without dislocating it. Figure 2-1 summarises the three alignment steps.

14
Figure 2-1: Alignment steps for the edge test method (Samei and Flynn, 1997)

On the X-ray beam, the central axis was identified and marked with metal maker on the collimator
front. In order to ensure that the central axis has not interpreted a radiograph was already taken.
The edge device on the holder was oriented on the receptor, with its centre intersecting on the
central axis of the X-ray beam. Depending on the direction in which the MTF was measured, the
edge was placed both horizontally and vertically with an angle varying between 1o and 6o. In the
second step, Figure 2-1b, a laser pointer was oriented on the collimator face with the source of the
laser on the central axis of the X-ray beam. The distance from the laser beam and the centre of the
edge was 1-2 mm. The reflection of the laser beam on the edge surface was identified and finally,
on Figure 2-1c, which was the last step, the edge device was tilted using adjustable screws on the
holder until the reflection spot corresponds with the laser beam. These three steps were done with
precaution in order to get the right alignment of the edge device. A radiograph of a properly aligned
edge device was taken. The focal spot blur was reduced by using a long source-to-image-distance
(SID), a small focal spot, a short distance between the detector and the edge device. The digital
image data of the radiograph was computed and processed to get the pre-sampled MTF which is
obtained using 8 × 8 cm2 sub-region radiographs containing data from the transferred radiographs
of the edge device. Samei et al, 1997, discusses the method used to get the computed ESF and

15
calculation method to obtain a differentiated LSF and finally, Fourier transform the LSF to get
pre-sampled MTF (Samei and Flynn, 1997).

Buhr et al. 2003 also shows the results of ESF measured with an edge method slightly angulated
with a detector grid and the ESF is generated. The ESF is differentiated to obtain the Line Spread
Function (LSF) and MTF is calculated by a Fourier transformation of the LSF (Buhr et al., 2003),
(Samei and Flynn, 1997). The benefit of the edge device includes high precision at very low spatial
frequencies, precise alignment and it is not complex to use

The slit and edge methods have been compared, with the edge method showing favourable results
when determining the MTF at low spatial frequency whereas the slit method shows more accurate
results when determining MTF at a high spatial frequency (Buhr et al., 2003). MTF basically is
the plot of the ratio of the output-to-input modulation transfer as a function of spatial frequency,
measured in cycles/mm (Kerr, 2010). If the plot yields a higher MTF, there is a better chance of
having good resolution and sharpness of an image(Samei, 2003)

Many authors have used a similar method to get the pre-sampled MTF curve using the edge test
method. However, they have applied different techniques to get to the MTF curve.

2.6 FRC/FSC theoretical behaviour

FRC is a mathematical function that calculates the correlation quantities between two-dimensional
volumes of images in Fourier space (van Heel et al., 1982). Both FSC and FRC have the same
metrics; the only difference is that FSC measures correlation in 3-D objects and FRC in 2-D
objects.

∑𝒓∈𝒓𝒊 𝑷𝟏 (𝒓)∗𝑷𝟐 (𝒓)∗

𝑭𝑺𝑪/𝑭𝑹𝑪(𝒓𝒊 ) = Eq.3
√∑𝒓∈𝒓𝒊 𝑷𝟐𝟏 (𝒓) ∗ ∑𝒓∈𝒓𝒊 𝑷𝟐𝟐 (𝒓)

Eq. 3 is the FSC/FRC formula that assesses the resemblances between two independent
reconstructions of the same object in frequency space in order to find the spatial resolution
(Banterle et al., 2013). FRC measures the normalised cross-correlation between two images over
resultant rings in spatial frequency (van Heel & Schatz, 2005). Eq. 3 describes the FRC/FSC

16
between two images in Fourier space where the summation are over the volume of radius r in rings
(or shells in 3D space) of each volume, 𝑃1 (𝑟) is complex structure factor at radius r in volume 1
and 𝑃2 (𝑟)∗ is the complex conjugate with radius r in volume 2 (Diebolder et al., 2015). The
denominator in this equation is a normalising factor. Two images are used because the objective
is to determine which image has the better spatial resolution keeping in mind that the two images
being used are two independent reconstructions imaged at the same position.

Van Heel et.al, 2005, discussed two FSC threshold curves, the sigma factor curve, and the bit-
based threshold curve. The sigma curve has different resolution criterion curve that has been used
and tested, the 2σ, 3σ, 5σ, 0.5 and 0.143. Various authors have used the resolution criterion to
apply it in different applications. However, recent studies show that the used criterion in
conjunction with FRC curves is the 0.5 threshold criterion. The 2σ threshold criterion was initially
introduced by Saxon and Baumeister in 1982 related to the definition of spatial frequency (van
Heel and Schatz, 2005). The 0.143 value was proposed to be the realistic value by Rosenthal et al.,
but van Heel et al., 2017, have criticised their finding. This is because they believe that the fixed
threshold value 0.143 is incorrect, as signal and noise cross terms were omitted. Eq.4 and Eq.5
will give a short description from van Heel et al., 2005.

𝑷𝟏 (𝒓) ≈ 𝑺(𝒓) + 𝑵𝟏 (𝒓) Eq.4

𝑷𝟐 (𝒓) ≈ 𝑺(𝒓) + 𝑵𝟐 (𝒓). Eq.5

Eq.4 and Eq.5 are two volumes containing the same data signal (S) and different random noise
(N). Using these two equations to find the cross-correlation between signal and noise, we have un-
normalized FRC, un-normalized means that the denominator of Eq.3 is not included, then Eq.6
yields the cross-correlation for the un-normalized FRC as;

𝑭𝑹𝑪𝒖 (𝒓𝒊 ) ≈ ∑𝒓∈𝒓𝒊 𝑷𝟏 (𝒓) ∙ 𝑷𝟐 (𝒓). Eq.6

Substituting Eq.4 and Eq.5 into Eq.6 gives:

𝑭𝑹𝑪𝒖 (𝒓𝒊 ) ≈ ∑𝒓∈𝒓𝒊 𝑺𝟐 (𝒓) + ∑𝒓∈𝒓𝒊 𝑺(𝒓) ∙ 𝑵𝟏 (𝒓) + ∑𝒓∈𝒓𝒊 𝑵𝟐 (𝒓) ∙ 𝑺(𝒓) +

17
 ∑𝒓∈𝒓𝒊 𝑵𝟏 (𝒓) ∙ 𝑵𝟐 (𝒓). Eq.7

The correlation between signal and noise is important when studying FRC. Many authors have in
their papers assumed that the middle term of Eq.7 is uncorrelated, meaning that it equals to zero
and falls off the equation. Van Heel et al., 2005, have emphasized that the cross-term is important
and should not be left out as the uncorrelated signal and noise does not mean that the middle vector
product is zero. The middle term should not be omitted during the derivations. Omitting it will
lead to incorrect results as this will mean that the correlation between signal and noise is orthogonal
(van Heel and Schatz, 2005, van Heel and Schatz, 2017).

A threshold curve is introduced as a measure to give a quantitative estimation of the image

resolution from FRC. The threshold curve is chosen as a logical expression independent of the
reconstruction data for the expected FRC images with a signal-to-noise ratio that is constant in
Fourier space. The ½ bit criterion was introduced in the work of Villa-Comamala et al., 2011 as a
measure that produced results similar to the resolution estimations used for X-ray crystallography
(Vila-Comamala et al., 2011).

