Bioimaging Systems

Dr. Zeyad Qasim Habeeb

Bioimaging Systems

• Image Processing

• Computer Vision

• Machine Learning

• Medical imaging
modalities
Motivation

Imaging sciences is experiencing a rapid growth

in the world. Some organizations recently ranked
biomedical jobs as the number one fastest
growing career field and listed bio-medical
imaging as the primary reason for the growth.
 This course will mostly focus on analysis of
biomedical images and Bioimaging Modalities,
and imaging part will be briefly taught
Syllabus
 Basics of Radiological Image Modalities and
their clinical use (MRI, PET, CT, fMRI, DTI, …)
Medical Image Registration
Medical Image Segmentation
Medical Image Visualization
Machine Learning in Medical Imaging
Shape Modeling/Analysis of Medical Images
Optional Reading List
 Visual Computing for Medicine: Theory,
Algorithms, and Applications. B. Preim, C. Botha.
Morgan Kaufmann, 2013.
 Medical Image Registration. J. Hajnal, D. Hill, D.
Hawkes (eds). CRC Press, 2001.
Medical Imaging Signals and Systems, by Jerry
Prince & Jonathan Links, Publisher: Prentice Hall
Biomedical Images
 (Bio)medical images are different from other
pictures
 They describe the various physical features measured from the
human body (or animal).

Analysis of biomedical images Focuses on:

 Automatic detection of tumors, characterizing their types
 Measurement of normal/abnormal structures
 Visualization of anatomy, surgery guidance, therapy
planning
 Exploring relationship between clinical, genomic, and
imaging based markers
Medical Image Formats
Dicom
Nifti
Analyze (img/hdr)
Raw data
…
DICOM (the mostly used)
 Digital Imaging and Communications in Medicine
standard
 Since its first publication in 1993, DICOM has
revolutionized the practice of radiology, allowing
the replacement of X-ray film with a fully digital
workflow.
 It is the international standard for medical images
and related information (ISO 12052)
 It is implemented in almost every radiology imaging,
and radiotherapy device (X-ray, CT, MRI, ultrasound,
etc.), and increasingly in devices in other medical
domains such as dentistry.
Medical Imaging
The most direct way to see inside the human (or
animal) body is cut it open (i.e., surgery)
We can see inside the human body in ways that
are less invasive or (completely non-invasive)
We can even see functional activities which are
not visible to naked eye
Medical Image Analysis
Because of the rapid technical advances in
medical imaging technology and the
introduction of new clinical applications,
medical image analysis has become a highly
active research field.
Improvements in image quality, changing
clinical requirements, advances in computer
hardware, and algorithmic progress in medical
image processing all have a direct impact on
the state of the art in medical image analysis.
Medical Image Analysis
Medical images are often multidimensional (2D,
3D, 4D,nD), have a large dynamic range, are
produced on different imaging modalities in the
hospital, and make high demands upon the
software for visualization and human–computer
interaction.
A high resolution MR image of the brain, for
instance, may consist of more than 200 slices of
512 x 512 pixels each, i.e., more than 50 million
voxels in total. (100MB)
Medical Image Analysis-Manual
Often accepted as replacement of the truth (if
biopsy or real ground truth is not available)
However, manual analysis is highly subjective
because it relies on the observer’s perception.
It is highly slow
Medical Image Analysis
Medical Image Analysis-Automated
Different strategies for image analysis exist.
However, few of them are suited for medical
applications
The reason is that both the medical image data
and the model or prototype (i.e., the a priori
description of the features to be analyzed), are
typically quite complex.
Brief Introduction to Imaging Modalities
Bioimaging Modalities
X-ray
Ultrasound
Computed Tomography (CT)
Magnetic Resonance Imaging (MRI)
Positron Emission Tomography (PET)
Diffusion Weighted Imaging (DWI)
Diffusion Tensor Imaging (DTI)
Magnetic Particle Imaging (MPI)
Optical Coherence Tomography (OCT)
Brief Introduction to Imaging Modalities
X-Ray Imaging / Radiography
X-Ray Imaging / Radiography
X-Ray Imaging / Sensitometric Curve
Basics Use of X-Rays
Clinical Examples – X-Rays
How Radiologists Search Abnormal Patterns
in Chest X-Rays?
Ultrasound Imaging
US is defined as any sound wave above 20KHz
In 1794, First to study US physics by deducing
bats used to US to navigate

