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Biomedical Imaging and Image Analysis
Lecture in Medical Informatics Course
Ewert Bengtsson
Professor of computerized image analysis Division of Visual Information and Interaction
Department of Information Technology
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The theme • Images are of central importance in medical
diagnosis • There has been a dramatic development in
medical imaging during the last few decades • In this lecture we will briefly describe different
ways of – Lecture 1: Creating
– Lecture 2: Analyzing
medical images
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Medical imaging vs. microscopy • There are two main types of medical images:
Microscopic and macroscopic. • The macroscopic images are typically taken in
situ from the patient while microscopic images are based on small samples taken out of the patient.
• The term “Medical imaging” is typically limited to images of the patient and his/her organs on a macroscopic scale.
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Medical imaging motivations • Medical imaging is used to
visualize and understand the patient – Anatomy
– Physiology (function)
– Discovering injuries or pathology
• Different imaging methods are
better at one or the other aspect
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Medical imaging modalities
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Imaging motivations - microscopy • Visual evaluation of tissue samples
in a microscope is usually the final basis for diagnosis of all cancers and many other diseases
• Used to be all optical Is rapidly becoming digital Also a rapid development of new microscopy imaging techniques
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Microscopic imaging modalities • Brightfield light microscopy
– The classical microscopy • Fluorescent microscopy
– Used for research – Several versions:
• Full field • Confocal • Two-photon • STED
• Electron Microscopy – The highest resolution but
complex and tedious
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Microscopic images • Brightfield microscopy
• Fluorescent microscopy
• Tissue microarray
• Electron microscopy
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Medical imaging
• Using different parts of the electromagnetic spectrum – PET – hard gamma rays,
511keV – X-ray images, CT – Visible light – Heat images, thermography – Radio waves from nuclear
spinn, MRT – The electric activity of the
body, EEG • Sound waves, ultrasound
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Classical X-ray projection, gives a 2D shadow image
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X-rays: Röntgen – the inventor
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X-ray technology trends
• Since about 100 years X-ray imaging through analogue electronic technology and photography
• Since about 30 years with digital technology
• Digital technology is rapidly taking over – in this field as in most other
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Fluoroscopy vs radiography
• Fluoroscopy –transillumination, – Creates a live image of
the patient – Can support real time
diagnosis – Shows dynamics – Can control certain
invasive diagnostic procedures
– Gives a relative high dose also to the medical doctor
• Radiography – X-ray photography • Creates a frozen
permanent image • Can be interpreted
without rush • Gives medical and
legal documentation
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Fluoroscopy
• Fluoroscope, originally zinkcadmiumsulphide screen, 7% efficiency
• Electro-optical image amplifiers with fluorescent screen (>10.000 x amplification)
• Image amplifier with TV-camera (tube or CCD) • Digitally registering the image from the TV-
camera – Digital fluoroscopy – Digital subtraction angiography
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Blood vessels - Angiography
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Digital fluoroscopy
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Radiography • Original direct film exposure, gives the sharpest
images but low efficiency, only used in special cases such as dental imaging
• Amplification screens converts X-rays to light, gain 100-10 000 x
• Can use secondary aperture, a grid to decrease scattered light and increase contrast
• The film can be replaced by image plates, gives a greater dynamic range and possibilities of directly digitizing and improving the image through image processing
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Muscles and bones
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Conventional vs digital, high-frequency amplified X-ray image
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Digital radiography, advantages
• Greater contrast range gives fewer retakes because of poor exposure
• Digital image handling gives fewer lost films and simplified archiving
• More enviromentally friendly through less use of film and chemicals
• Easier to consult other experts over the network
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Computed Tomography (CT)
Creates images of slices through the body
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How the tomograph functions
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CT-functional principles
• In a large number of projection rays though the body the X-ray absorption is measured, this yields many density profiles.