The 2 sigma threshold criterion was applied by Banterle et al., 2013, 70 rings were assigned into
the images after they were Fourier transformed, in order to have that 2 sigma cut-off frequency,
the pixel size was adjusted and the cut-off was found to be between ring 20th and 30th (Banterle et
al., 2013). In most cases, radiation damage is often the main factor when it comes to the resolution
limit (Diebolder et al., 2015).

FRC plot is a one-dimensional curve, approaching zero at high spatial frequencies and fluctuating
around the zero mark (Van Heel and Schatz, 2017). Filtering is applied to the FRC curve if data
does not give the expected FRC curve, this may be caused by under-sampling or over-sampling.
Apodization is one type of filtering that is applicable to FRC to give the expected FRC curve.

2.7 Filtering methods

The world of digital imaging is evolving and the method of recording or transmitting these digital
images is usually affected by many factors including faulty detectors, inaccuracy or even quality
of the system. Filters are invented for such cases so that we can have good filtered images, without
18
losing the important details of an image. Filtering is a method or technique used to modify an
image or hide the unwanted artefacts in an image. This technique may also be used to enhance
some features of an image such as edges, brightness, colour, contrast and increase or decrease pixel
size. Different methods of filtering are used in different fields such as medical, industrial and
photography. They either use filtering in real space or Fourier space.

Filters may be categorised in two classes, linear and non-linear filters. Linear filters contain an
arrangement of pixel values of an input image, the sum, and averages whereas non-linear filters
consist of combinations of median, minimum and maximum. Linear filter may be demonstrated as
convolution and can be analysed in Fourier space. The convolution theorem can function both in
real and Fourier space. The convolution operator in real space may be expressed as in Eq.8 and in
Fourier space may be expressed as in Eq.9.

𝒈(𝒊, 𝒋) = 𝒇(𝒊, 𝒋)⨀𝒉(𝒊, 𝒋) Eq.8

𝑓(𝑖, 𝑗) 𝑎𝑛𝑑 ℎ(𝑖, 𝑗), being the input image and filter function respectively, and 𝑔(𝑖, 𝑗) being the
output filtered image.

𝒈(𝒌, 𝒍) = ℱ −1 {𝑭(𝒌, 𝒍)𝑯(𝒌, 𝒍)} Eq.9

where; 𝑔(𝑘, 𝑙) is the output or filtered image, and 𝐹(𝑘, 𝑙)𝐻(𝑘, 𝑙), are both inverse Fourier
transforms of input image of Eq.8 and filter function of Eq.9, respectively. The following form
part of the filters in Fourier space.

Low-pass filter is a linear type of filter, which works in such a way that it allows low frequency to
pass un-attenuated and reducing or even completely blocking high frequencies from passing. The
high frequency that is attenuated may be usable to decrease the random noise in the input image.
The low spatial frequency in an image will be used to verify the characteristics of an image; this
blurs the image and diminishes the image edges, sharpness and noise associated with high spatial
frequencies.

High-pass filter is the opposite of low-pass filter; only high spatial frequencies are allowed to pass
whereas low spatial frequencies are attenuated. The high-pass filter improves the edges in images.
These improvement effects are associated with un-attenuated high frequencies and thus vary in
real space and in Fourier space.
19
Band pass filter is the type of filter that can pass low-pass and high-pass frequencies. But only to
a certain frequency range.

2.7.1 Apodization

Apodization may be defined as an ideal window function used to remove the side-lobes in a signal.
In simple terms, it is a filtering function used to remove unwanted artefacts in a signal (Qi et al.,
2013). Zhou (2011), defines apodization as the suppression of side-lobes (Zhou, 2011).
Traditionally apodization methods have been there and used for adjusting the main-lobes of an
imaging signal and reducing the side-lobes (Reeg, 2016). Main-lobe is the highest peak of the
signal pattern produced either by the antenna or radiation pattern. Side-lobes are the local peaks in
signal patterns lower than the main-lobe. These side lobes in signal processing are usually
considered as noise if they are too many to interpret well.

The apodization method was developed by Dolph in 1946. He used Chebyshev polynomials (a
sequence of orthogonal polynomials) for a collection of linear antenna that formed its radiation
pattern such that the base main-lobe width was achieved for a set maximum side-lobe level. In
1954, Taylor enhanced Dolph’s method by improving the distribution function of the linear array
and the result located the side-lobes farther away from the main-lobes. Different types of
apodization techniques have been tried and tested. T’Hoen (1982), studied these different methods
in the search for a better method to apply on linear ultrasound array and the effects each
apodization technique has on image quality. From his findings, he concluded that only four
apodization techniques such as Hamming, cosine, sine and 10% reduced Gaussian give appropriate
results when compared to the mostly used rectangular apodization function (Dolph, 1946, Reeg,
2016, Taylor, 1955, t'Hoen, 1982).

Apodization has been applied in ultrasound images to increase the main-lobe and decrease the
side-lobes. Spatial resolution in ultrasound distinguishes between two points at different positions
in space, and consists of two components, axial and lateral resolution. It is important to distinguish
between two. The axial resolution or longitudinal or linear resolution as referred to in some
context; is the resolution of an image parallel in direction to the ultrasound beam. This axial
resolution may detail out the smallest tissue layer density and has the ability to detect the smallest
anatomical details in an ultrasound imaging system. The axial resolution is dependent on the length

20
of the pulse and many methods already exist to improve this resolution (Almualimi et al., 2018,
Reeg, 2016). However, only a few methods have been established to improve the lateral resolution.
Lateral resolution is the ability of the system to differentiate between two points in the
perpendicular direction to the ultrasound beam. This resolution is in most cases affected by the
width of the ultrasound beam. For instance, if the beam of the ultrasound is wide, the lateral
resolution will decrease and this will result in bad quality images (Qasim and Raina).

Reeg, 2006 proposed a method of apodization to improve the lateral resolution and proved that the
method was better than rectangular apodization function and has used apodization function to
achieve better resolution of the imaging system in ultrasound. This lateral resolution was improved
by a factor of 25 times when comparing it with the rectangular apodization method and for this the
side-lobes were low. The proposed method by Reeg (2006), was tested using two approaches, the
masking and bridging approach of apodization. The masking approach was tested in simulation
and subtracted an image with zero mean apodization from a scaled rectangular apodization
function. This subtraction was done so that the beam patterns of the zero mean, images' two main-
lobes to be masked by the main-lobe of the rectangular images. Masking approach was used by
Savoia et al., 2014, and minimal improvements in the lateral resolution were attained; this was
with suppression of side-lobes (Reeg, 2016). The bridging approach was also tested using two
images. The two images were constructed using zero mean apodization separately. This was
because both images were apodized on collection and a constant was added to the apodization
function.

In Zhou’s 2011 thesis, Fourier transform infrared emission spectroscopy was used to measure
spatially resolved flame temperature and species concentration. Apodization function was applied
in emission spectra in Fourier space. The type of apodization function applied was boxcar and it
was used to find emission spectra in Fourier transform calculations. This is because integration of
Fourier transform is done in the time domain from negative infinity to positive infinity and that is
not practical, hence the boxcar apodization function was applied (Zhou, 2011).