Ultrasound Imaging
Principle of US Imaging
Features of US Imaging
Clinical Use of US Imaging
Clinical Use of US Imaging
Computed Tomography (CT)

 A computerized tomography (CT) scan combines a

series of X-ray images taken from different angles
around your body and uses computer processing to
create cross-sectional images (slices) of the bones,
blood vessels and soft tissues inside your body.
 CT scan images provide more-detailed information than
plain X-rays
Computed Tomography (CT)

Computed Tomography (CT)

3D Nature of CT

3D Nature of CT

3D Nature of CT

Clinical Use of CT Imaging
Standard imaging technique in many organs,
particularly gold standard for lung imaging
Fast
Radiation exposure
Often used in surgery rooms
Show anatomy

Magnetic Resonance Imaging (MRI)

How the MRI Works(1)
Magnetic resonance imaging (MRI) uses a large
magnet and radio waves to look at organs and
structures inside your body.
Health care professionals use MRI scans to
diagnose a variety of conditions, from torn
ligaments to tumors.
MRIs are very useful for examining the brain and
spinal cord
How the MRI Works(2)

MRIs employ powerful magnets which produce

a strong magnetic field that forces protons in
the body to align with that field.
When a radiofrequency current is then pulsed
through the patient, the protons are stimulated,
and spin out of balance, straining against the
pull of the magnetic field.
How the MRI Works(3)
 When the radiofrequency field is turned off, the
MRI sensors are able to detect the energy released
as the protons realign with the magnetic field.
 The time it takes for the protons to realign with the
magnetic field, as well as the amount of energy
released, changes depending on the environment
and the chemical nature of the organs.
 Physicians are able to tell the difference between
various types of tissues based on these magnetic
properties.
Magnetic Resonance Imaging (MRI)

MRI Basics
Repetition Time (TR) is the amount of time
between successive pulse sequences applied to
the same slice.
Time to Echo (TE) is the time between the
delivery of the RF pulse and the receipt of the
echo signal.
Types of MRI

Safety in MRI

Diffusion Tensor Imaging (DTI)
Diffusion tensor imaging (DTI) is a magnetic
resonance imaging technique that enables the
measurement of the restricted diffusion of water
in tissue
MRI (sub-)modality
useful for tumor characterization (densely
cellular tissues exhibit lower diffusion).
Diffusion Tensor Imaging (DTI)
Diffusion Weighted Imaging (DWI)
Diffusion Weighted Imaging (DWI)
 It is a form of MR imaging.
 DWI is the use of specific MRI sequences as well as
software that generates images from the resulting
data that uses the diffusion of water molecules to
generate contrast in MR images
 A special kind of DWI, diffusion tensor imaging (DTI),
has been used extensively to map (white matter
tractography) in the brain.
 White matter refers to areas of the central nervous
system (CNS)
 tractography is a 3D modeling technique used to
visually represent nerve tracts using data collected
by diffusion MRI
DTI and DWI
Diffusion-weighted and diffusion tensor imaging
(DWI/DTI) has revolutionized clinical
neuroimaging.
Pathology may be detected earlier and with
greater specificity than with conventional
magnetic resonance imaging sequences.
In addition, DWI/DTI allows exploring the
microarchitecture of the brain.
Functional MRI (fMRI)
measures brain activity through oxygen
concentration in the blood flow.
when area of the brain is active (in use), blood
flow to that area also increases
which part/location of the brain is activated
when reading?
which part/location of the brain is activated
when listening music?
which part/location of the brain is activated
when searching puzzle?
Functional MRI (fMRI)
Nuclear Medicine Imaging – PET/SPECT
Nuclear medicine imaging is a method of
producing images by detecting radiation from
different parts of the body after a radioactive
tracer is given to the patient
it records radiation emitting from within the body
rather than radiation that is generated by
external sources like X-rays.
In nuclear medicine imaging, radioactive
compound are taken internally, for example,
intravenously or orally. Then, external detectors
capture and form images from the radiation
emitted by the radioactive compound.
Nuclear Medicine Imaging – PET/SPECT
 Nuclear medicine scans differ from radiology,
as the emphasis is not on imaging anatomy, but
on the function
PET: Positron Emission Tomography
SPECT: Single Photon Emission Tomography
Positron Emission Tomography (PET)
 Late 1950s, David L. concept of emission and
transmission molecular activity is measured.
Positron emission tomography (PET) is a
functional imaging technique that uses
radioactive substances known as (radiotracers
)to visualize and measure changes in blood
flow, regional chemical composition, and
absorption
Basics of PET Imaging
PET uses short-lived positron emitting isotopes
PET scanners can incorporate a CT scanner and
are known as PET-CT scanners
What to Measure in PET?
Metabolic lesion/tumor volume (MTV)
Shape information of lesion
Texture information of lesion (heterogeneous vs
homogeneous)
Number and distribution of the lesions (focal,
multi-focal)
Basics of PET Imaging
Single Photon Emission Tomography(SPECT)
Positron emission tomography (PET):
 is very expensive
 uses positron emitting radioisotope (tracer)
 fluorine-18
 gives better contrast and spatial resolution (cf. SPECT)

