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Chapter 2: Mathematical PreliminariesIterative Reconstruction Methods
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Contents
• Reconstruction and general linear inverse problems
• Statistical description of the data
• Image reconstruction criteria
• General structure of iterative reconstruction methods
• Maximum Likelihood Expectation Maximization (MLEM)algorithm
• Other related reconstruction methods
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
The inverse problem:
?
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019 Signals and Systems
General Inverse Problem and Image Reconstruction
• Given a set of measured output signal
• Given a known system response function
• Given the statistical description of the data
what should be the input signal that gave rise to the output data?
Projection Data from Early X-ray CT Systems
From Computed Tomography, Kalender, 2000.
b
a
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dttIIeII
b
a )()/ln( 0
)(
0
:object the through passing
after beam the of intensity The
Data measured bytranslating the detector is atypical projection data.
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019 Signals and Systems
Radon Transform
×
x’
2-D integral
The value of the projection function p(x’)at this point is the integral of the functionof f(x,y) along the straight line:x’=xcos+ysin
dxdyxyxyxfxp )sincos(),(),(
The integral of a line impulse function and a given 2-D signal gives theprojection data from a given view …
Central Slice Theorem
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
http://engineering.dartmouth.edu/courses/engs167/12%20Image%20reconstruction.pdf
The nature of the 1/r blurring:Radon transform produced equally spaced radial sampling in Fourier domain.
Simple Back-projection and the 1/r Blurring
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Simple Back Projection from Projection Data
Projection data p(, x’)
y
xr x’
IncidentX-rays
f(x,y)
Detected p(, x’)
R
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
dxdyxyxyxf
xp
)sincos(),(
),(
Simple Back Projection from Projection Data
From Medical Physics and Biomedical Engineering, Brown, IoP Publishing
Simple Back-projection and the 1/r Blurring
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Simple Backprojection and Inverse Radon Transform
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Crude Idea 1: Take each projection and smear it back along the lines of integration it was calculated over.
Result from a back projection from a single view angle:
b (x,y) = ∫ p (x’) (x cos + y sin - x’) dx’
Adding up all the back projections from all the angles gives,
fback-projection (x,y) = ∫ b (x,y) d
𝒇^
𝑥, 𝑦 𝑑𝜙 𝐹 𝐹 𝑝 𝑥′ 𝑤 𝛿 𝑥cos𝜙 𝑦sin𝜙 𝑥′ 𝑑𝑥′
𝒇^ 𝑥, 𝑦 𝑑𝜙 𝑝 𝑥′ 𝛿 𝑥cos𝜙 𝑦sin𝜙 𝑥′ 𝑑𝑥′
Review of Fourier Transform and Filtering Spectral Filtering
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Review of Fourier Transform and Filtering Spectral Filtering
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Filtered Back-projection
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Filtered Back-Projection
Sampled version
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Simple Backprojection, Inverse Radon Transform and Filtered Backprojection (FBP)
Result from a back projection from a single view angle:
b (x,y) = ∫ p (x’) (x cos + y sin - x’) dx’
Adding up all the back projections from all the angles gives,
fback-projection (x,y) = ∫ b (x,y) d
𝒇^
𝑥, 𝑦 𝑑𝜙 𝐹 𝐹 𝑝 𝑥′ 𝑤 𝛿 𝑥cos𝜙 𝑦sin𝜙 𝑥′ 𝑑𝑥′
𝒇^ 𝑥, 𝑦 𝑑𝜙 𝑝 𝑥′ 𝛿 𝑥cos𝜙 𝑦sin𝜙 𝑥′ 𝑑𝑥′
𝒇^
𝑥, 𝑦 𝑑𝜙 𝐹 𝐹 𝑝 𝑥′ 𝐻 𝑤 𝛿 𝑥cos𝜙 𝑦sin𝜙 𝑥′ 𝑑𝑥′
As a matter of fact, FBP provides almost optimum image quality with goodquality projection data, but performs poorly when the projection datacontains significant noise.
Why?
Are we missing something in the design of the FBP or BPF methods?
