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Biomedical Imaging


Biomedical Imaging Eugen Kvasnak, PhD. Department of Medical Biophysics and Informatics 3rd Medical Faculty of Charles University Content Microscopy Ultrasound ... – PowerPoint PPT presentation

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Title: Biomedical Imaging

Biomedical Imaging
Eugen Kvasnak, PhD. Department of Medical
Biophysics and Informatics 3rd Medical Faculty of
Charles University
  • Microscopy
  • Ultrasound Sonography
  • SPECT Gamma Camera
  • CT
  • NMR fMRI
  • PET

  • main branches optical, electron and scanning
    probe microscopy. ( less used X-ray microscopy)
  • Optical and electron microscopy involves the
    diffraction, reflection, or refraction of
    radiation incident upon the subject of study, and
    the subsequent collection of this scattered
    radiation in order to build up an image.
  • Scanning probe microscopy involves the
    interaction of a scanning probe with the surface
    or object of interest.

Optical microscopy - definition
  • Optical or light microscopy involves passing
    visible light transmitted through or reflected
    from the sample through a single or multiple
    lenses to allow a magnified view of the sample.
  • The resulting image can be detected directly by
    the eye, imaged on a photographic plate or
    captured digitally.
  • The single lens with its attachments, or the
    system of lenses and imaging equipment, along
    with the appropriate lighting equipment, sample
    stage and support, makes up the basic light

Optical microscopy - scheme
Optical microscopy - magnification

Optical microscopy - limitations
  • OM can only image dark or strongly refracting
    objects effectively.
  • Out of focus light from points outside the focal
    plane reduces image clarity. Compound optical
    microscopes are limited in their ability to
    resolve fine details by the properties of light
    and the refractive materials used to manufacture
    lenses. A lens magnifies by bending light.
    Optical microscopes are restricted in their
    ability to resolve features by a phenomenon
    called diffraction which, based on the numerical
    aperture AN of the optical system and the
    wavelengths of light used (?), sets a definite
    limit (d) to the optical resolution. Assuming
    that optical aberrations are negligible, the
    resolution (d) is given by
  • In case of ? 550 nm (green light), with air as
    medium, the highest practical AN is 0.95, with
    oil, up to 1.5.
  • Due to diffraction, even the best optical
    microscope is limited to a resolution of around
    0.2 micrometres.

Optical microscopy - types
  • Optical microscopy techniques
  • Bright field optical microscopy
  • Oblique illumination
  • Dark field optical microscopy
  • Phase contrast optical microscopy
  • Differential interference contrast microscopy
  • Fluorescence microscopy
  • Confocal laser scanning microscopy
  • Deconvolution microscopy
  • Near-field Scanning OM

Electron Microscopy - definition and types
  • developed in the 1930s that use electron beams
    instead of light.
  • because of the much lower wavelength of the
    electron beam than of light, resolution is far
  • Transmission electron microscopy (TEM) is
    principally quite similar to the compound light
    microscope, by sending an electron beam through a
    very thin slice of the specimen. The resolution
    limit (in 2005) is around 0.05 nanometer.
  • Scanning electron microscopy (SEM) visualizes
    details on the surfaces of cells and particles
    and gives a very nice 3D view. The magnification
    is in the lower range than that of the
    transmission electron microscope.

Transmission Electron Microscopy (TEM)
  • beam of electrons is transmitted through a
    specimen, then an image is formed, magnified and
    directed to appear either on a fluorescent screen
    or layer of photographic film or to be detected
    by a sensor (e.g. charge-coupled device, CCD
  • involves a high voltage electron beam emitted by
    a cathode, usually a tungsten filament and
    focused by electrostatic and electromagnetic
  • electron beam that has been transmitted through a
    specimen that is in part transparent to electrons
    carries information about the inner structure of
    the specimen in the electron beam that reaches
    the imaging system of the microscope.
  • spatial variation in this information (the
    "image") is then magnified by a series of
    electromagnetic lenses until it is recorded by
    hitting a fluorescent screen, photographic plate,
    or CCD camera. The image detected by the CCD may
    be displayed in real time on a monitor or