• These can be reprojected into the slice through Radons formula or through filtered back projection
• CT gives good contrast resolution and very good geometric accuracy
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Computed tomography
CT gives anatomical information
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CT image properties
• CT measures X-ray density in absolute units according to the Hounsfields scale – -1000 for air – 0 for water – +1000 for bone
• Through different contrast windows in the display different tissues can be displayed optimally
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A modern CT can have 64 parallel channels
• Typical specifications; • 64 x 0.625mm acquisition • 0.34mm x 0.34mm x 0.34mm isotropic resolution • 0.4 second rotation time • Up to 24 Lp/cm ultra-high spatial resolution • High resolution 768 and 1024 reconstruction matrices • Reconstruction up to 40 images per second
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CT examples
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Magnetic Resonance Tomography (MRT)
Based on magnetic pulse sequences in a strong magnetic field
Different pulse sequences gives different contrast
The orientation of the slices can be chosen freely through manipulation of the magnetic fields
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Magnetic Resonance Imaging
MRI gives anatomical information
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Magnetic Resonance Imaging
MRI the main parts of the machine
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How MRT works • Nuclei with odd number of protons/neutrons has
spin
• The spin vector can be aligned to a (very) strong magnetic field
• Can be disturbed by a radio signal in resonance with the spin frequency, the so called Larmorfrequency
• When the atoms returns to rest position they become radio transmitters which can be detected by sensitive receivers
• Through conrol of field gradients and pulse sequences one can determine which atoms are activated and listened to respectively and thus images can be created in 2D and 3D
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Some fundamental MR-concepts
• MR-images can be weighted to show two time constants giving different contrast:
• T1 is the time constant that determines how fast the spin MZ returns to equilibrium, it is called spin lattice relaxation time Mz = Mo ( 1 - e-t/T1 )
• T2 is the time constant that determines the return to equilibrium for the transversal magnetisation MXY, it is called spin-spin relaxation time MXY =MXYo( e-t/T2)
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MRT image properties
• Very good contrast resolution for soft tissue • Very flexible, different pulse sequences
gives different contrast • Usually not possible to determine the signal
levels in absolute terms • Poor geometric precision • No known harmful effects • Still under strong development
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MR Neuro
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Muscles and bones (joints)
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Microscopic resolution for orthopedics
• 0.078 mm in-plane resolution of wrist
• Observe clear delineation of fine structures such as the vessel walls
• Technical details: – T1 FLASH – TR 591 ms, – TE 7.5 ms, – TA 6:09 min, – SL 3 mm, – slices 19, – matrix 1024, – FoV 80 mm.
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Whole body MR imaging
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Neurological
Multiple sclerosis
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Angiography
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The heart
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MRT technologies • The image properties are influenced by many
factors: • Radio antenna coils can be adapted to anatomy and
pathology – Closer coil gives better image
• Different pulse sequences gives different contrast, resolution, signal noise and registration times
• Triggering by heart beat, blood motion and breading can increase the resolution
• Contrast media can enhance certain structures • With functional MR, fMRI activity in the brain can be
registered and imaged
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MRT technologies • The image properties are influenced by many
factors: • Radio antenna coils can be adapted to anatomy and
pathology – Closer coil gives better image
• Different pulse sequences gives different contrast, resolution, signal noise and registration times
• Triggering by heart beat, blood motion and breading can increase the resolution
• Contrast media can enhance certain structures • With functional MR, fMRI activity in the brain can be
registered and imaged
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Functional imaging
SHOWS WHERE THE BRAIN IS PARTICULARLY ACTIVE
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Functional imaging - how it works
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MR diffusion tensor imaging
• Showing the connections of “fibers” in the brain
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Brain fiber visualization by Anders Brun CMIV/CBA
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For further studies about MRT
• A good description of the MRI technology at: http://www.cis.rit.edu/htbooks/mri/inside.htm
• A good popular description at: – http://www.nobel.se/medicine/laureates/2003/pre
ss-sv.html • A leading research group in MR and other
medical image visualisation, CMIV: – http://www.cmiv.liu.se
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Positron Emission Tomograpy (PET) PET shows the concentration and distribution of positron emitting tracer substances in the patient.