Review of 2-D Analytical Reconstruction MethodsFiltered Back Projection
Problems of FBP:
Review of 2-D Analytical Reconstruction MethodsFiltered Back Projection
Based on somewhat idealistic geometry …
Lack of an accurate statistical description of the projection data …
Limitation of incorporating other physical effects associated with certainimaging modalities …
Imaging systems in real world have all kinds of imperfection …
What is the Central Problem to be Solved with Statistical Imaging Reconstruction Methods?
50 000 counts 100 000 counts 200 000 counts
500 000 counts 1 million counts 2 million counts
4.8mm 6.4mm
11.1mm
12.7 mm
The Importance of Counts
7.9 mm
9.5mm
Noise In PET Images Noise in PET images is dominated by the counting statistics of the
coincidence events detected. Noise can be reduced at the cost of image resolution by using an
apodizing window on ramp filter in image reconstruction (FBP algorithm).
105 106 107 counts
Unapodized ramp filter
Hanning window, 4mm
Hanning window, 8mm
Scatteredcoincidences component
Attenuation
Random coincidencescomponent
Detector efficiencyeffects True
coincidencescomponent
An Example of PET Image Reconstruction Data corrections are necessary
the measured projections are not the same as the projections assumed during image reconstruction
Object(uniformcylinder)
projectionmeasured
projectionassumed
integral of the activity along the line or tube of response
An Example of PET Image Reconstruction
Figure 3: Comparison of EM reconstruction with FBP for different total counts. Note particular the streaking and noise appearance at low counts using FBP. Figures indicate the noise (standard deviation / mean) for a region in the liver.
http://web.uchile.cl/vignette/borrar3/alasbimn/CDA/sec_a/0,1205,SCID%253D470%2526PRT%253D455%2526LNID%253D10,00.html
Comparison of emission images when real clinical data were used: (a) FBP method; (b) ML‐EM method; (c) MAP method; (d) TV‐MAP method; (e) MC‐MAP method; and (f) GC‐MAP method.
Fig. 5. Enlargement part of the reconstructed images. Projections with 1× 106 counts Poisson noise. The iterative number is set to 40 for all algorithms: (a) synthetic phantom; (b) FBP; (c) ML‐EM; (d) MAP; (e) TV‐MAP; (f) MC‐MAP; and (g) GC‐MAP.
Analytical Methods
Advantages Fast Simple Predictable, linear behaviour
DisadvantagesNot very flexible Image formation process is not modelled image properties
are sub-optimal (noise, resolution)
Statistical Methods Advantages
Can accurately model the image formation process (use with non-standard geometries, e.g. not all angles measured, gaps)
Allow use of constraints and a priori information (non-negativity, boundaries)
Corrections can be included in the reconstruction process (attenuation, scatter, etc)
Disadvantages Slow Less predictive behaviour (noise? convergence?)
The solution:
Review of 2-D Analytical Reconstruction MethodsFiltered Back Projection
Put what ever we know about the system into the model.
Try to model the projection data with better accuracy.
Using iterative optimization methods to get around the numericalstability problem in large scale inverse (reconstruction) problem.
A basic problem for image reconstruction in emission tomography
Image Reconstruction and General Linear Inverse Problem
An Emission Tomography System
Image Reconstruction and General Linear Inverse Problem
How Do We Describe the Problem?
Linear imaging systems – An alternative representation
Image Reconstruction and General Linear Inverse Problem
_
How Do We Solve the Problem?
The Statistical Approach
The Basic Idea of Statistical Reconstruction
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
The likelihood function:
In very non-technical terms, the probability of the underlyingsource function that results in the measurement.
The basic idea of statistical reconstruction is simple:
We chose the solution (estimated source function) thatmaximizes the likelihood function, or
The solution that is the most likely to produce the measureddata.
The Basic Idea of Statistical Reconstruction
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
An simple example: estimate the source strength from the measured count rate
The answer? -- pick the source intensity that is most likely to give the observedcount rate.
What do we need to know? -- (a) The probability of a photon reaching thedetector surface (assuming 100% detection) and (b) how reliable is themeasurement (the statistical fluctuation of the counts measured)
Two Key Challenges
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Evaluating the likelihood. What is the likelihood of a givensource function that produces the measured data?
Finding the maximum likelihood solution. There are oftenan infinite number of possible source functions to chose from,each is associated with a likelihood (or a probability). How dowe search through the source space to decide which one givesthe maximum likelihood?