In Akhter's 2012 thesis, different weighting functions are evaluated to control side-lobes on ultra-
wideband (UWB) Synthetic Aperture Radar (SAR) images. SAR is a comprehensible sensor that
is capable of producing images of earth's surface with high resolution. The SAR images relate to
backscattered electromagnetic energy. The SAR images need to be processed before use, and they

21
apply two dimensional Fourier transform to the raw images for processing. After Fourier
transformation, the output spectrum has main-lobes and side-lobes. SAR images always have side-
lobes which severely misrepresent the images. Side-lobes are a concern and need to be dealt with
and that's when apodizing function comes in. This technique is well known for reducing side-lobes
level but still giving a clear image resolution. Different weighting functions are tested, both linear
and non-linear, the Hamming, Hanning, Blackman, and Taylor were used in SAR images to
decrease the impulse response (IPR) side-lobes and increases the IPR main-lobe width (Akhter,
2012).

Akhter (2012), proposed a new linear weighting function and applied it to SAR images which then
showed that it is better than the traditional apodizing technique when it comes to preserving lower
side-lobes. Linear and non-linear apodization techniques may be applied to SAR images and both
are capable of decreasing the side-lobes but linear apodization technique decreases the side-lobes
and leads to a loss in image resolution whereas on the other method non-linear can decrease the
side-lobes without causing any changes to the image resolution. Non-linear apodization technique
is not used because Akhter (2012), believes that it is not the best technique to use because it is not
easy to find a relation between the apodized image and the real image, and also mentions that for
non-linear weighting function two or more weighting functions are required in UWB SAR imaging
(Akhter, 2012).

A rectangular approximation, a general apodization technique, is used on two-dimensional

weighting functions and applied in a narrow beam and narrow band SAR images. This technique
only induces orthogonal side-lobes but in UWB SAR images even non-orthogonal images are
induced. In SAR images, where the narrow beam and narrowband spectrum is estimated to a
rectangular area, there is a loss in spatial resolution and which is still acceptable. For UWB SAR
images this is a different case, the loss in spatial resolution is not acceptable at any level (Akhter,
2012).

The new proposed linear weighting function is,

𝒌𝒙 𝒌𝒙
𝟐𝝅 (𝒂𝒕𝒂𝒏 ) 𝟔𝝅 (𝒂𝒕𝒂𝒏 )
𝒌𝒓 𝒌𝒓
𝒘(𝒌𝒙 , 𝒌𝒓 ) = [𝟎. 𝟔𝟑 −∝𝒌 𝒄𝒐𝒔 ( ) − 𝜷𝒌 𝒄𝒐𝒔 ( )]
∅𝒐 ∅𝒐
𝟐 𝟐

22
 𝟐𝝅(√𝒌𝟐𝒙 +𝒌𝟐𝒚 −𝒌𝒄 ) 𝟔𝝅(√𝒌𝟐𝒙 +𝒌𝟐𝒚 −𝒌𝒄 )
[𝟎. 𝟔𝟑 −∝𝒌 𝒄𝒐𝒔 ( ) − 𝜷𝒌 𝒄𝒐𝒔 ( )] Eq.10
𝒌𝒎𝒂𝒙 −𝒌𝒎𝒊𝒏 𝒌𝒎𝒂𝒙 −𝒌𝒎𝒊𝒏

where ∝𝑘 is 0.45,

𝛽𝑘 is 0.002,

𝑘𝑥 is azimuth wave number,

𝑘𝑟 is range wave number,

𝑘𝑐 center wavelength of SAR system,

𝑘𝑚𝑎𝑥 𝑎𝑛𝑑 𝑘𝑚𝑖𝑛 are the wavenumbers that correspond to the lowest and highest signal frequencies.

This linear weighting reduces the side-lobes for both orthogonal and non-orthogonal and still keeps
the image resolution unchanged. The spectrum was generated using different angles proportional
to the bandwidths and inverse Fourier transform was applied to the spectrum. The loss of image
resolution was calculated and the linear weighting function was applied in all directions, azimuth,
range, and angular direction. Figure 2-2 to Figure 2-10 shows how Akhter (2012), came to the
conclusion that the linear method is best when compared to traditional apodization function
(Akhter, 2012).

Figure 2-2: Non-apodized real SAR image (Akhter, 2012).

23
Figure 2-3: Apodized real SAR image by implementing the proposed weighting function (Akhter,
2012).

Figure 2-4: SAR non-apodized image with different (10-110) integration angle (Akhter, 2012).

24
Figure 2-5: Apodized image using rectangular weighting function (Akhter, 2012).
Figure 2-5, the rectangular weighting function was implemented to decrease the orthogonal side-
lobes but did not decrease them as expected.

Figure 2-6: Apodized image using Hanning weighting function (Akhter, 2012).
25
Figure 2-7: Apodized image using Hanning weighting function in the angular direction (Akhter,
2012).

In Figure 2-6 and Figure 2-7, Hanning weighting function was applied in azimuth and angular
direction respectively. It was observed that when Hanning weighting function was applied to the
azimuth direction, Figure 2-6, 60% of resolution was lost even though the orthogonal side-lobes
are adequately decreased. In Figure 2-7, about 45% of resolution was lost with sufficient side-
lobes suppression when Hanning weighting function was applied in the angular direction.

26
Figure 2-8: Apodized image by Hanning weighting function (Akhter, 2012).

Figure 2-9: Apodized image by Hamming weighting function in the angular direction (Akhter,
2012).

27
Figure 2-8 and Figure 2-9, the Hamming weighting function was applied in the azimuth direction
and angular direction respectively, 45% loss of resolution was calculated on both directions with
reduced orthogonal side-lobes.

Figure 2-10: SAR apodized image after applying proposed new linear weighting function (Akhter,
2012).

In Figure 2-10, the proposed linear weighting function was applied in azimuth, range and angular
directions. The side-lobes in orthogonal and non-orthogonal were reduced and resolution loss was
measured to be 33.34% (azimuth direction) and 36.58% (range direction). The resolution loss is
better than the other traditional weighting functions. Akhter (2012), mentioned in her thesis that
the resolution in angular direction is much less than the two other directions (azimuth and range)
and did not state by what percentage was the resolution loss in angular direction. The proposed
weighting function was verified to be accurate to use on SAR images because it was proven to
reduce side-lobes yet retain spatial resolution on SAR images (Akhter, 2012).

28
2.7.1.1 Different types of apodizing functions

There are many different types of apodizing functions or weighting functions as referred in most
studies. The weighting functions that are classified as the classic functions are Hamming, Hanning,
Blackman, and Taylor. These weighting functions are commonly used in apodization technique.
The following subsection is the description of each weighting function and its related theory.

2.7.1.1.1 Hamming window

Hamming window is used in many applications, such as speech and sound processing. It is used
because of its great ability to reduce side-lobes while retaining the main-lobes (Akhter, 2012). The
coefficient of Hamming window is computed from Eq.11.

𝟐𝝅𝒏
𝒘𝒉𝒎 (𝒏) = 𝜶 − 𝜷 𝒄𝒐𝒔 ( ) Eq.11
𝑴

where α is 0.54 and

β is 0.46.

2.7.1.1.2 Hanning

Hanning window is generally used when doing operational noise and vibration measurements. It
is often used with random data because of its moderate impact on frequency resolution and
amplitude precision of the resulting frequency spectrum. Eq.12 and Eq.13 are applied in Hanning
window operations.

