Solving problems in biology and
medicine using engineering methods
and technology (e.g., research, design
and development of biomedical
Image is an Artifact that
reproduce the likeness of
some subjects usually a
Images are pictures!
A picture that represents visual
Used to save visual experiences.
A picture is worth a 1000 words…I
How are non-digital images stored?
Imaging is the process of acquiring images.
Shorthand for image acquisition.
Process of sensing our surroundings and then
representing the measurements that are made in
the form of an image.
Passive imaging – employs energy sources
that are already present in the scene.
Active imaging – involves use of artificial
energy sources to probe our surroundings.
Passive imaging is subject to the limitations of
existing energy sources.
Active imaging is not restrictive in this way
but is invariably a more complicated &
Active imaging predominates in medical field,
where precise control over radiations sources
Active imaging is also an important tool in
DICOM - Digital Imaging and Communications in Medicine
User Consortia (e.g., HL7)
Organizations (e.g., NEMA, IEEE)
US Government Agencies (e.g., ANSI, NIST)
Foreign Government Agencies (e.g., CEN)
United Nations (e.g., ISO, CCITT)
The name was changed to separate the standard
from the originating body
1991 - Release of Parts 1 and 8 of DICOM
1992 - RSNA demonstration, Part 8
1993 - DICOM Parts 1-9 approved,
RSNA demonstration of ALL parts
1994 - Part 10: Media Storage and File Format
1995 - Parts 11,12, and 13 plus Supplements
Information Management System
Query/Retrieve, Patient & Study Management
Information Object DIMSE Service Group
Study Content Notification
Basic Print Management
Joint CEN-DICOM development
Medicom = DICOM
MIPS 95 work is underway with JIRA
IS&C Harmonization is also in progress
HL7 Harmonization continuing interest
New DICOM organization
Companies: NEMA and non-NEMA
ACR, ACC, CAP, ...
Networking is a critical component of all
medical imaging systems
Support for Open Communication Standards is a
DICOM is here, NOW
DICOM products exist on the market
DICOM is emerging as THE common protocol for
medical image communication - WORLD WIDE!
JPEG - Joint Photographic Experts Group
JPEG is designed with photographs in mind.
It is capable of handling all of the colors needed.
JPEGs have a lossy way of compressing images.
At a low compression value, this is largely not
noticeable, but at high compression, an image can
become blurry and messy. .jpg
• Images with hard edges, high contrasts, angular areas, and
text suffer from JPEG compression.
• Scanned “natural” photographs do not lose much,
especially at High or Maximum quality.
• Only save finished images as JPEGs, every time you open
and save again, even if you don’t edit, you lose quality.
• Always keep the original non-JPEG version (the native .psd
So why use JPEG?
• It is the best format for photographic images on the Web.
• It’s compression ability is very great.
GIF - Graphics Interchange Format
GIF is the most popular on the Internet, mainly because of its
small file size. It is ideal for small navigational icons and simple
diagrams and illustrations where accuracy is required, or
graphics with large blocks of a single color. The format is loss-
less, meaning it does not get blurry or messy.
The 256 color maximum is sometimes tight, and so it has the
option to dither, which means create the needed color by
mixing two or more available colors.
GIF use a simple technique called LZW compression to reduce
the file sizes of images by finding repeated patterns, but this
compression never degrades the image quality.
The GIF format is one of the most commonly used
graphic file formats, especially on the Internet.
The GIF format is exceedingly useful in that it can
contain animations. Its internal structure is such
that it can store multiple images and the controls to
make them appear as real time animation
The GIF format also allows a special color as to be
specified as "using the background." This results in
the image looks like transparent
Portable Network Graphic (PNG) which is
pronounced as “Ping”.
Alternative to GIF, a lossless compression
scheme is used.
Support three image type: true color,
grayscale, palette-based (8-bit).
JPEG supports the first 2.
GIF supports the 3rd one.
○ Deflate is an improved version of the Lempel-Ziv compression
○ Display image quicker than Interlaced GIF.
True Color and Transparency
○ Support 16-bit (Grey scale) or 48-bit (True Color)
○ 16-bit for alpha channel (Transparency).