Source of Noise
Source of noise:
Measurement error, instrument malfunction …
Random fluctuation in the number of counts detected by detectors
Other additive noise
In emission tomography systems, detector readout noise is generally muchsmaller than the statistical fluctuation associated with the counting process.
Noise introduced by other physical effects. The general frame work ofiterative (or some-times called statistical) reconstruction methods allows oneto incorporate many other effects …
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Chapter 2: Mathematical Preliminaries
Bernoulli ProcessConsider the radioactive disintegration process in a sample, it follows the followingfour conditions:
It consists of N trails.
Each trail has a binary outcome: success or failure (decay or not).
The probability of success (decay) is a constant from trail to trail – all atoms haveequal probability to decay.
The trails are independent.
In statistics, these four conditions characterize a Bernoulli process.
Binomial Distribution
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
The binomial distribution gives the discrete probability distribution ofobtaining exactly k successes out of N Bernoulli trials (where the result ofeach Bernoulli trial is true with probability p and false with probability 1-p ).The binomial distribution is therefore given by
)!(!!
)1(),(
kNkN
kNwhere
ppkN
pNkp kNk
Binomial Distribution and Imaging Applications
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Suppose we have a point source generated N gamma rays and we have apixilated detector for detecting these photons
kNk ppkN
pNkp
)1(),(
Each gamma ray photon has a fixed probability p of reaching a givendetector element. p is defined by the relative distance between the sourceand the pixel and the collimation configuration used.
So the probability of detecting k gamma rays on the pixel is given as
Furthermore, the number of counts detected on different pixels areindependent …
Chapter 6: Counting Statistics
Binomial Distribution
What are the mean and standard deviation of a Binomial distribution?
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Chapter 2: Mathematical Preliminaries
Binomial Distribution
NpqPn
and
NpqPn
N
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For a binomial distribution, the mean or the expectation of the number ofdisintegration in time t is given by
and the fluctuation on the number of disintegrations is given by the variance or thestandard deviation of the
NpqpnN
nPnN
n
nNnN
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NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Chapter 2: Mathematical Preliminaries
Binomial Distribution
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Considering a realistic case, in which we use an detector to measure the number ofcounts and use the measured count rate to infer to the activity of the source.
Given (a) each disintegration yield one single particle and (b) the detection efficiency ofthe detector is , then
The prob. of detecting a count within a time t is
Therefore, we can use the binomial distribution to describe the counting statistics as
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Chapter 2: Mathematical Preliminaries
Binomial Distribution
The prob. of detecting n count within a time t is
The mean number of detected counts is
detector theof efficiencydetection : t timea within atesdisintergr atoman of prob. :
1*
p
ppnN
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and the variance on number of detected counts is
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Chapter 2: Mathematical Preliminaries
Bernoulli ProcessConsider the radioactive disintegration process in a sample, it follows the followingfour conditions:
It consists of N trails.
Each trail has a binary outcome: success or failure (decay or not).
The probability of success (decay) is a constant from trail to trail – all atoms haveequal probability to decay.
The trails are independent.
In statistics, these four conditions characterize a Bernoulli process.
Poisson Distribution
The counting statistics related to nuclear decay processes is often more conveniently described by the Poisson distribution, is related to situations that involves a collection of multiple trails that satisfy the following conditions:
1. The number of trails, N, is very large, e.g. N>>1.2. Each trail is independent.3. The probability that each single trail is successful is a constant and approaching
zero, p<<1. So the number of successful trails is fluctuating around a finite number.
Poisson DistributionThe probability of having n successful trails can be approximated with the Poisson distribution.
en
nPn
!|
NpnStd )(
pNnMean )(
and the mean and the variance of number of successful trail are given by
NPRE 441, Principles of Radiation Protection, Spring 2016
Chapter 6: Counting Statistics
Poisson Distribution
Remember the conditions for Binomial distribution to be approximated by PoissonDistribution:
1. The number of trials, N, is very large, e.g. N>>1.
2. Each trial is independent.
3. The probability that each single trial is successful is a constant and approachingzero, p<<1. So the number of successful trials is fluctuating around a finitenumber.