𝟏 𝟐𝝅𝒏
𝒘(𝒏) = 𝟐 (𝟏 − 𝒄𝒐𝒔 (𝑵−𝟏)) Eq.12

or

𝝅𝒏
𝒘(𝒏) = 𝒔𝒊𝒏𝟐 (𝑵−𝟏). Eq.13

2.7.1.1.3 Blackman window

Blackman window uses a cosine function to reduce the side-lobes of the signal, it is defined in
Eq.14.
29
 𝟐𝝅𝒏 𝟒𝝅𝒏
𝒘𝒃𝒍𝒌 (𝒏) = 𝒂𝟎 − 𝒂𝟏 𝒄𝒐𝒔 (𝑵−𝟏) + 𝒂𝟐 𝒄𝒐𝒔 (𝑵−𝟏) Eq.14

1−𝛼 1 𝛼
where 𝑎0 = 𝑎1 = 2 𝑎2 =
2 2

for 0 ≤ 𝑛 ≤ 𝑀.

2.7.1.1.4 Triangular

𝑵−𝟏
𝒏−
𝟐
𝒘(𝒏) = 𝟏 − | 𝑳 | Eq.15
𝟐

2.7.1.1.5 Cosine

Cosine window functions are commonly used in signal processing. Eq.16 mathematically defines
the Cosine window,

𝝅𝒙
𝒘(𝒙) = 𝒄𝒐𝒔 (𝟐𝒂). Eq.16

2.7.1.1.6 Gaussian

Gaussian window is applied in both signal processing and uses a standard deviation and an eigen
function of the Fourier transform. Eq.17 is the confined Gaussian window and Eq.18 is the
Gaussian window function which uses the standard deviation.

𝟏
𝑮(− )[𝑮(𝒏+𝑵)+𝑮(𝒏−𝑵)]
𝟐
𝒘(𝒏) = 𝑮(𝒏) − 𝟏 𝟏 Eq.17
𝑮(− +𝑵)+𝑮(− −𝑵)
𝟐 𝟐

𝑵−𝟏
𝒙−
−( 𝟐 )
𝟐𝝈𝒕
𝑮(𝒙) = 𝒆 Eq.18

for 𝜎𝑡 < 0.14𝑁,

30
2.7.2 Filtering using ImageJ

ImageJ is digital image processing and analysis software which was inspired by the National
Institute of Health (NIH) in the USA. It is a Java-based image processing software developed by
Wayne Rasband. It is an open source and may be used online or offline (Rasband, 2018).

2.7.2.1 Types of filtering in ImageJ

The following are the built-in filtering modes in ImageJ.

2.7.2.1.1 Mean

In the mean filter, also known as box filter, average filter is used to smooth an image to remove
all the artefacts contained in the image. It decreases the quantity of intensity variation between one
pixel and the next. What the filter does is, it calculates the mean or the average by adding up all
the numbers in the data set and dividing by the total; Eq.19 present the mean formula (Paul-
Scherrer-Institute, 2019);

∑ 𝒙𝒊
𝒎𝒆𝒂𝒏 = Eq.19
𝒏

where 𝑥𝑖 is numbers in the individual data set and 𝑛 represent how many numbers are in the data
set. On the software one gets to select radius. With the choice of radius selected, the mean is
calculated and each pixel value is replaced by the mean value of its neighbour.

2.7.2.1.2 Median

Median filter is a non-linear filter used to remove noise and smooth an image. Median filter is
usually used in real space images and is not only limited to real space images but can also be
applied in Fourier space. Median is defined as the number that represents the middle of the
distribution. Before calculating the median, the data set needs to be sorted first from smallest to
largest and the median value may be determined from the sorted data set. In simple, median is
calculated as in Eq.20;

𝒏+𝟏
𝒎𝒆𝒅𝒊𝒂𝒏 = Eq.20
𝟐

31
where 𝑛 represent the numbers of data sets. Note that for odd and even data set the median is
calculated differently. Just like in mean filter, ImageJ gives an option to select the radius, within a
specified radius median is calculated and each pixel value is replaced by the median value.

2.7.2.1.3 Gaussian blur

Gaussian blur is a type of filters that blurs the image artefacts and removes noise. It works similar
to the mean filter but does not average the neighbouring pixels. Eq.21 represent Gaussian function
in one dimension

−𝒙𝟐
𝑮(𝒙) = 𝒂𝒆 𝟐𝝈𝟐 Eq.21
1
where 𝑎 = and substituting 𝑎 gives:
√2𝜋𝜎

−𝒙𝟐
𝟏
𝑮(𝒙) = 𝒆 𝟐𝝈𝟐 Eq. 22
√𝟐𝝅𝝈

where 𝜎 is the standard deviation, 𝑥 is the distance from the origin on the horizontal axis. Eq.23
applies for 2D

−𝒙𝟐 +𝒚𝟐
𝟏
𝑮(𝒙, 𝒚) = 𝒆 𝟐𝝈𝟐 . Eq. 23
√𝟐𝝅𝝈

The idea of Gaussian blur is to remove unwanted details in an image but still keep the edges. The
Gaussian blur filter depends on the standard deviation.

2.7.2.1.4 Minimum and maximum filter

Minimum and maximum filter are morphological filters. Morphological filters are non-linear
filters which use mathematical operators to detect edges of an image. Morphology is a wide-range
imaging process technique that uses operators to transform images based on their structure.
Originally, morphology filter was typically applied to binary images, but the application expanded
and it is now applied to grayscale images too. They use dilation and erosion operation to detect
edges. The morphological filters may be applied in real and Fourier space. Morphological methods
32
analysis images with a small shape known as structuring element (SE) (Gopal and Svalbe, 2018).
Morphological filters are split into two methods which are; minimum and maximum filters. These
two filters are opposite of each other, minimum filter is known as erosion and maximum filter as
dilation (resizing). The erosion and dilation operators are used to find the minimum and maximum
of the pixel values within a specified radius in an image.

Maximum- to calculate dilation of an image (grayscale image in this case), each pixel in an input
image is considered. The rudimentary effect of the dilation operator is to enlarge the image pixels
especially the foreground pixels. In simple terms, the maximum filter applied on text, the text will
gradually become thicker.

2.7.2.1.5 Un-sharp Mask

Un-sharp mask is another form of filtering that sharpens the edges of an image; this is done by
removing the un-sharpness or blurredness on the original image and inventing a new form of image
from the filtered original image. This type of filter is equivalent to adding a high pass filter to an
image. Using un-sharp mask as a filter, there are three settings that needs to be well understood;
amount, radius and threshold. Amount controls the magnitude of the contrast that is added to the
edges of an image, it determines how much lighter or darker the edges of an image become. Radius
influences the size of the edges to be improved. A smaller radius will improve smaller scale details
whereas a higher radius will cause halos at the edges of an image. Threshold controls the contrast
of an image and determines the minimal brightness change before the filter applies any changes.
This setting is also used to sharpen more definite edges while leaving subtler edges untouched.

33
Chapter 3: Methodology

3.1 Introduction

This chapter focuses on outlining the methodology and the choice of research method for testing
the theoretical framework and addresses the research question, objectives and research problem.
The research methodology is a key activity that supports the choice of research design and includes
a step by step process of how the research was carried out. The research design of choice was
quantitative using an experimental approach. Data was obtained from digital neutron radiographs
with values ranging from 0 – 65535 for a 16-bit image format obtained from PSI. The images are
2160 by 2560 pixels. Within the quantitative approach, the experiment was conducted to obtain
data which was analysed to provide results with regards to spatial resolution.