○ Store the gamma setting of the platform of the creator.
Not support by old browsers (Netscape 2,3,4 and IE 2,3,4)
TIFF - Tagged Image File Format
Widely used cross platform file format also designed for printing.
A bitmap image format.
TIFF supports lossless LZW compression which also makes it a
good archive format for Photoshop documents.
A popular format for grayscale images (8 bits/pixel)
Closely-related formats are:
PBM (Portable Bitmap), for binary images (1 bit/pixel)
PPM (Portable Pixelmap), for color images (24 bits/pixel)
- ASCII or binary (raw) storage
FITS - Flexible Image Transport System
Format of a FITS file (http://fits.gsfc.nasa.gov)
Primary Header: metadata describing
instrument, observation & file contents
Primary Data Array: array of 0-999
dimensions – usually a 2D image
+ none or more Extensions:
Array, ASCII Table or Binary Table, each with
(New FITS-inspired XML format – VOTable)
BMP - Bitmap Format
uses a pixel map which contains line by line information.
It is a very common format, as it got its start in Windows.
This format can cause an image to be super large.
Image Processing is any form of signal processing for
which our input is an image, such as photographs or
frames of video and our output can be either an image or
a set of characteristics or parameters related to the
Image Processing generally refers to processing
of two dimensional picture and by two
dimensional picture we implies a digital image.
A digital image is an array of real or complex
numbers represented by a finite number of bits.
But now in these days optical and analog image
processing is also possible.
Is enhancing an image or extracting information
or features from an image.
Computerized routines for information extraction
(eg, pattern recognition, classification) from
remotely sensed images to obtain categories of
information about specific features.
Image processing are of two
improving the visual appearance
of images to a human viewer
preparing images for
measurement of the features
and structures present.
❶ Acquisition of Image
Medical image data is acquired one slice at a time.
Resulting data set comprises n slices, each containing w x h
Basic Steps for Image Processing
❷ Data Storage
Array starts with the ﬁrst row of the ﬁrst slice and so on until the end of
the ﬁrst slice.
Next, the array continues with the ﬁrst row of the second slice, then the
second row of the second slice, and so on.
A single slice corresponds to a k
space plane acquired in real-time
The “K-Space” undergoes an Inverse
Following this mathematical step,
we finally have an image
❸ Image Formation
❹ Data Visualisation
Medical image data is commonly visualised by two
Since the digital image is “invisible” it must be
prepared for viewing on one or more output
device (laser printer, monitor, etc.,)
It might be possible to analyze the image in the
computer and provide cues to the radiologists to
help detect important/suspicious structures (e.g.:
Computed Aided Diagnosis, CAD)
Why do we need Image Processing
Image processing can be done using various
software's and languages such as:-
How Image Processing is done?
Early 1920’s: One of the first applications of digital
imaging was in the newspaper industry
The Bartlane cable picture
Images were transferred by
submarine cable between London
and New York
Pictures were coded for cable
transfer and reconstructed at the
receiving end on a telegraph printer
Early digital image
Mid to late 1920’s: Improvements to the Bartlane
system resulted in higher quality images
digital image Early 15 tone digital
New reproduction processes
based on photographic
Increased number of tones in
1960’s: Improvements in computing technology
and the onset of the space race led to a surge of
work in digital image processing
A picture of the moon taken
by the Ranger 7 probe
minutes before landing
1964: Computers used to
improve the quality of images of
the moon taken by the Ranger 7
Such techniques were used in
other space missions including
the Apollo landings
1970’s: Digital image processing begins to be
used in medical applications
Typical head slice CAT
1979: Sir Godfrey N. Hounsfield & Prof.
Allan M. Cormack share the Nobel Prize
in medicine for the invention of
tomography, the technology behind
Computerised Axial Tomography (CAT)
1980’s - Today: The use of digital image processing
techniques has exploded and they are now used for all kinds
of tasks in all kinds of areas
Human computer interfaces
Primary purpose is to identify pathologic conditions.
Requires recognition of normal anatomy and
Create image of body part
Medical imaging is the technique and
process used to create images of
the human body or it’s parts for clinical
Non-invasive visualization of internal
organs, tissue, etc.