Transmission Electron Microscopy (TEM)
Neuron growing on astroglia
Black Ant
House Fly
House Fly
Human stem cells
Human red blood cells
Neurons CNS
Scanning Electron Microscopy (SEM)
  • type of electron microscope capable of producing
    high-resolution images of a sample surface.
  • due to the manner in which the image is created,
    SEM images have a characteristic 3D appearance
    and are useful for judging the surface structure
    of the sample.
  • Resolution
  • depends on the size of the electron spot, which
    in turn depends on the magnetic electron-optical
    system which produces the scanning beam.
  • is not high enough to image individual atoms, as
    is possible in the TEM so that, it is 1-20 nm

X-ray microscopy
  • less common,
  • developed since the late 1940s,
  • resolution of X-ray microscopy lies between that
    of light microscopy and the electron microscopy.
  • X-rays are a form of electromagnetic radiation
    with a wavelength in the range of 10 to 0.01
    nanometers, corresponding to frequencies in the
    range 30 PHz to 30 EHz.

Ultrasound (Sonography) - basics
  • It is used to visualize muscles, tendons, and
    many internal organs, their size, structure and
    any pathological lesions with real time
    tomographic images. They are also used to
    visualize a fetus during routine and emergency
    prenatal care.
  • The technology is relatively inexpensive and
    portable, especially when compared with
    modalities such as magnetic resonance
    imaging(MRI) and computed tomography (CT).
  • It poses no known risks to the patient, it is
    generally described as a "safe test" because it
    does not use ionizing radiation, which imposes
    hazards (e.g. cancer production and chromosome
  • However, it has two potential physiological
    effects it enhances inflammatory response and
    it can heat soft tissue.

Ultrasound how does it work?
  • the same principles involved in the sonar used by
    bats, ships and fishermen.
  • when a sound wave (frequency 2.0 to 10.0
    megahertz ) strikes an object, it bounces
    backward or echoes.
  • by measuring these echo waves it is possible to
    determine how far away the object is and its
    size, shape, consistency (solid, filled with
    fluid, or both) and uniformity.
  • a transducer both sends the sound waves and
    records the echoing waves. When the transducer is
    pressed against the skin, it directs a stream of
    inaudible, high-frequency sound waves into the
    body. As the sound waves bounce off of internal
    organs, fluids and tissues, the sensitive
    microphone in the transducer records tiny changes
    in the sound's pitch and direction. These
    signature waves are instantly measured and
    displayed by a computer, which in turn creates a
    real-time picture on the monitor.

Ultrasound - biomedical applications
  • heart and blood vessels, incl. the abdominal
    aorta and its major branches
  • liver
  • gallbladder
  • spleen
  • pancreas
  • kidneys
  • bladder
  • uterus, ovaries, and unborn child (fetus) in
    pregnant patients
  • eyes
  • thyroid and parathyroid glands
  • scrotum (testicles)

Ultrasound limitations
  • Ultrasound waves are reflected by air or gas
    therefore ultrasound is not an ideal imaging
    technique for the bowel.
  • Ultrasound waves do not pass through air
    therefore an evaluation of the stomach, small
    intestine and large intestine may be limited.
    Intestinal gas may also prevent visualization of
    deeper structures such as the pancreas and aorta.
  • Patients who are obese are more difficult to
    image because tissue attenuates (weakens) the
    sound waves as they pass deeper into the body.
  • Ultrasound has difficulty penetrating bone and
    therefore can only see the outer surface of bony
    structures and not what lies within.

Single Positron Emission Computed Tomography
  • Single Photon Emission Computed Tomography.
  • gamma ray emissions are the source of information
  • (contrary to X-ray transmissions used in
    conventional CT)
  • allows to visualize functional information about
    a patient's specific organ or body system
    (similarly to X-ray Computed Tomography (CT) or
    Magnetic Resonance Imaging (MRI)

SPECT - how does it work?
  • Internal radiation is administered by means of a
    pharmaceutical which is labeled with a
    radioactive isotope / tracer / radiopharmaceutical
    , is either injected, ingested, or inhaled.
  • The radioactive isotope decays, resulting in the
    emission of gamma rays. These gamma rays give us
    a picture of what's happening inside the
    patient's body.