3.2 Facilities – neutron sources

There are several instruments that can be utilised to obtain neutron radiographs or images. The
data was collected from PSI in the Neutron Transmission Radiography (NEUTRA) facility. Figure
3-1 is an aerial view of PSI campus in Switzerland. PSI has four large facilities; the Switzerland
X-ray free-electron laser (SwissFEL) which is focused on matters in biology, chemistry and
material science. The Swiss Light Source (SLS) is the third generation synchrotron light source at
PSI and it is part of the photon science division focusing on research in chemistry, biology and
material science for in-depth 3D imaging. The other two large facilities are Spallation neutron
source (SINQ) and the Swiss Muon Source (SμS) (Paul-Scherrer-Institute, 2019). Each large
facility has different beam lines for different uses. SINQ is used for neutron radiography and
tomography, it has both cold and thermal neutrons. The facilities are discussed in the section 3.2.1.

34
Figure 3-1: PSI campus (Paul-Scherrer-Institute, 2019)

3.2.1 NEUTRA

NEUTRA is thermal neutron radiography and tomography facility at PSI. It is one of the leading
radiography facilities in Europe because of its steady-state (Lehmann et al., 2001) proton beam
current of 850µA and driven by 590MeV energy (Alam et al., 2006). NEUTRA has three key
components which are, the working room with a shielded concrete assembly block, the outer and
the inner collimator (Lehmann et al., 2001) as shown in Figure 3-2. The inner collimator is located
within the target shielding block and the outer collimator is an evacuated divergent aluminum tube.
They are described in detail by (Alam et al., 2006).

35
Figure 3-2: Graphic layout of the NEUTRA facility at PSI thermal beam line of SINQ (Lehmann
et al., 2003).

The great thing about the outer collimator is that it can be fragmented into two or more parts to
perform different investigations at positions of choice under suitable conditions. It has a high
neutron flux, which makes it appropriate for irradiation experiments. The properties of the beam
positions were verified at the facility by Lehmann et.al, 2001. The L/D verification was done
following the same method which was applied by (Kobayashi and Kiyanagi, 1996). The L/D of
500 is advantageous when performing experiments which require a larger distance between the
detector and the sample, Table 3-1 and Table 3-2 show properties of the system and different
positions at NEUTRA facility that are available to use.

Table 3-1: Properties of the NEUTRA (Lehmann et al., 2001)

Position number
System Characteristic 1 2 3
Distance from the target centre (mm) 6404 9876 13131
Distance from the aperture (mm) 3820 7292 10547
Beam diameter (mm) 150 290 400
Neutron flux (cm-2s-1mA-1) 1.6 x 107 5 x 106 3 x 106
L/D 200 350 550

36
Table 3-2: Properties of NEUTRA imaging detector system (Lehmann et al., 2001).

System Characteristic Imaging Plates Scintillator & CCD X-ray film &digital
camera transmission scanner

Inherent spatial resolution 50 µm 500 µm 20 µm

Typical exposure time for 20 sec 10 sec 5 min

generation of good images
Number of pixels per line 4000 x 8000 512 x 512 9000 x 12000

Detector area 20 cm x 40 cm 25 cm x 25 cm (given 18 cm x 24 cm (given by the

(given by the IP) by the scintillator) vacuum cassette & film)

Dynamic image 105 (linear) 105 (linear) 105 (linear)

Applicability for Yes Yes Yes

quantitative studies

3.2.2 ICON

Imaging with Cold Neutrons (ICON) is a beamline attached to the cold neutron source of SINQ
based in Switzerland, PSI, which started its operation in 2005 and has provided services for both
science and industry. The facility as its name suggests it uses cold neutrons for investigations. The
objects that are sampled at ICON are often thinner because of the high attenuation coefficient when
using cold neutrons. The neutrons generated from this sector are moderated by a liquid deuterium
(D2) tank at a temperature of 25 K.

Cold neutrons also have an advantage for use on several applications including and not limited to
neutron imaging, neutron diffraction, material science and archaeology (Kaestner et al., 2011).
The advantage of using cold neutrons compared to thermal neutrons of NEUTRA is that it permits
diverse investigations and high contrast images can be obtained. It also allows larger macroscopic
cross-section for materials as a result of the energy dependence of absorption cross-sections. Table
3-3 summarizes the camera system and Table 3-4 summarizes beam parameters.

37
Table 3-5 is the resolution and scintillation available at ICON with different experimental
positions.

Table 3-3: Properties of camera system used at ICON (Kaestner et al., 2011).

System Property Andor DW434 Andor DV436 PCO. 4000 PI-MAX 1300
Pixels 1024 x 1024 2048 x 2048 4032 x 2688 1340 x 1300
Dynamic 16 bits 16 bits 14 bits 16 bits
Exp. Pos. 2.3 2 2.3 2.3
Camera box Midi/maxi Micro Micro/midi/maxi Midi/maxi
Ext. trigger - - Yes Yes
On-chip memory - - 4 GB -
Photomultiplier - - - Yes

Table 3-4: Resolution and scintillators accessible at ICON (Kaestner et al., 2011)

Scintillator material 6Li Gadolinium

Thickness (µm) 50 100 10 20
Resolution (lp/mm at10%MTF) 12.7 11.8 24.6 18.0
Resolution (µm) 39.4 42.4 20.3 27.8
Sensitivity (count/s.mA 226.5 515.8 61.46 95.35

38
Table 3-5: Resolution and scintillators accessible at ICON (Kaestner et al., 2011).

System Value at Experimental Position

Characteristic 2 3
Aperture 1 10 20 40 80 1 10 20 40 80
diameter (mm)
L/D Range 6864 686 343 172 86 12083 1208 604 302 151
Neutron Flux - 3.2x 1.3x - 1.4x - - 3.9x - 5.2x
(cm-2s-1mA-1) 106 107 108 106 107
Spectral ∆λ⁄λ = 15 ∆λ⁄λ = 15
Resolution (%)
at 20 mm
aperture
diameter
Wavelength 2.5 – 9 2.5 – 9
range (Å)
FOV (mm2) 27 x 27 120 x 200 except 80 mm aperture

3.3 Neutron radiography setup

This section discusses the methodology used to analyse the results to obtain spatial resolution in
digital neutron radiography using FRC and MTF/SFR methods.

39
In neutron radiography the method used to obtain radiographs is standard and consists of the
following: Image acquisition, pre-processing of images, processing of images, analysis of images
and finally the results. Image acquisition is basically the act of retrieving an image from a
hardware-based source such as a CCD camera, in order to get the images for analysis. Figure 3-3
shows the basic neutron radiography setup.

Figure 3-3: Neutron radiography setup.

The research design was quantitative, data used was measured at the thermal neutron imaging
instrument, NEUTRA at the SINQ spallation neutron source, PSI. Gadolinium knife edge. Figure
3-4 was used as a test object to acquire images that were used for analyses to obtain the results.
The test object consisted of gadolinium sheet fixed in two aluminium layers. The aluminium layers
were there to hold and support the Gadolinium sheet. Gadolinium was used because of its greatest
ability to absorb neutrons. Gadolinium consists of six stable isotopes, 154Gd, 155Gd, 156Gd, 157Gd,
158 160
Gd and Gd with natural abundance of 2.18%, 14.8%, 20.5%, 15.7%, 24.8% and 21.9%
152
respectively and one radioactive isotope Gd with half-life of 1.08x1014 years. In the nuclear
industry, 155Gd and 157Gd are the two stable isotopes used because of their high neutron absorption
cross-section. Their absorption cross-sections are 61 000 b and 254 00 b respectively (Power, 2018,
Radebe, 2017).