These images are functional, not anatomical, i.e. they show physiological parameters
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PET – functional principle
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PET functional principles
• A positron emitting compound is injected into the body (must be produced in an accelerator)
• The positrons will, within a couple of mm, collide with an electron and create two co-linear 511keV gamma rays
• These are detected by two detectors located in opposite locations in rings around the person and based on this one can figure out where the event took place
• Re-projection based on the tomographic principle
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Positron Emission Tomography
PET gives functional information
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Positron Emission Tomografi : accelerator for creating the radioactive
tracer substances
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The properties of PET images • Gives functional images with rather good
resolution at least 1 cm • Glucose can be labelled with C11 and this
makes it possible to see where in the brain “fuel” is needed i.e. where the brain is working
• Very specific substances can be labelled so PET has many applications in pharmaceutical research
• The need for an accelerator and a chemical lab which can handle high speed synthesis of radioactive compounds makes the technology very expensive
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PET in Uppsala • The PET-research in Uppsala is in the international
front-line • In 2001 the university PET-centre was sold to
Amersham-Biosciences and Imanet AB was created • Amersham-Biosciences was bought by GE Medical a
few years later • Now the PET-centre medical activity is back at
Uppsala university hospital • Will get the first PET-MR system in Sweden next year
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Typical result from PCA image enhancement of PET images HV NK1-receptor tracer GLD
Pasha Razifar PhD thesis work at IMANET AB and CBA
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Single Photon Emission Computed Tomography (SPECT)
SPECT is
similar to PET and shows the concentration and distribution of a radioactive tracer in the patient. The images are functional, not anatomical.
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Scintigraphy - SPECT camera
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SPECT functional principles • A radioactive tracer is injected into the body • With a matrix of detectors arranged above the
body the location of the radioactive disintegrations is approximately determined
• The detector can be moved into different positions, which makes tomographic reconstruction possible
• Alternatively a collimator with slanted holes can be used - ectomography
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Single Photon Emission Tomography
SPECT gives functional information
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The SPECT image properties
• SPECT gives a functional image with relatively low resolution, some cm
• The images are intrinsically 3D • The radioactive compounds can be
obtained from long lived mother isotopes which is much cheaper than accelerators
• Dynamic processes can be studied through long registrations
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Ultrasound, US • Based on the sonar, acoustic echo
principle. Sound with high frequency, typically a few MHz is sent into the body and the echoes are studied.
• Can with a small, compact equipment give dynamic images in 2D or 3D.
• The images has problems with coherent noise, specle, and with non-linearities in the sound propagation.
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Ultrasound equipment
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Ultrasound, best at showing soft tissue
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Heart
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Ultrasound images of a heart
Sharp images of structures in a moving heart
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Ultrasound for fetal examinations
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3D rendering of dynamic Ultrasound
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Ultrasound can show flow through Doppler technology
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Digital image analysis
• Most modern medical imaging devices are digital • This creates opportunities for also using digital
image processing techniques to help interpret the images
• Actually digital techniques are necessary even for being able to handle some types of images
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Advantages of digital technology • Can create images with greater contrast range with
less radiation • Can handle the images more efficiently through
PACS – Picture Archiving and Communication Systems
• Can create completely new types of images – Slice images, computer tomography – Three dimensional volume images – Images of new physiological aspects e.g. oxygen
consumption or flow • Can visualize the images in new ways, 3D • Can extract quantitative information from the images
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Man vs computer • Man is superior when it comes to
recognising and interpreting patterns • The computer is superior when it comes to
– Store – Transport – Present – Count and measure
• The computer can make the images better for human visual analysis
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PACS – the computer as an administrative tool
• Large amounts of images are registered dayly at a modern hospital. Administration and storage of these requires great resources
• A Picture Archiving and Communication System, PACS, can make this more rational
• Requires high capacity storage units and networks. Typically several TB needs to be handled and stored.