Medical imaging has come a long way since 1895
when Röntgen first described a ‘new kind of ray’.
That X-rays could be used to display anatomical
features on a photographic plate was of immediate
interest to the medical community at the time.
Today a scan can refer to any one of a number of
medical-imaging techniques used for diagnosis and
Medical Imaging using Ionising Radiations
The transmission and detection of X-rays still lies at the heart of
radiography, angiography, fluoroscopy and conventional
However, traditional film-based scanners are gradually being
replaced by digital systems
The end result is the data can be viewed, moved and stored without
a single piece of film ever being exposed.
X-rays: A form of Electromagnetic
Energy travelling at the speed of
*No mass *No charge *Energy
Wavelength – Range of 0.01 to 10
X-rays: a form of electromagnetic energy
Travel at the speed of light
Gamma Rays X-rays
Visible light Infrared light
X-Rays are associated with inner shell electrons
As the electrons decelerate in the target
through interaction, they emit electromagnetic
radiation in the form of x-rays.
patient is located between an x-ray source and
a film -> radiograph
cheap and relatively easy to use
potentially damaging to biological tissue
X-Rays - Visibility
Bones contain heavy atoms -> with many electrons,
which act as an absorber of x-rays
Commonly used to image gross bone structure and
Excellent for detecting foreign metal objects
Main disadvantage -> Lack of anatomical structure
All other tissue has very similar absorption
coefficient for x-rays
Three things can happen
Pass all the way through the body
Be deflected or scattered
Where on this image
have x-rays passed
through the body
to the greatest degree?
X-rays Passing Through Tissue
Depends on the energy of the x-ray
and the atomic number of the tissue
Higher energy x-ray - more likely to
Higher atomic number - more likely
to absorb the x-ray
X-rays that pass through the body to
the film render the film dark (black).
X-rays that are totally blocked do not
reach the film and render the film
Air = low atomic no. = x-rays get through
= image is dark
Metal = high atomic no. = x-rays blocked
= image is light (white)
How do x-rays passing through
the body create an image?
5 - Basic Radiographic Densities
X-Rays - Images
X-Rays can be used in computerized tomography
Computerized (Axial) Tomography
Introduced in 1972 by Hounsfield and Cormack
Natural progression from X-rays
Based on the principle that a three-dimensional object can be
reconstructed from its two dimensional projections
From 2D to 3D !
CT (or) CAT
• Johan Radon (1917) - Showed how a reconstruction from
projections was possible.
• Cormack (1963,1964) - Introduced Fourier transforms into the
• Hounsfield (1972) - Invented the X-ray Computer scanner for
medical work, (which Cormack and Hounsfield shared a Nobel
• EMI Ltd (1971) - Announced development of the EMI scanner
which combined X-ray measurements and sophisticated
algorithms solved by digital computers.
measures the attenuation of
X-rays from many different angles
a computer reconstructs the
organ under study in a series of
cross sections or planes
combine X-ray pictures from
various angles to reconstruct 3D
Linear advancement (slice by slice)
tumor might fall between ‘cracks’
takes long time
5-8 times faster
A whole set of trade-offs
1. Scanning the patient
2. Data Acquisition
Tube and detector move
measurements are taken
3. Image reconstruction
4. Image Display
5. Image archival (recording)
1.X-ray tube and detector rotate 360°
2.Patient table is stationary with X-ray’s “on”
3.Produces one cross-sectional image
4. Once this is complete patient is moved to
Process starts again at the beginning
1.X-ray tube and detector rotate 360°
2.Patient table moves continuously
With X-ray’s “on”
3.Produces a helix of image information
4.This is reconstructed into 30 to 1000 images
Helical or spiral CT
Medical Applications Type of Tomography
Full body scan X-ray
Respiratory, digestive systems,
PET Positron Emission
Respiratory, digestive systems. Radio-isotopes
Whole Body Magnetic Resonance (MRI, NMR)
PET scan on the
MRI and PET showing
lesions in the brain.