40
The two aluminium layers used were 2 mm in thickness; this allowed room for the gadolinium
sheet to be exposed to the detector. The object were sampled in two dimensional, vertical and
horizontal planes. The gadolinium knife edge test object was placed close to the detector, the
ODD≈0 mm, and the collimation L/D=800 mm with an exposure time of 35 seconds, which was
sufficient to provide statistical accuracy. The imaged radiographs have statistical consistency in
order to minimise noise. In radiography, noise is the unwanted details in an image that affect its
visualization and interpretation (Samei, 2003). Statistics here is described as signal-to-noise-ratio
(SNR). The same gadolinium knife edge test object was imaged at different ODD of 12.0 mm,
32.0 mm and 104 mm to determine which ODD gives the best spatial resolution.

Aluminium

Air

Gadolinium

Figure 3-4: Gadolinium knife edge test object (Radebe, 2017).

The gadolinium knife edge was imaged twice at the same distance and properties. The resultant
images are shown in Fig 3-5a and Fig 3-5b.

3.4 Determination of spatial resolution

This subsection details out the method to determine the spatial resolution of an image using the
proposed method, the FRC method. By definition spatial resolution is the ability of an imaging
instrument to be able to differentiate between two features that are close to each other. The test
object was imaged twice at the same position, in order to have two images with the same SNR.

41
Both images were in real space and were analysed in Fourier space. A method on how real space
images were analysed in Fourier space follows in section 3.4.1

3.4.1 Matrix Laboratory (MATLAB)

MATLAB is a multi-paradigm numerical coding and programming language. It is a product of the

MathWorks, Inc., developed by Cleve Moler in the late 1970’s. It is a powerful language for
technical computing and an accessible environment where problems and solutions are expressed
in mathematical notation. MATLAB has two kinds of program files, scripts and functions. Both
program files have .m extension. In these two files, a series of commands can be written which
wants to be executed together. MATLAB has an image processing toolbox which allows the user
to perform noise reduction, background subtraction, segmentation, image enhancement and
geometric transformation. And this can be applied to different image formats as MATLAB is
capable of reading numerous image formats (Jalalvand et al., 2019).

3.4.2 Fourier Ring Correlation method

FRC is mainly used to characterise the spatial resolution in nanoscopy, X-ray crystallography,
microscopy and diffraction applications. It hasn't been used in digital neutron radiography and X-
ray imaging. In this research, the FRC method was proposed to measure spatial resolution with
different threshold criterion available.

Two images were acquired in real space using neutron beamline, and were analysed and compared
against one another because in nature cross-correlation compares one thing to the other. Therefore,
two images were compared to determine the spatial resolution. A mathematical approach Fourier
Ring Correlation (FRC) was used to find the resolution of an image. To find the suitable threshold
criteria, different threshold criterion including (the σ factor, 2σ, 3σ, ½ bit, 1 bit, 0.143 and 0.5)
were tested for the FRC method using a MATLAB program and the suitable threshold criterion
was 0.5 threshold, and was used to present the results. The criteria used to determine the suitable
threshold was, on the FRC MATLAB code, different threshold criterion were tested. The other
criterion could not give the output as close as expected. Literature shows that FRC was applied to
assess spatial resolution in microscopy and nanoscopy (Nieuwenhuizen et al., 2013). The FRC
formula to be applied, is a criterion on its own, and the criterion work in a way that two images
42
must be sampled. The FRC equation is mathematically described as in Eq.3. The two images were
put as an input in the FRC MATLAB function, the code ran to display the FRC and spatial
frequency curve as an output results.

An algorithm of how the FRC MATLAB function calculates FRC and spatial frequency curve to
determine the spatial resolution is described in the following steps;

 Two independent reconstructions (image 1 and image 2) of the same object were required.
 The number of rings and image pixel size are also required for the input.
 Apply Fourier transform on each independent reconstruction,
 Assign rings on the two independent reconstructions in the same manner; every ring differs
with thickness and radii.
 Image 1 is calculated as it is, the complex conjugate of image 2 is calculated as in Eq.3
 Take ring one of image one and ring one of the complex conjugate of image two, find
artefacts (pixels) in each ring and get the products of artefacts in image one and image two
and sum up all the artefacts of ring one.
 Do the same for ring two till the nth ring (on image one and image two). To normalise the
method, the square of artefacts in ring one of image one is summed up and the square of
artefact in ring one of image two are summed up and the product of the two are over the
square root in Fourier space. This is done on the denominator of Eq.3.
∑𝑟∈𝑟 𝑃1 (𝑟)∗𝑃2 (𝑟)∗
𝑖
𝐹𝑆𝐶/𝐹𝑅𝐶(𝑟𝑖 ) = , and
√∑𝑟∈𝑟𝑖 𝑃12 (𝑟) ∗ ∑𝑟∈𝑟𝑖 𝑃22 (𝑟)

 Plot the FRC and threshold versus spatial frequency curve on the x-y plane.

The FRC measurements are based on statistical accuracy. A resolution limit is determined from
the curve, where the FRC and threshold curve meet. Figure 3-5 summarises the workflow used to
compute the FRC curve using the FRC MATLAB function to determine spatial resolution. Fig 3-
5a and Fig 3-5b are the images of gadolinium knife edge imaged twice at the same position. The
two images are Fourier transformed to form Fig 3-5c and Fig 3-5d. These results were plotted on
an x-y plane where FRC is on the y-axis and spatial frequency is on the x-axis as in Fig 3-5e. The
MTF/SFR method which is the standard method that has been applied in neutron radiography is
detailed in section 3.4.3. The FRC results were then compared with the results obtained from the
MTF/SFR.
43
Figure 3-5: Computational steps on how to compute FSC/FRC. Fig 3-5e is the FRC/Resolution
curve (Radebe, 2017).
44
3.4.3 Modulation Transfer Function (MTF) method

To compute the spatial resolution using the standard method MTF/SFR, sfrmat was used as a
MATLAB function to provide an MTF/SFR and ESF from digital images containing slanted-edge
features. Sfrmat is a spatial frequency response MATLAB function developed by Peter Burns in
order to obtain the MTF curve from an edge image (Burns, 2009). The precise edge-gradient
algorithm follows the same standard of the ISO 12233, which was developed for resolution
measurements of the electronic still images (Burns, 2003).

An sfrmat on MATLAB was launched, once opened, the run button on the MATLAB toolbar was
selected to run the script, the slanted-edge analysis window appeared to select an image to be
analysed. The Gadolinium edge image was selected (same image as in Figure 3-5a and Figure
3-5b). Only images with the following extensions can be used (Dicom, JPEG, GIF, BMP, RVG
and RAW) otherwise the script won’t run. A display of data sampling window in pixel/inch (ppi)
or millimetre (mm) appeared, this was for selecting the correct sampling data that the user want to
be sampled. To select the region of interest (ROI) on gadolinium knife edge images, 50% of the
Gadolinium edge and 50% of air was selected in an upright rectangular shape because if incorrectly
selected the sfrmat function interpret the results incorrectly. The ROI was selected as shown in
Figure 3-6.