SPECT /Gamma camera - how does it work?
  • The Gamma camera collects gamma rays that are
    emitted from within the patient, enabling us to
    reconstruct a picture of where the gamma rays
    originated. From this, we can determine how a
    particular organ or system is functioning.
  • The gamma camera can be used in planar imaging to
    acquire 2-dimensional images, or in SPECT imaging
    to acquire 3-dimensional images.

Gamma Camera
  • Once a radiopharmaceutical has been administered,
    it is necessary to detect the gamma ray emissions
    in order to attain the functional information. 
  • The instrument used in Nuclear Medicine for the
    detection of gamma rays is known as the Gamma
    camera. The components making up the gamma camera
    are the collimator, detector crystal,
    photomultiplier tube array, position logic
    circuits, and the data analysis computer. 

Gamma Camera - how does it work?
Gamma Camera - Collimator
- the first object that an emitted gamma photon
encounters after exiting the body. The collimator
is a pattern of holes through gamma ray absorbing
material, usually lead or tungsten, that allows
the projection of the gamma ray image onto the
detector crystal.  The collimator achieves this
by only allowing those gamma rays traveling along
certain directions to reach the detector. 
Gamma Camera - Scintillation Detector
  • In order to detect the gamma photon we use
    scintillation detectors.  A Thallium-activated
    Sodium Iodide NaI(Tl) detector crystal is
    generally used in Gamma cameras.  This is due to
    this crystal's optimal detection efficiency for
    the gamma ray energies of radionuclide emission
    common to Nuclear Medicine. 
  • A detector crystal may be circular or
    rectangular. It is typically 3/8" thick and has
    dimensions of 30-50 cm. A gamma ray photon
    interacts with the detector by means of the
    Photoelectric Effect or Compton Scattering with
    the iodide ions of the crystal.  This interaction
    causes the release of electrons which in turn
    interact with the crystal lattice to produce
    light, in a process known as scintillation.

Gamma Camera Photoelectric effect
Gamma Camera Compton Scattering
Gamma Camera - Scintillation
Gamma Camera - Photomultiplier
  • - instrument that detects and amplifies the
    electrons that are produced by the photocathode
    which, when stimulated by light photons ejects
  • For every 7 to 10 photons incident on the
    photocathode, only one electron is generated. 
    This electron from the cathode is focused on a
    dynode which absorbs this electron and re-emits
    many more electrons (6 to 10).

Gamma Camera - Planar Dynamic Imaging
  • Since the camera remains at a fixed position in a
    planar study, it is possible to observe the
    motion of a radiotracer through the body by
    acquiring a series of planar images of the
    patient over time. 
  • Each image is a result of summing data over a
    short time interval, typically 1-10 seconds. 

SPECT - Imaging
  • If one rotates the camera around the patient, the
    camera will acquire views of the tracer
    distribution at a variety of angles.
  • After all these angles have been observed, it is
    possible to reconstruct a three dimensional view
    of the radiotracer distribution within the body. 

SPECT - Applications
  • Heart Imaging
  • Brain Imaging
  • Kidney/Renal Imaging
  • Bone Scans

Computed Tomography Scan (CT)
CT - basics
  • CT scans use a series of X-ray beams
  • It creates cross-sectional images, e.g. of the
    brain and shows the structure of the brain, but
    not its function.
  • Digital geometry processing is used to generate a
    three-dimensional image of the internals of an
    object from a large series of two-dimensional
    X-ray images taken around a single axis of

CT - basics
  • CT's primary benefit is the ability to separate
    anatomical structures at different depths within
    the body.
  • A form of tomography can be performed by moving
    the X-ray source and detector during an exposure.
  • Anatomy at the target level remains sharp, while
    structures at different levels are blurred.
  • By varying the extent and path of motion, a
    variety of effects can be obtained, with variable
    depth of field and different degrees of blurring
    of 'out of plane' structures.