Single-photon emission computed tomography (SPECT):

 is lower cost
 uses gamma emitting radioisotope (tracer):
 technetium-99m
 iodine-123
 iodine-131
 gives poorer contrast and spatial resolution (cf. PET)
Single Photon Emission Tomography(SPECT)
The main difference between SPECT and PET scans
is the type of radiotracers used.
While SPECT scans measure gamma rays, the
decay of the radiotracers used with PET scans
produce small particles called positrons.
 A positron is a particle with roughly the same mass
as an electron but oppositely charged.
PET/CT and MRI/PET (Hybrid Imaging)
MRI/PET
positron emission tomography–magnetic resonance
imaging (PET–MRI) is a hybrid imaging technology
that incorporates magnetic resonance imaging (MRI)
soft tissue morphological imaging and positron
emission tomography (PET) functional imaging.
The combination of PET and MRI was mentioned in
a 1991 Phd thesis by R. Raylma
PET/MR detection was first demonstrated in 1997,
however it took another 13 years, and new detector
technologies, for clinical systems to become
commercially available.
MRI/PET
Several companies offer clinical and pre-clinical
combined PET-MR system, clinical systems are
available from Philips, Siemens, GE.
There are varying approaches to the combination of
the two technologies. Some designs are essentially
separate machines, in the same room, with a bed
that can transfer a patient from one scanner to
another.
Fully integrated systems are the most technically
challenging to achieve, but provide greatest benefits
in terms of the ability to make simultaneous, exactly
aligned, acquisitions
Serial and Simultaneous MRI/PET
PET/CT
Positron emission tomography–computed
tomography (better known as PET-CT or PET/CT)
is a nuclear medicine technique which
combines, in a single gantry, a positron emission
tomography (PET) scanner and an x-ray
computed tomography (CT) scanner
It acquires sequential images from both devices
in the same session, which are combined into a
single image
PET/CT
PET-CT has revolutionized medical diagnosis in
many fields.
For example, many diagnostic imaging
procedures in surgical planning, radiation
therapy and cancer staging have been
changing rapidly under the influence of PET-CT
availability, and centers have been gradually
abandoning conventional PET devices and
substituting them by PET-CTs.
Although the combined/hybrid device is
considerably more expensive
PET/CT
The combination of PET and CT scanners was first
suggested by R. Raylman in his 1991 Ph.D thesis
The first commercial system reached the market by
2001, and by 2004, over 400 systems had been
installed worldwide
 takes from 5 minutes to 40 minutes depending on
the acquisition protocol and technology of the
equipment used
Basics of PET PET-CT Imaging
Comparison of Imaging Methods

Chest Abdomen Head/Neck Cardiovascular Skeletal

Need
gold contrast for Good for Gold Gold
CT
standard excellency, trauma standard standard
widely used

no use Problems
US except heart Poor Poor Elastography
with gas

Extensive
use in heart CT or MRI is Perfusion(the
Nuclear PET bone marrow
and therapy merged passage of blood)
in lung

Will replace
growing Increased Gold
MRI CT in near Excellent
role of MRI standard
future
Thanks