Figure 3-6: Region of interest selection on Gadolinium edge with 50% Gadolinium edge selection
and 50% air selection.
45
Figure 3-7: Cropped Gadolinium knife edge image to display ROI with 50% selection on
Gadolinium edge and 50% air selection.

After the selection of the ROI, the Edge Spread Function ESF and MTF/SFR graphs were
automatically displayed as an output as in Figure 3-8 and Figure 3-10 and the output data points
were saved as an MS EXCEL spreadsheet. These MS EXCEL data points were used to plot the
Line Spread Function (LSF). The LSF was obtained by differentiating the ESF output.

46
Figure 3-8: Edge Spread Function (ESF) curve of Gadolinium knife edge test object.

The ESF output saved as MS EXCEL data points was used to derive Line Spread Function (LSF).
The LSF is equal to the first derivative of ESF which is differentiated using numerical method as
shown in equation Eq.24

𝑬𝑺𝑭𝒊+𝟏 −𝑬𝑺𝑭𝒊
𝑳𝑺𝑭 = Eq. 24
𝟐(𝒙𝒊+𝟏 −𝒙𝒊 )

where i = 1, 2, 3…n-1 and xi is the position of the ith pixel. Figure 3-9 shows the LSF output.

47
 ESF derivative
0,08
0,07
0,06
0,05
0,04
LSF

0,03
0,02
0,01
0
-0,01 0 50 100 150 200 250 300 350
-0,02
X-value

Figure 3-9: Line Spread Function which is the ESF derivative.

LSF can also generate an MTF curve by Fourier transforming the LSF data point.

Figure 3-10: MTF/SFR curve with sampling efficiency of 17%.

48
Chapter 4: Results and discussion

4.1 Introduction

This chapter discusses the results obtained using the methods described in chapter 3 and has three
sections detailing out the results. Section 4.2 of this chapter focusses on FRC results using FRC
script as an input in MATLAB whereas section 4.3 focusses on the results obtained using the
standard method MTF. Section 4.4 is the comparison of the two methods, the proposed FRC
method in neutron radiography and the standard method used in neutron radiography MTF/SFR.
The remainder of this chapter summarises the results and the aim of this study.

4.2 Fourier Ring Correlation results

The edge images used on fig 3-5a and fig 3-5b were used to compute the results. These two images
(fig 3-5a and fig 3-5b) are the original images as obtained from the NEUTRA facility before any
image analysis. The FRC MATLAB function was ran using two input images to produce the FRC
curve as a function of spatial frequency. To give a measureable estimate of the image resolution
from the FRC, a threshold criteria was used. The FRC curve produced has two curves in one
Cartesian plane, the threshold curve and the FRC curve. This is shown in Figure 4-1. The FRC
curve and the threshold curve are used to characterize a resolution limit of images.

49
Figure 4-1: FRC and spatial frequency curve.
The FRC curve generated from MATLAB utilised Eq.3 with two slanted gadolinium edge images
as in the input. The resulting FRC and threshold curves were evaluated to determine the spatial
resolution of the images. For Figure 4-1, the 0.5 threshold criterion was used to measure the spatial
resolution of an image. According to literature, there are different threshold criterion for FRC
method being the σ factor, 2σ, 3σ, ½ bit, 1 bit, 0.143 and 0.5 criterion. The 0.5 threshold criterion
was used in this study because it was fitted to be the one to give the solution for the resolution
limit. Figure 4-2 show the solution of the spatial resolution.

Figure 4-2: FRC curve and spatial resolution solutions at approximately 0 mm ODD.

According to Figure 4-2, the two curves are equal in four positions at 0.5 threshold criterion cut-
off; therefore there are solutions at four positions. According to literature, the FRC curve
approaches unity and decays to zero (Banterle et al., 2013), before it approaches zero it cuts-off
the threshold curve. That is where the spatial resolution result is recorded. For this case where
there are four possible solutions, the results for the spatial resolution was recorded at position A
in Figure 4-2 because it is where the two curves are equal after the FRC curve approached unity.
The spatial resolution at position A is approximately 0.16 spatial frequency, nm-1. FRC is measured
in nanometres (nm) or angstrom (Å). Here the FRC curve do not decay to zero as expected, instead
it floats. This is because of unfiltered noise in the input images. Images were not filtered because

50
the integrity of the spatial resolution was to be lost as filtering may alter the spatial resolution of
images.

4.3 Modulation Transfer Function

The FRC spatial resolution results were compared with the MTF or SFR, this was because the
MTF method is the established metric to characterise spatial resolution performance in
radiography system especially the X-ray radiography community and is used as a standard method
to evaluating the spatial resolution.

The MTF/SFR curve, Figure 4-3 was obtained from the sfrmat MATLAB Function. This curve
can also be attained using the LSF output by Fourier transforming the output to get the MTF curve.

Figure 4-3: MTF/SFR curve with the threshold curve to determine the spatial resolution.

The SFR and frequency curve in Figure 4-3: was obtained from running an sfrmat MATLAB
function. The SFR curve is expected to approach zero and float on the x-axis but never to touch it.
The SFR decaying to zero at 0.5 frequency (half-sampling), would yield good image resolution;
as the higher the MTF/SFR value the better the spatial resolution. The FRC results were compared
with the MTF/SFR method to evaluate the spatial resolution in digital neutron radiography. In
51
Figure 4-3 the MTF/SFR curve decays to zero approximately at 0.085 frequency, cy/pixel because
of the unfiltered noise on the images used. In Figure 4-3 the spatial resolution solution is observed
approximately at 0.085 frequency, cy/pixel at 10% threshold and 17% sampling efficiency.

Sampling efficiency is determined by the limiting resolution (also known as spatial resolution) and
the sampling resolution. A limiting resolution is the cut-off between the MTF/SFR and the
frequency (measured in cy/mm or cy/pixel), meaning where the two curves intersect. The sampling
resolution is defined by the half-sampling frequency. Half-sampling frequency is the halfway of
the frequency on an x-axis plane. It is measured in cy/pixel. Sampling efficiency is defined
mathematically as in Eq.25.

𝐥𝐢𝐦𝐢𝐭𝐢𝐧𝐠 𝐫𝐞𝐬𝐨𝐥𝐮𝐭𝐢𝐨𝐧
𝐄𝐕 = 𝐬𝐚𝐦𝐩𝐥𝐢𝐧𝐠 𝐫𝐞𝐬𝐨𝐥𝐮𝐭𝐢𝐨𝐧 Eq.25

where EV , is the sampling efficiency measured in percentage. Sampling efficiency is the results of
sampling frequency (number of pixels per spatial unit) which estimates the good or bad of image
quality and differentiating between a sharp and blurred image. An image with a good resolution
has a sampling efficiency of 80% and above (Burns and Williams, 2008).

4.4 Comparisons of the FRC method with the standard method (MTF/SFR)

In Figure 4-2 the spatial resolution for FRC is observed to be approximately at 0.16 spatial
frequency, nm-1. And the spatial resolution in figure 4-3 is observed at 0.085 frequency, cy/pixel.
The spatial resolution from FRC is twice the one from the MTF/SFR at ODD of approximately 0
mm.