CT - principle
  • Because contemporary CT scanners offer isotropic,
    or near isotropic, resolution, display of images
    does not need to be restricted to the
    conventional axial images.
  • Instead, it is possible for a software program to
    build a volume by 'stacking' the individual
    slices one on top of the other. The program may
    then display the volume in an alternative manner.

CT - diagnostic use
  • Cranial
  • diagnosis of cerebrovascular accidents and
    intracranial hemorrhage
  • CT generally does not exclude infarct in the
    acute stage of a stroke. For detection of tumors,
    CT scanning with IV contrast is occasionally used
    but is less sensitive than magnetic resonance
    imaging (MRI).

CT - diagnostic use
  • Chest
  • CT is excellent for detecting both acute and
    chronic changes in the lung parenchyma.
  • A variety of different techniques are used
    depending on the suspected abnormality.
  • For evaluation of chronic interstitial processes
    (emphysema, fibrosis, and so forth), thin
    sections with high spatial frequency
    reconstructions are used - often scans are
    performed both in inspiration and expiration.
    This special technique is called High resolution
    CT (HRCT).
  • For detection of airspace disease (such as
  • pneumonia) or cancer, relatively thick
  • sections and general Purpose image
  • reconstruction techniques may be adequate.

CT - diagnostic use
  • Cardiac
  • With the advent of subsecond rotation combined
    with multi-slice CT (up to 64-slice), high
    resolution and high speed can be obtained at the
    same time, allowing excellent imaging of the
    coronary arteries (cardiac CT angiography).
  • Images with an even higher temporal resolution
    can be formed using retrospective ECG gating. In
    this technique, each portion of the heart is
    imaged more than once while an ECG trace is
    recorded. The ECG is then used to correlate the
    CT data with their corresponding phases of
    cardiac contraction. Once this correlation is
    complete, all data that were recorded while the
    heart was in motion (systole) can be ignored and
    images can be made from the remaining data that
    happened to be acquired while the heart was at
    rest (diastole). In this way, individual frames
    in a cardiac CT investigation have a better
    temporal resolution than the shortest tube
    rotation time.

CT - diagnostic use
  • Abdominal and pelvic
  • CT is a sensitive method for diagnosis of
    abdominal diseases. It is used frequently to
    determine stage of cancer and to follow progress.
    It is also a useful test to investigate acute
    abdominal pain.
  • Renal/urinary stones, appendicitis, pancreatitis,
    diverticulitis, abdominal aortic aneurysm, and
    bowel obstruction are conditions that are readily
    diagnosed and assessed with CT.
  • CT is also the first line for detecting solid
    organ injury after trauma.

CT step by step
CT step by step
CT step by step
CT step by step
Magnetic Resonance Imaging (MRI)
MRI fMRI - basics
  • An MRI uses powerful magnets to excite hydrogen
    nuclei in water molecules in human tissue,
    producing a detectable signal. Like a CT scan, an
    MRI traditionally creates a 2D image of a thin
    "slice" of the body.
  • The difference between a CT image and an MRI
    image is in the details. X-rays must be blocked
    by some form of dense tissue to create an image,
    therefore the image quality when looking at soft
    tissues will be poor.
  • An MRI can ONLY "see" hydrogen based objects, so
    bone, which is calcium based, will be a void in
    the image, and will not affect soft tissue views.
    This makes it excellent for peering into joints.
  • As an MRI does not use ionizing radiation, it is
    the preferred imaging method for children and
    pregnant women.

MRI fMRI - basics
  • Magnetic resonance imaging (MRI), formerly
    referred to as magnetic resonance tomography
    (MRT) and, in scientific circles and as
    originally marketed by companies such as General
    Electric, nuclear magnetic resonance imaging
    (NMRI) or NMR zeugmatography imaging, is a
    non-invasive method using nuclear magnetic
    resonance to render images of the inside of an
  • It is primarily used in medical imaging to
    demonstrate pathological or other physiological
    alterations of living tissues.
  • MRI also has uses outside of the medical field,
    such as detecting rock permeability to
    hydrocarbons and as a non-destructive testing
    method to characterize the quality of products
    such as produce and timber.