Non Medical Applications Type of Tomography
Oil Pipe Flow
Flame Analysis Optical Tomography
ECT on industrial pipe flows
Significantly more data is collected
Superior to single X-ray scans
Far easier to separate soft tissues other than bone from one
another (e.g. liver, kidney)
Data exist in digital form -> can be analyzed quantitatively
Adds enormously to the diagnostic information
Used in many large hospitals and medical centers throughout
significantly more data is collected
soft tissue X-ray absorption still relatively similar
still a health risk
MRI is used for a detailed imaging of anatomy – no X rays
1979 “For the Development of
computer assisted tomography (CAT)”
– Hounsfield & Cormack
2003 “For the Discoveries
concerning magnetic resonance
imaging (MRI)” - Paul Lauterbur &
Nuclear Magnetic Resonance (NMR) (or Magnetic
Resonance Imaging - MRI)
Most detailed anatomical information
High-energy radiation is not used, i.e. this is “safe
Based on the principle of nuclear resonance
(medicine) Uses resonance properties of protons
MRI (or) NMR
Magnetic resonance imaging (MRI),
Magnetic resonance imaging (MRI), is a
non-invasive method used to render
images of the inside of an object. It is
primarily used in medical imaging to
demonstrate pathological or other
physiological alterations of living tissues.
Hydrogen nuclei(protons) under a strong magnetic field in
phase with one another and align with the field.
Relaxed protons induce a measurable radio signal.
Main modality for image guided surgery.
Ability to discriminate between subtle surfaces.
--Not effective for bone scanning.
Positron Emission Tomography
Single Photon Emission
involves the emission of particles of
antimatter by compounds injected
into the body being scanned
follow the movements of the
injected compound and its
reconstruction techniques similar to
CT - Filter Back Projection & iterative
•Positron Emission Tomography
(PET) is a nuclear medicine medical
imaging technique which produces
a three-dimensional image or map
of functional processes or
Metabolic Activities in the body.
To conduct the scan, a short-lived radioactive tracer isotope,
which decays by emitting a positron, which also has been
chemically incorporated into a metabolically active molecule,
is injected into the living subject (usually into blood
The data set collected in PET is much poorer than CT, so
reconstruction techniques are more difficult (see section
below on image reconstruction of PET).
the use of high-frequency sound (ultrasonic) waves to
produce images of structures within the human body
above the range of sound audible to humans (typically
piezoelectric crystal creates sound waves
aimed at a specific area of the body
change in tissue density reflects waves
echoes are recorded
Delay of reflected signal and amplitude determines the position of
still images or a moving picture of the inside of the body
there are no known examples of tissue damage from conventional
commonly used to examine fetuses in utero in order to ascertain
size, position, or abnormalities
also for heart, liver, kidneys, gallbladder, breast, eye, and major
by far least expensive
1D, 2D, 3D scanners
irregular sampling -
Mammography is a radiographic examination that is
specially designed for detecting early breast cancer,
yielding a significant improvement in breast cancer
Mammography has been used in clinical practice since 1927
in the diagnosis of breast abnormalities.
In the late 1950s, the pioneering work of Gershon – Cohen
and Egan demonstrated that even clinically occult cancers
of early detection of breast cancer by screening asymptotic
Since the first mammography units (xeromammography
and screen-film mammography in the 1970’s) became
available, both the equipment and the examination
procedure have changed and progressed.
A high degree of accuracy was developed with this
technique to differentiate between Benign and
Computed radiography (CR)
Computed Aided Diagnosis
Tomosynthesis - 3D
Improved detection efficiency
A linear dynamic range
Increased signal-to-noise ratio (SNR)
Excellent Image Handling
Data in Digital form
Computer Aided Detection
Compatibility with PACS and Telemammography
Early Detection Is Your
If breast cancer is found and treated early, the five-year survival rate is 98
The social prejudices and stigma associated in screening of breast is to be
The success of the scheme depends upon the involvement of radiologists
and lab attendants who have to handle with delicate and humane.
Another success of the scheme rests upon instead of bringing the people
to lab, the lab itself has to go in search of the patient. For which a handy
and portable mammogram has to developed for instant and hassle free
GE unveiled an impressive portable
mammography concept as part of a
portfolio of integrated technologies aimed
at combating cancer.