Using Eq.25 to calculate the limiting resolution of MTF/SFR curve at approximately 0 mm ODD
yields

𝑙𝑖𝑚𝑖𝑡𝑖𝑛𝑔 𝑟𝑒𝑠𝑜𝑙𝑢𝑡𝑖𝑜𝑛 = EV × 𝑠𝑎𝑚𝑝𝑙𝑖𝑛𝑔 𝑟𝑒𝑠𝑜𝑙𝑢𝑡𝑖𝑜𝑛

𝑙𝑖𝑚𝑖𝑡𝑖𝑛𝑔 𝑟𝑒𝑠𝑜𝑙𝑢𝑡𝑖𝑜𝑛 = 0.17 × 0.5

𝑙𝑖𝑚𝑖𝑡𝑖𝑛𝑔 𝑟𝑒𝑠𝑜𝑙𝑢𝑡𝑖𝑜𝑛 = 0.085

52
4.4.1 FRC and MTF/SFR comparisons at different object-detector-distance.

The same test object of gadolinium knife edge was imaged at different ODDs. The results are
graphically presented. Different ODDs measured in millimetres at 12, 32 and 104. The results for
the spatial resolution on Figure 4-4, figure 4-5, Figure 4-6, figure 4-7, Figure 4-8 and figure 4-9
are presented.

Figure 4-4: FRC curve at 12 mm ODD.

53
Figure 4-5: MTF/SFR curve at 12 mm ODD.

𝑙𝑖𝑚𝑖𝑡𝑖𝑛𝑔 𝑟𝑒𝑠𝑜𝑙𝑢𝑡𝑖𝑜𝑛 = EV × 𝑠𝑎𝑚𝑝𝑙𝑖𝑛𝑔 𝑟𝑒𝑠𝑜𝑙𝑢𝑡𝑖𝑜𝑛

𝑙𝑖𝑚𝑖𝑡𝑖𝑛𝑔 𝑟𝑒𝑠𝑜𝑙𝑢𝑡𝑖𝑜𝑛 = 0.56 × 0.5

𝑙𝑖𝑚𝑖𝑡𝑖𝑛𝑔 𝑟𝑒𝑠𝑜𝑙𝑢𝑡𝑖𝑜𝑛 = 0.28

54
Figure 4-6: FRC curve at 32 mm ODD.

Figure 4-7: MTF/SFR curve at 32 mm ODD.

The spatial resolution on figure 4-6 is observed at approximately 0.25 nm-1

𝑙𝑖𝑚𝑖𝑡𝑖𝑛𝑔 𝑟𝑒𝑠𝑜𝑙𝑢𝑡𝑖𝑜𝑛 = EV × 𝑠𝑎𝑚𝑝𝑙𝑖𝑛𝑔 𝑟𝑒𝑠𝑜𝑙𝑢𝑡𝑖𝑜𝑛

𝑙𝑖𝑚𝑖𝑡𝑖𝑛𝑔 𝑟𝑒𝑠𝑜𝑙𝑢𝑡𝑖𝑜𝑛 = 0.54 × 0.5

𝑙𝑖𝑚𝑖𝑡𝑖𝑛𝑔 𝑟𝑒𝑠𝑜𝑙𝑢𝑡𝑖𝑜𝑛 = 0.27

55
Figure 4-8: FRC curve at 104 mm ODD.

Figure 4-9: MTF/SFR curve at 104 mm ODD

56
The spatial resolution for sampling efficiency of 30% at 104 mm ODD is calculated as,

𝑙𝑖𝑚𝑖𝑡𝑖𝑛𝑔 𝑟𝑒𝑠𝑜𝑙𝑢𝑡𝑖𝑜𝑛 = EV × 𝑠𝑎𝑚𝑝𝑙𝑖𝑛𝑔 𝑟𝑒𝑠𝑜𝑙𝑢𝑡𝑖𝑜𝑛

𝑙𝑖𝑚𝑖𝑡𝑖𝑛𝑔 𝑟𝑒𝑠𝑜𝑙𝑢𝑡𝑖𝑜𝑛 = 0.30 × 0.5

𝑙𝑖𝑚𝑖𝑡𝑖𝑛𝑔 𝑟𝑒𝑠𝑜𝑙𝑢𝑡𝑖𝑜𝑛 = 0.15

Table 4-1 summarizes the results of spatial resolution measured using two methods compared at
different ODD. The MTF/SFR curves with x-axis measurements are for frequency in cy/pixel.
Burns et.al, 2008, explains that MTF/SFR is a function of spatial frequency and that spatial
frequency when expressed in pixel, 1 cy/mm is 0.5 cy/pixel. FRC as a function of spatial frequency
and measured in nm-1. Comparing two measurements, cy/mm with nm-1. Both methods are
function of frequency. This shows that the spatial resolution of an FRC can be compared with that
of MTF/SFR.

Table 4-1: Summary of FRC and MTF/SFR results at different ODD

ODD (mm) FRC MTF/SFR % difference

0.0 0.16 0.085 88.24
12 0.29 0.28 3.57
32 0.26 0.27 3.70
104 0.19 0.15 26.67

The percentage difference is made on the ratio of FRC vs MTF/SFR using Eq.26;

𝑭𝑹𝑪
((𝑴𝑻𝑭/𝑺𝑭𝑹) − 𝟏) × 𝟏𝟎𝟎% Eq.26

57
CHAPTER 5: Conclusion and recommendation

5.1 Conclusion

In this study the scope to characterize spatial resolution using the adapted method from cryo-
electron microscopy, FRC was evaluated using digital neutron radiographs. The method was
evaluated on digital neutron radiographs obtained at NUETRA facility, PSI at different ODDs.

Determining the spatial resolution of neutron radiographs was achieved using FRC mathematical
algorithm on the FRC MATLAB script (Vila-Comamala et al., 2011). MATLAB was a very useful
tool to find the spatial resolution of an image, it was used to compute both results for FRC and
MTF/SFR. MTF/SFR was applied on the images obtained at different ODDs to evaluate the spatial
resolution. The methods (FRC and MTF/SFR) were compared to find the spatial resolution. It
showed that the spatial resolution at 0 mm ODD was twice than expected, whereas at 12 mm, 32
mm and 104 mm ODDs yielded approximately the same results.

The spatial resolution values obtained at different ODDs were compared using the percentage
difference shows that the two methods are comparable even though the 0 mm ODD spatial
resolution was not as expected. The highest percentage difference calculated was 88.24%, this is
the spatial resolution difference at approximately 0 mm ODD. From this it can be concluded that
imaging the test object closer to the detector is not ideal. Even though the FRC curves do not decay
to zero as expected from the literature and as the MTF curves, this comparisons shows that the
FRC method can be adapted to assess and evaluate the spatial resolution in digital neutron
radiography. The FRC curves do not decay to zero as expected because of the unfiltered noise in
the images as SNR was not evaluated when analysing the images. Reason for not evaluating the
SNR was the limitation of the FRC MATLAB function.

5.2 Recommendation

For future work the study needs to look at apodization method to filter out the noise on the original
images before analysis. The SNR needs to be evaluated in order for the FRC curves to decay to
zero. Different filtering methods also need to be assessed to determine which one is best suited to
determine the spatial resolution in digital neutron radiography. It is recommended that FRC

58
method to be applied with filtering before it can be adapted to be used in digital neutron
radiography to determine the spatial resolution. The current edge analysis of the MTF/SFR is
complex and sensitive in terms of finding the best edge angle.

59
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