Binomial and Poisson Random Variable
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
When N and p0, k follows the Poisson distribution, whose probabilityfunction is
Np
ek
kpppkN
pNkp
N
kkNk
lim as defined ariablePoission v theof valueexpected theis where
!)( )1(),(
Other examples of Poisson variables:The number of phone calls received by a telephone operator in a 10-minuteperiod.
Binomial
distribution
Poisson
distribution
The number of flaws in a bolt of fabric.
The number of typos per page.
The Basic Idea of Statistical Reconstruction
An Emission Tomography System
Image Reconstruction and General Linear Inverse Problem
An Emission Tomography System
Image Reconstruction and General Linear Inverse Problem
Image Reconstruction CriteriaMaximum Likelihood (ML)
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Suppose that for any given source function f, the probability of observing adata set g is given by a known probability law p(g|f).
p(g|f) is called the Likelihood function, which is sometimes denoted as L(f)or L(f,g).
A typical image reconstruction problem is that we have a set of measured datag, how to determine the original source function f?
The ML criterion:
Chose the source function f that maximize the likelihood function p(g|f).
Image Reconstruction CriteriaMaximum Likelihood (ML)
f̂
ff ˆE
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Properties of images reconstructed with the ML criterion:
• Asymptotically unbiased. If there are sufficiently large number ofcounts in the data g, then
• Asymptotically efficient. If there are sufficiently large number of counts inthe data g, the ML solution has the lowest variance amongst all possiblesolutions.
ggfgff dp )|()(ˆ ˆE
The Maximum Likelihood Reconstruction
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NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Recall that the likelihood function, L(f,g), of a possible source function f is
So that the maximum likelihood solution (the image that maximizing thelikelihood function) can be found as
Poisson Statistics of the Projection Data
m# pixeldetector on counts ofnumber for the valueexpected theis where!
)()()|( 11
m
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NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Measured no. ofcounts on detectorpixel m.
The probability of a given projection data g=(g1, g2, g3,…, gM) is
The Maximum Likelihood Reconstruction
M
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NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
For data that follows Poisson distribution, the likelihood function, L(f,g), ofa possible source function f is
m. pixeldetector on counts ofnumber measured theis
m. pixeldetector on counts ofnumber expected theis ,
!)()|()(
1
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The log-likelihood function is
Linear imaging systems – An alternative representation
Image Reconstruction and General Linear Inverse Problem
_
N
nnmnm pfg
1
An Typical Imaging System Described in Matrix Form
The source object.
The number of photons
being emitted from each
source voxel
Everything we know about the
imaging system – The system
response function
Expected number of
photons detected on each
detector element
NMNMMM
N
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Poisson Statistics of the Projection Data
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NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
N
nnmnm pfg
1Remember that
Measured no. ofcounts on detectorpixel m.
The probability of a given projection data g=(g1, g2, g3,…, gM) is
In the context of emissiontomography, pnm is theprobability of a gamma raygenerated at a source pixel n isdetected by detector element m.
The Maximum Likelihood Reconstruction
M
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!loglog!
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NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
For data that follows Poisson distribution, the likelihood function, L(f,g), ofa possible source function f is
m. pixeldetector on counts ofnumber measured theis
m. pixeldetector on counts ofnumber expected theis ,
!)()|()(
1
11
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The log-likelihood function is
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The Maximum Likelihood Reconstruction
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NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
So the ML reconstruction for Poisson distributed data is
The Maximum Likelihood Expectation Maximization (MLEM) Algorithm
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
The source (image) function f that has the maximum likelihood of giving riseto the observed data g can be found by the following iterative updatingscheme
m pixeldetector in counts ofnumber observed the:melement detector by the detected and
pixel sourcein generatedray gamma a ofy probabilit the: pixel source theof estimate updated the:
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where
1,2,...,Nnpfp
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p
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The Maximum Likelihood Expectation Maximization (MLEM) Algorithm
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Each iteration updates all elements in the source function f sequentially.
1,2,...,Nnpfp
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p
ffM
mnmN
n
oldnmn
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Each iteration is guaranteed to provide a new image function that has anincreased likelihood compared to the previous image function (unless themaximum likelihood solution has been achieved).
Structure of MLEM Algorithm
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
M
mnmN
n
oldnmn
mM
mnm
oldnnew
n pfp
g
p
ff1
1
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1
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Properties of MLEM Algorithm
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Advantages
• Relatively simple but highly useful.