The SenoCase is mobile mammography
system which can be folded and easily
stored in a car boot.
According to GE, such portability could remove geographical barriers to
regular breast screening for many women on a global scale.
The system could also be more cost effective than conventional
mammography systems, making it more accessible to smaller practices
A standard field of view Cesium Iodide
Similar image quality to a full-field digital
A user-friendly interface, operable by a
Digital Portable Mammography
model was preferred in employee
Employee feedback confirmed
that Women Diagnostic Center
mammograms are more convenient,
private and familiar because
employees feel more comfortable.
Digital mammography has proven to be
an essential tool in the diagnosis,
treatment and fight against breast cancer.
And studies have shown that routine
mammograms can help reduce breast
The important thing is that you make
annual mammography screening a top
priority for yourself and the women you
As defined at the beginning of this chapter,
angiography refers to radiologic imaging of blood
vessels after injection of a contrast medium.
To visualize these low-contrast structures, contrast
media is injected by a catheter that is placed in the vessel
Positive contrast media are more commonly used, but
there are instances when use of negative contrast media
is indicated. Highly specialized imaging equipment is
required for these procedures.
Fluoroscopy is a technique in which a
continuous beam of x-rays is used to produce
It is used to show movement in the digestive
system (which may require ingestion of a
high-contrast liquid such as barium) and the
circulatory system (angiograms).
X-ray transmitted trough patient
The photographic plate replaced by fluorescent screen
Screen fluoresces under irradiation and gives a live image
Older systems— direct viewing of screen
Screen part of an Image Intensifier system
Coupled to a television camera
Radiologist can watch the images “live” on TV-monitor; images can
Fluoroscopy often used to observe digestive tract
Upper GI series, Barium Swallow
Lower GI series Barium Enema
(Still in use in some countries)
Staff in DIRECT beam
• AVOID USE OF DIRECT FLUOROSCOPY
• Directive 97/43Euratom Art 8.4.
In the case of fluoroscopy, examinations without an
image intensification or equivalent techniques are
not justified and shall therefore be prohibited.
• Direct fluoroscopy will not comply with BSS
Performance of diagnostic radiography and
fluoroscopy equipment and of nuclear medicine
equipment should be assessed on the basis of
comparison with the diagnostic reference levels
Remote control systems
Not requiring the presence of
medical specialists inside the X
Mostly used in surgical theatres.
Interventional radiology systems
Requires specific safety considerations.
In interventional radiology the physician
can be near the patient during the
Multipurpose fluoroscopy systems
Can be used as a remote control system
or as a system to perform simple
Techniques which are well established in traditional engineering
applications need new hardware and software to work efficiently in the
biomedical arena. Much of our work includes fusing multiples sources of
data, or fusing data with underlying models of movement or tissue
properties to improve predictions, sometimes with the development of
Current applications are in cancer diagnosis and therapy, stroke
rehabilitation and orthopaedics. Recent projects have included monitoring
heat distribution and tissue changes from ultrasound images in cancer
therapy (HIFU), developing protocols and instrumentation to assess arm
movement (with immediate application in stroke rehabilitation), and
ultrasound and microwave measurements on soft tissue.
We are pursuing methods to integrate the detection of electrical as well as
mechanical properties of tissue. 117
Recognising abnormal states; adaptive stimulation
At present, stimulation is continuous and this gives poor battery usage and can cause
The goal is to make the next generation of stimulators adaptable to particular patients
through demand driven stimulation - altering the pattern and duration of stimulation to
the brain's own signals.
Tremor in Parkinson's disease (PD) is clearly detectable in the beta wave brain activity (as
well of course from external instrumentation such as accelerometers), but its onset is
We have developed methods using autorgressive models, coherence measures and
Hidden Markov modelling to detect the change of state associated with onset of tremor
from signals received from implanted electrodes in the subthalmic nucelus (which is a
prime target for stimulation in PD patients).