MRI fMRI - basics
  • MRI should not be confused with the NMR
    spectroscopy technique used in chemistry,
    although both are based on the same principles of
    nuclear magnetic resonance.
  • In fact MRI is a series of NMR experiments
    applied to the signal from nuclei (typified by
    the hydrogen nuclei in water) used to acquire
    spatial information in place of chemical
    information about molecules.
  • The same equipment, provided suitable probes and
    magnetic gradients are available, can be used for
    both imaging and spectroscopy.

MRI fMRI - basics
  • The scanners used in medicine have a typical
    magnetic field strength of 0.2 to 3 Teslas.
    Construction costs approximately US 1 million
    per Tesla and maintenance an additional several
    hundred thousand dollars per year.
  • Medical Imaging MRI, or "NMR" as it was
    originally known, has only been in use since the
    1980's. Effects from long term, or repeated
    exposure, to the intense magnetic field is not
    well documented.
  • Functional MRI detects changes in blood flow to
    particular areas of the brain. It provides both
    an anatomical and a functional view of the brain.
  • MRI uses the detection of radio frequency signals
    produced by displaced radio waves in a magnetic
    field. It provides an anatomical view of the

MRI fMRI dis/advantages
  • Advantages
  • No X-rays or radioactive material is used.
  • Provides detailed view of the brain in different
  • Safe, painless, non-invasive.
  • No special preparation (except the removal of all
    metal objects) is required from the patient.
    Patients can eat or drink anything before the
  • Disadvantages
  • Expensive to use.
  • Cannot be used in patients with metallic devices
  • Cannot be used with uncooperative patients
    because the patient must lie still.
  • Cannot be used with patients who are
    claustrophobic (unless new MRI systems with a
    more open design are used).

  • Functional MRI
  • A fMRI scan showing regions of activation in
    orange, including the primary visual cortex (V1,
  • Functional MRI (fMRI) measures signal changes in
    the brain that are due to changing neural
    activity. The brain is scanned at low resolution
    but at a rapid rate (typically once every 2-3
    seconds). Increases in neural activity cause
    changes in the MR signal via T2 changes this
    mechanism is referred to as the BOLD
    (blood-oxygen-level dependent) effect. Increased
    neural activity causes an increased demand for
    oxygen, and the vascular system actually
    overcompensates for this, increasing the amount
    of oxygenated hemoglobin (haemoglobin) relative
    to deoxygenated hemoglobin.

  • Because deoxygenated hemoglobin attenuates the MR
    signal, the vascular response leads to a signal
    increase that is related to the neural activity.
    The precise nature of the relationship between
    neural activity and the BOLD signal is a subject
    of current research. The BOLD effect also allows
    for the generation of high resolution 3D maps of
    the venous vasculature within neural tissue.
  • While BOLD signal is the most common method
    employed for neuroscience studies in human
    subjects, the flexible nature of MR imaging
    provides means to sensitize the signal to other
    aspects of the blood supply. Alternative
    techniques employ arterial spin labeling (ASL) or
    weight the MRI signal by cerebral blood flow
    (CBF) and cerebral blood volume
  • (CBV). The CBV method requires injection of a
  • of MRI contrast agents that are now in human
  • trials.

MRI fMRI - principle
  • Modern 3 Tesla clinical MRI scanner.
  • Medical MRI most frequently relies on the
    relaxation properties of excited hydrogen nuclei
    in water and lipids. When the object to be imaged
    is placed in a powerful, uniform magnetic field,
    the spins of atomic nuclei with a resulting
    non-zero spin have to arrange in a particular
    manner with the applied magnetic field according
    to quantum mechanics. Nuclei of hydrogen atoms
    (protons) have a simple spin 1/2 and therefore
    align either parallel or antiparallel to the
    magnetic field.