• Sectra-Imtec in Linköping is a leading company in this field
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Digital image enhancement
• When the images are available in digital format the computer can be used to help presenting them optimally
• In order to enhance the images they are filtered – point-wise – through neighbourhood filters – or in the spectral domain
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Point-wise greyscale transforms
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Example of simple greyscale transforms: Contrast inverted mammograms
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Contrast-enhancement
with non-linear
greyscale-transform
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Image subtraction image with contrast – image without
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Spatial filtering
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Mean filtering
Linear quadratic mean filter with increasing size 3,5,9,15,35
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Noise reducing filtering
Original image 3x3 mean filter 3x3 medianfilter
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Laplace filter 3x3
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Edge sharpening filter
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Image filtering example a) Whole body
image
b) Laplace filtered
c) Sum a and b
d) Sobel filtered a
e) 5x5 mean of a
f) c*e
g) a+f
h) Greyscale transf. of g
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Image enhancement with the Context Vision method (adaptive neighboorhood filtering)
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Context Vision filtering of MR
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Medical image analysis: CAD - Computer Aided Diagnosis
• To filter an image so that it becomes significantly better for visual analysis is difficult, the visual system is very adaptive and can handle rather poor images
• To automatically find abnormalities in images is even harder, requires advanced image analysis
• The techology is about to mature in this area
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Typical Mammography image
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Typical Mammography image
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Typical Mammography image
Automated detection of suspicious cancerous lesions
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Quantitative Microscopy
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Exp_Wt7777, number of blobs per cell
0
50
100
150
200
250
300
350
400
0 50 100 150
red
gree
n
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BlobFinder Special features •z-stack input and enhancement slice by slice •zooming •slide-bar for object thresholding in real time (at configuration setup)
GUI by Amin Allalou
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An MR camera gives a 3D image. Classical X-ray image handling works with 2D film. 3D images gives a whole stack of 2D images to be interpreted jointly
3D MRI
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Volume rendering An imaginative light ray is sent through each pixel
in the image plane. The colour and intensity is determined through the interaction between the ray and the volume elements in the volume in combination with different light sources.
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Volume rendering methods • Single modalities
– Greylevel gradient shading – Maximum intensity projection (MIP) – Integrated projection
• Multiple modalities – Combined rendering – Implicit segmentation
– Surface projection of cortical activity
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Greylevel gradient shading • A greylevel threshold is set and rays are sent into the volume
until a volume element with a value greater than the threshold is encountered
• The intensity gradients at these positions are combined with the light sources to render the the image
• Cutting planes can be used to remove parts of the volume to make other parts more visible
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3D volume rendering used for CT
Much easier than for MR because of fixed Hounsfield units
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Maximum intensity
projection (MIP) • Along each ray the maximal density/intensity value is determined
• This is particularly useful for small intense structures such as the vessels in angiography
• Can become complex if several vessels are crossing and overlapping each other
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MIP projections of a contrast enhanced MRA volume. Original MIP Arteries Veins
With special image analysis (based on greyscale connectivity) the different vessel
can be separated
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Rotating MIP gives good 3D effect
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Image Fusion
• Different modalities give complimentary information, anatomy and physiology respectively. There are therefore needs to fuse data from different modalities
• Image fusion includes – spatial registration – combined visualisation – combined analysis
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05-10-10 103
Choose starting par
Transform Study
Evaluate similarity (cost function)
Converged?
Choose new set of parameters
Reference Study
No Yes
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PET-MRI
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SPECT-MRI
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Multimodal registration can also be combined with 3D visualization
- =
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Surface projection of cortical activity
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05-10-10 108
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Stereo rendering
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05-10-10 111
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3D visualisation requires segmentation
• Small differences in the properties of different tissue types makes advanced segmentation methods necessary
• High demands of correct reproduction of small details in the anatomy
• Need for rapid interaction between man and the system
• Greate needs for research
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Summary
• Humans are good at recognising patterns • Computers are good at counting and measuring • The 3D reality is hard to represent accurately in
2D images • Computers can significantly improve and
facilitate medical diagnostics • So far mainly by producing new types of images • In the future 3D visualisation and CAD will
probably also have great importance
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THE END
That's all, thanks for your attention!