• Provides room for incorporating a wide range of physical effects anddetector system characteristics and therefore provide an improvedimage quality for low statistics data.
• Consistent and predictable behavior.
• Automatically incorporates non-negativity constraint. So the imagevalues are always non-negative.
• Provides theoretically optimum solution (Please be careful whensaying this!!).
Properties of MLEM Algorithm
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Shortcomings
• Relatively slow convergence. For typical 3-D reconstruction, it takesseveral tens of iterations to converge. In principle, each iteration takessimilar amount of computation to that for a complete FBP reconstruction!
• Tends to yield noisy reconstructions when projection data has lowstatistics.
What exactly is the problem?
The algorithm tends to fit to the noise in the (observed) projection data!
Properties of MLEM Algorithm
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
With noise free data
With noisy data
With noisy data
MLEM and filtering
Properties of MLEM Algorithm
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
How to improve?
Adding extra (or sometime called a priori) information in the reconstructionprocess.
This can be done using two numerically equivalent approaches
• This can be done by trying to discourage possible image solutions that has large fluctuations (noisy images). – Penalized Maximum Likelihood (PML) methods.
• Using the Bayes’ law to incorporate the a priori information – Maximum a posteriori (MAP) methods.
Further Improvements – Penalized ML Algorithms
)()( argmaxˆ fgf,ff
Ul
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
The basic idea:
Instead of finding the original image by maximizing the likelihood function:
We can use a different selection criterion
)( argmax)|(argmaxˆ gf,fgfff
lp
Probability of a measurement ggiven the underlying image f
The so-called log-likelihood
function
The so-called penalty function that
has increased value when an
undesired imaging feature
presents in the solution.
is a scaling constant that controls
“how strong the penalty is for the
presence of a given feature”
So by minimizing, we are selecting an
image by dis-encouraging the undesired
features to be presented in the image.
Penalized Maximum Likelihood (PML) reconstruction …
Further Improvements –Maximum A Posteriori (MAP) Algorithms
)()()()(
gff|g
g|fp
ppp
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
We have to change our mind a little bit … by considering that the image to beestimated is itself an random variable that follows some statistical law p(f).
The Bayis’s law:
Suppose we know something about the
underlying image and we can describe
this knowledge with a statistical law
This leads to the maximum a posteriori (MAP) approach…
And, we know that if the underlying image
is f, the probability of observing a given
measurement g is
The a posteriori probability.
So the underlying image can be best
estimated by maximizing this
probability
Further Improvements –Maximum A Posteriori (MAP) Algorithms
)()( if ff Up
)(log)( log argmax )(
)()(log argmax)(logargmaxˆ
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g|ff
f
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MAPf
PML ppUp
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
The a priori probability of the data. This is
where you can fold in your prior knowledge
about the underlying image … for example, the
image “should” be relatively smooth …
The maximum a posteriori (MAP) approach…
The likelihood function
This is numerically equivalent to PML approach is we recognize that
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
The simplest form of imaging problem:
Isotropic point source, single detector,
How to estimate the source intensity from the measured number of counts/sec?
The answer? -- pick the source intensity that is most likely to give the observedcount rate.
What do we need to know? -- (a) The probability of a photon is detected by theand (b) how reliable is the measurement (the statistical fluctuation of the countingerror)
Summarizing the Key Concepts (1)The Basic Image Reconstruction Problem
Summarizing the Key Concepts (2)
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Many common imaging system can be represented in simple linear systemform.
The model H tells that for a signal (agamma ray) generated in any givenlocation in the object, what is theprobability of this signal being detectedby each detector element
Summarizing the Key Concepts (3)The System Response Function Matrix (H)
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
as defined average), weighted(theoperator n expectatio theis E where
3
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2232221
1131211
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L
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The system response function matrix governs the transform between the underlying image parameters and the measured projection data.
Summarizing the Key Concepts (4)Commonly Used Statistical Models for Projection Data
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Binomial Distribution and Imaging Applications
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Suppose we have a point source generated N gamma rays and we have apixilated detector for detecting these photons
kNk ppkN
pNkp
)1(),(
Each gamma ray photon has a fixed probability p of reaching a givendetector element. p is defined by the relative distance between the sourceand the pixel and the collimation configuration used.