MRI fMRI - principle
  • The spin polarization determines the basic MRI
    signal strength. For protons, it refers to the
    population difference of the two energy states
    that are associated with the parallel and
    antiparallel alignment of the proton spins in the
    magnetic field and governed by Boltzmann
    statistics. In a 1.5 T magnetic field (at room
    temperature) this difference refers to only about
    one in a million nuclei since the thermal energy
    far exceeds the energy difference between the
    parallel and antiparallel states. Yet the vast
    quantity of nuclei in a small volume sum to
    produce a detectable change in field. Most basic
    explanations of MRI will say that the nuclei
    align parallel or anti-parallel with the static
    magnetic field however, because of quantum
    mechanical reasons, the individual nuclei are
    actually set off at an angle from the direction
    of the static magnetic field. The bulk collection
    of nuclei can be partitioned into a set whose sum
    spin are aligned parallel and a set whose sum
    spin are anti-parallel.

MRI fMRI - principle
  • The magnetic dipole moment of the nuclei then
    precesses around the axial field. While the
    proportion is nearly equal, slightly more are
    oriented at the low energy angle. The frequency
    with which the dipole moments precess is called
    the Larmor frequency. The tissue is then briefly
    exposed to pulses of electromagnetic energy (RF
    pulses) in a plane perpendicular to the magnetic
    field, causing some of the magnetically aligned
    hydrogen nuclei to assume a temporary non-aligned
    high-energy state. Or in other words, the
    steady-state equilibrium established in the
    static magnetic field becomes perturbed and the
    population difference of the two energy levels is
    altered. The frequency of the pulses is governed
    by the Larmor equation to match the required
    energy difference between the two spin states.

MRI fMRI - applications
  • Clinical practice, MRI is used to distinguish
    pathologic tissue (such as a brain tumor) from
    normal tissue. One advantage of an MRI scan is
    that it is thought to be harmless to the patient.
    It uses strong magnetic fields and non-ionizing
    radiation in the radio frequency range. Compare
    this to CT scans and traditional X-rays which
    involve doses of ionizing radiation and may
    increase the risk of malignancy, especially in a
  • While CT provides good spatial resolution (the
    ability to distinguish two structures an
    arbitrarily small distance from each other as
    separate), MRI provides comparable resolution
    with far better contrast resolution (the ability
    to distinguish the differences between two
    arbitrarily similar but not identical tissues).
    The basis of this ability is the complex library
    of pulse sequences that the modern medical MRI
    scanner includes, each of which is optimized to
    provide image contrast based on the chemical
    sensitivity of MRI.
  • For example, with particular values of the echo
    time (TE) and the repetition time (TR), which are
    basic parameters of image acquisition, a sequence
    will take on the property of T2-weighting. On a
    T2-weighted scan, fat-, water- and
    fluid-containing tissues are bright (most modern
    T2 sequences are actually fast T2 sequences).
    Damaged tissue tends to develop edema, which
    makes a T2-weighted sequence sensitive for
    pathology, and generally able to distinguish
    pathologic tissue from normal tissue. With the
    addition of an additional radio frequency pulse
    and additional manipulation of the magnetic
    gradients, a T2-weighted sequence can be
    converted to a FLAIR sequence, in which free
    water is now dark, but edematous tissues remain
    bright. This sequence in particular is currently
    the most sensitive way to evaluate the brain for
    demyelinating diseases, such as multiple
  • The typical MRI examination consists of 5-20
    sequences, each of which are chosen to provide a
    particular type of information about the subject
    tissues. This information is then synthesized by
    the interpreting physician.

Positron Emission Tomography (PET)
Positron Emission Tomography (PET)
  • A scanner detects radioactive material that is
    injected or inhaled to produce an image of the
  • Commonly used radioactively-labeled material
    includes oxygen, fluorine, carbon and nitrogen.
  • When this material gets into the bloodstream, it
    goes to areas of the brain that use it. So,
    oxygen and glucose accumulate in brain areas that
    are metabolically active.
  • When the radioactive material breaks down, it
    gives off a neutron and a positron.
  • When a positron hits an electron, both are
    destroyed and two gamma rays are released.
  • Gamma ray detectors record the brain area where
    the gamma rays are emitted. This method provides
    a functional view of the brain.

Positron Emission Tomography (PET)
  • Advantages
  • Provides an image of brain activity.
  • Disadvantages
  • Expensive to use.
  • Radioactive material used.

For images thanks to
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Diagnostic Medical Imaging
  • Thank you for your attention!