More generic work in this area has developed HMM models to identify state transitions
between different regions to identify brain networks using MEG imaging. This work is
currently been demonstrated on resting state data but will soon be applied to tremor
MEG (Magneto encephalography) imaging and application to
chronic pain patients
MEG is the only technology suitable for functional imaging for DBS patients as they have
metal implanted in the skull so fMRI cannot be used. MEG uses a set of very sensitive
magnetic sensors placed around the head to detect the magnetic fields associated with the
Once the signal have been acquired, an image is formed using a technique known as beam
forming which uses them to reconstruct the sources within the brain, a technique known as
The signals acquired are typically with low signal to noise ratio, non-Gaussian distribution
and correlated. Beam forming is therefore challenging. It is particularly difficult for DBS
patients because artefacts arise from the coil of wire left beneath the burr hole (through
which wires are taken to the battery.
Microwave imaging to diagnose breast cancer
Microwaves are an attractive imaging method for finding breast
tumours as the contrast between healthy tissue and tumour is
very high. However the resolution is low.
We are working to improve the interpretation of the data
gathered from both phantoms and clinical images using
microwave clinical imaging system developed in Bristol
A spin out company from Bristol University has one of the few
clinical systems in use worldwide, which has been used in trials
in Frenchay Hospital. This work is funded by EPSRC.
Imaging for medical purposes involves the services of
radiologists, radiographers, medical physicists and
biomedical engineers working together as a team for
maximum output. This ensures the production of
high quality of radiological service with consequent
improvement of health care service delivery.
Technological advances have made human imaging possible at
scales from a single molecule to the whole body.
By linking the anatomical data collected with emerging imaging
technologies to computer simulations, researchers now can
form truly functional images of individual patients.
These images will allow physicians not only to see what a
patient’s organs look like but also how they are functioning
even at the smallest dimensions.
A major challenge is how to store, analyze, distribute,
understand and use the enormous amount of data associated
with thousands of images.
Biomedical engineering stands at the forefront of this effort
because its researchers are able to integrate the engineering
tools needed to solve the technological problems of image
analysis with the deeper knowledge of the underlying biological
Already, members of the Department of Biomedical
Engineering, in close collaboration with the Departments of
Applied Mathematics and Statistics, Computer Science,
Electrical and Computer Engineering, and Radiology, have
pioneered the use of imaging technology in computational
anatomy, neuropsychiatry, computer-integrated surgery and
Now, researchers are expanding their imaging efforts
into other modalities and organ systems.
Ultimately, their work will contribute to advancing
image-guided therapy and to the early diagnosis and
treatment of a host of disorders, including heart
disease and brain dysfunction.
Included in Medical Imaging Research
Creating new systems and methods for measuring and analyzing
imaging data in humans, developing mathematical and computational
approaches to compare data across individuals, and applying these
techniques to understand, diagnose and treat disease.
Using novel imaging techniques to provide information on three-
dimensional structure and function at the molecular, cellular, tissue,
organ and organism level.
Improving ways to image blood flow and cardiac motion with magnetic
resonance imaging, computed tomography, ultrasound and
Finding and modeling the cerebral cortex to understand both normal
and abnormal shape and the relation to genetic and environmental
Developing bio-inspired algorithms for recognizing objects and
actions in video. 125
Research - Biomedical Imaging
New developments in biomedical imaging provide a window
into complex biological phenomena.
Imaging enables researchers to track the movements of
molecules, cells, fluids, gases, or sometimes even whole
Imaging techniques such as x-ray crystallography and magnetic
resonance imaging can also yield information about important
biological structures from single proteins to the human brain.
The frontiers of biomedical imaging promise to make diagnosis
of disease more accurate and less invasive, and to improve our
understanding of disease.
Imaging research encompasses
Imaging of protein complexes involved in synaptic communication in the
Fluorescence tagging of molecules involved in intracellular signalling
Non-invasive imaging of cancer
Imaging of human movement using dynamic MR, motion capture systems,
and ultrasonic imaging
Molecular and biochemical imaging with PET, SPECT, and optical imaging
Three-dimensional medical imaging of blood flow, blood vessels, and
Functional human brain mapping
Strategies for fusing images across modalities (e.g., CT and MR)
Ultrasonic diagnostic technology in medicine
Computational analysis and reconstruction of complex imaging data