So the probability of detecting k gamma rays on the pixel is given as
Furthermore, the number of counts detected on different pixels areindependent …
Binomial and Poisson Random Variable
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
When N and p0, k follows the Poisson distribution, whose probabilityfunction is
Np
ek
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Binomial and Poisson Random Variable
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!)()(
11
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NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
For an imaging system that contains M detector elements, observing aprojection data that has g=(g1, g2, g3, … gM) counts in each detector elementis
Poisson distribution is normally a good description of the counting statisticsfor an imaging system.
Poisson Statistics of the Projection Data
m# pixeldetector on counts ofnumber for the valueexpected theis where!
)()( 11
m
M
m
g
m
gm
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egggpp m
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NMNMMM
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NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
N
nnmnm pfg
1Remember that
Measured no. ofcounts on detectorpixel m.
The probability of a given projection data g=(g1, g2, g3,…, gM) is
In the context of emissiontomography, pnm is theprobability of a gamma raygenerated at a source pixel n isdetected by detector element m.
Gaussian Statistics of the Projection Data
ek
kpk
!)(
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
For a random variable follows Poisson distribution, whose probabilityfunction is defined as
When is greater than 20, the distribution of k can be approximated as aGaussian distribution, so that
on.distributi theofdeviation standard the: variable theof valueexpected the:
where21)(
2
2
)(21
x
exp
Gaussian Statistics of the Projection Data
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
The probability of observing a particular set of projection data is
constant. scaling a is where
)()( 1
22
21
1
21
1
A
AeeAgppM
m m
mm
m
mmgggM
m
gggM
mm
g
Gaussian statistics is a good approximation for the random counting noise onprojection data when in high count rate imaging situation. For example in X-ray CT case…
This equation holds only when the observed
counts on deferent detector elements are
independent to each other …
Summarizing the Key Concepts (5)Criteria for Estimate the Underlying Image
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
The Maximum Likelihood Reconstruction
)|()( fggf, pL
)(log)(function likelihood-log theis )( where
)( argmax)(logmaxargˆlyequivalentor
)( argmaxˆ
gf,gf,
gf,
gf,gf,f
gf,f
ffML
fML
Lll
lL
L
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Recall that the likelihood function, L(f,g), of a possible source function f is
So that the maximum likelihood solution (the image that maximizing thelikelihood function) can be found as
The Maximum Likelihood Reconstruction
M
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get we, offunction not is since
!loglogmaxarg )(maxargˆ
ffML
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gf,f
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gf,f
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
So the ML reconstruction for Poisson distributed data is
Further Improvements – Penalized ML Algorithms
)()( argmaxˆ fgf,ff
Ul
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
The basic idea:
Instead of finding the original image by maximizing the likelihood function:
We can use a different selection criterion
)( argmax)|(argmaxˆ gf,fgfff
lp
Probability of a measurement ggiven the underlying image f
The so-called log-likelihood
function
The so-called penalty function that
has increased value when an
undesired imaging feature
presents in the solution.
is a scaling constant that controls
“how strong the penalty is for the
presence of a given feature”
So by minimizing, we are selecting an
image by dis-encouraging the undesired
features to be presented in the image.
Penalized Maximum Likelihood (PML) reconstruction …
Further Improvements –Maximum A Posteriori (MAP) Algorithms
)()()()(
gff|g
g|fp
ppp
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
We have to change our mind a little bit … by considering that the image to beestimated is itself an random variable that follows some statistical law p(f).
The Bayis’s law:
Suppose we know something about the
underlying image and we can describe
this knowledge with a statistical law
This leads to the maximum a posteriori (MAP) approach…
And, we know that if the underlying image
is f, the probability of observing a given
measurement g is
The a posteriori probability.
So the underlying image can be best
estimated by maximizing this
probability
Further Improvements –Maximum A Posteriori (MAP) Algorithms
)()( if ff Up
)(log)( log argmax )(
)()(log argmax)(logargmaxˆ
ff|g
gff|g
g|ff
f
ffMAP
ppp
ppp
)(log)( log argmaxˆ)()( log argmaxˆ ff|gfff|gff
MAPf
PML ppUp
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
The a priori probability of the data. This is
where you can fold in your prior knowledge
about the underlying image … for example, the
image “should” be relatively smooth …
The maximum a posteriori (MAP) approach…
The likelihood function
This is numerically equivalent to PML approach is we recognize that
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
1,2,...,Nnpfp
g
p
ffM
mnmN
n
oldnmn
mM
mnm
oldnnew
n
,1
1
)(
1
)()(
The Maximum Likelihood Expectation Maximization (MLEM) Algorithm
Summarizing the Key Concepts (6)
Methods to Estimate the Underlying Image
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
A Final Remark for Reconstruction Methods
So far, we have discussed several reconstruction methods such as FBP,MLEM, PML and MAP.
It should be remember that it is not the reconstruction method that makesthe differences between the resulting images.The keys to a good reconstruction is How well you know your imagingsystem and How faithful is your model to the system.
A Brief Introduction on Matlab Functions Related to Image Processing
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
OverviewGetting Help2D Matrix / Image
• Coordinate system• Display• Storing images
2D FunctionsDiscrete Fourier Transform
• 1D DFT• fftshift• 2D DFT: zero-filling and shifting the image
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Getting Help in Matlab
Online Help
• Help Browser (? In toolbar or >>helpbrowser)
• Help Functions ( >>help functionname )• Matlab website: www.mathworks.com
• Demos
Documentation
• Online as pdf files
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
2D Matrix2D matrix has M rows and N columns
Example• >>m=zeros(400,200);• >>m(1:50,1:100) = 1;
Note:• Index 1 to M, not 0 to M-1• Origin of coordinate system is in upper
left corner• Row index increases from top to bottom• Coordinate system is rotated in respect
to ‘standard’ x-y coordinate system
123
M
1 2 3 N…
…r
c
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Image TypesMedical images are mostly represented asgrayscale images
• Human visual system resolveshighest spatial resolution forgrayscale contrast
• Color is sometimes used tosuperimpose information onanatomical data
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Save Image MatrixMATLAB binary format
• >>save example -> writes out example.mat
Standard image format (bmp,tiff,jpeg,png,hdf,pcx,xwd)
• >>imwrite(m,’example.tif ’,’tif ’)-> writes out example.tif
• Warning: imwrite expects data in range [0…1]• If data range outside this [0…1], use
mat2gray• >>m_2 = mat2gray(m);• >>imwrite(m_2,’example.tif ’,’tif ’)
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Save Figure (incl. labels etc)
Save in Matlab Figure Format: • >File>Save As> in Figure Window
-> writes out example.figStandard image formats
• >File>Export in Figure Window• E.g. jpg, tif, png, eps, …
• Alternatively, use print, e.g.>>print –deps2 example.eps
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Loading 2D Data and Images
Load matrix from MATLAB binary format>>load example (loads example.mat)
Load matrix from standard image format>>m_in = imread(’example.tif ’,’tif ’);
To check on an image: >>imfinfo(’example.tif ’,’tif ’)
Load figure from Matlab Figure Format (*.fig): • >File>Open> ‘example.fig’ in Figure Window
->Check loaded matrices• >>whos
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Some Common Image Formats• TIF (TIFF)
• Very common, compatible, all purpose image format• Allows for lossless compression
• JPEG• Allows for lossy compression (small file size)• Very common for internet
• PNG (portable network graphics)• Good for saving MATLAB images for importing into Microsoft documents such as
Word• Dicom
• THE medical imaging format• Lots of header information (patient name & ID, imaging parameters, exam date,
…) can be stored• Allows for lossy and lossless compression• Matlab function ‘dicomread’, ‘dicomwrite’
• EPS (Encapsulated Postscript)• Graphics format rather than an image format• Great for best quality print results• Large file size
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
2D Functions• Create a matrix that evaluates 2D Gaussian: exp(-
p/2(x2+y2)/s2)• >>ind = [-32:1:31] / 32;• >>[x,y] = meshgrid(ind,-1*ind);• >>z = exp(-pi/2*(x.^2+y.^2)/(.25.^2));• >>imshow(z)• >>colorbar
x’
y’
x
y
64x64 matrix
-1
0
31/32-1
Discrete Fourier Transform in 1-D Revisited
0uu- esfrenquenci negative the toingcorrespond are 1-N..., N/2,nuu0 esfrenquenci positive the toingcorrespond are 1-N/21,...,n
zero) is frenquency (spatialcomponent DC the toingcorrespond 0n
1-1,2,...N,0n ,
c
c
1
0
2
N
k
Nnkj
kn efF
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
The discrete Fourier transform (DFT) is defined as
And the inverse DFT is defined as
1-1,2,...N,0k ,1 1
0
2
N
n
Nnkj
nk eFN
f
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
FT Conventions - 1D1D Fourier Transform
• >>l = z(33,:);• >>L = fft(l);
sample #
10 20 30 40 50 600
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
l
10 20 30 40 50 600
2
4
6
8
10
12
10 20 30 40 50 60-4
-2
0
2
4
sample #
phas
e (L
)ab
s (L
)
1 33 64
u0 fNfN/2
1 33 64
x [Matlab]0 xmax
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
1D FT - fftshift
Use fftshift>>L1 = fft(fftshift(l));
sample #
l
sample #
phas
e (L
1)ab
s (L
1)
1 33 64
0 fNfN/2
1 33 64
0 xmax
10 20 30 40 50 600
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
10 20 30 40 50 600
2
4
6
8
10
12
10 20 30 40 50 60-4
-2
0
2
4
x [Matlab]
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
1D FT - 2xfftshift
Center Fourier Domain: >>L2 = fftshift(fft(fftshift(l)));
phas
e (L
2)ab
s (L
2)10 20 30 40 50 60
0
2
4
6
8
10
12
10 20 30 40 50 60-4
-2
0
2
4
sample #1 33 64
0-fN/2u
(N-1)/N*fN/2
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
fftshift in 2D
Use fftshift for 2D functions >>smiley2 = fftshift(smiley);
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
2D Discrete Fourier Transform
20 40 60
20
40
60
20 40 60
20
40
600
50
100
-2
-1
0
1
2x 10-14
Real (Z) Imag (Z)
• >>Z=fftshift(fft2(fftshift(z)));• >>whos• >>figure• >>imshow(real(Z))• >>imshow(real(Z),[])• >>colorbar
• >>figure• >>imshow(imag(Z),[])• >>colorbar
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
2D DFT - Zero FillingInterpolating Fourier space by zerofilling in image space
• >>z_zf = zeros(256);• >>z_zf(97:160,97:160) = z;• >>Z_ZF = fftshift(fft2(fftshift(z_zf)));• >>figure• >>imshow(abs(Z_ZF),[])• >>colorbar
• >>figure• >>imshow(angle(Z_ZF),[])• >>colorbar
50 100 150 200 250
50
100
150
200
250-3
-2
-1
0
1
2
3
50 100 150 200 250
50
100
150
200
2500
20
40
60
80
100
120
Magnitude (Z_ZF) Phase (Z_ZF)
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
2D DFT - Voxel ShiftsShift image: 5 voxels up and 2 voxels left
• >>z_s = zeros(256);• >>z_s(92:155,95:158) = z;• >>Z_S = fftshift(fft2(fftshift(z_s)));• >>figure• >>imshow(abs(Z_S),[])• >>colorbar
• >>figure• >>imshow(angle(Z_S),[])• >>colorbar
-3
-2
-1
0
1
2
3
50 100 150 200 250
50
100
150
200
250
0
20
40
60
80
100
120
Magnitude (Z_S) Phase (Z_S)
50 100 150 200 250
50
100
150
200
250
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Review of functions …
Input / Output• >>imread• >>imwrite• >>imfinfo
Image Display• >>imshow
Others• >>axis• >>colorbar• >>colormap• >>meshgrid• >>fft, fft2• >>fftshift
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
More useful functions …Image Display
• >>title• >>xlabel, ylabel• >>subimage• >>zoom• >>mesh
Others• >>imresize• >>imrotate• >>imhist• >>conv2• >>radon• >>roipoly
Demos in Image Processing Toolbox• >>help imdemos
Matlab Examples
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Matlab Examples
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Matlab Examples
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Matlab Examples
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019
Matlab Examples
NPRE 435, Principles of Imaging with Ionizing Radiation, Fall 2019