Introduction au cours

Fund BioImag 20131-11: Introduction to the courseHow is the course organized ?What is Bio-imaging ? What is the importance of biomedical imaging ?ExamplesTour of the Imaging Centre (CIBM)After this course youknow the course organization and coverage of topics;know the contribution of bio-imaging to life science and why it is an interdisciplinary effort. know the main elements required for bio imaging; are able to perform contrast to noise and signal to noise calculations;are familiar with noise error propagation calculations1Fund BioImag 20131-21-1. How is the course organized ?Exercises (Fri 15:15 CE 1):Handed out by assistant on day of lectureAvailable on moodleSolution of selected problems of prior weekIf you miss a course The course given in 2011 was filmed the link is provided on moodleppt animation do not showyoutube videos do not play fullyCourse web site (moodle, physics, master):moodle.epfl.ch/course/view.php?id=250If we havent enrolled you yet: Enrollment key = bioimaging13Copies of the presentationWill be provided on moodle (pdf) ppsx : provided as link at lesson No. ()Please take notes during lecture without using polycopiesIf the lecture is unclear, holler !90% chance you are not the only oneThere are no stupid questions (I will take any question seriously)You can also approach me in the breakI will be present in the exercises

Your participation wanted!2Fund BioImag 20101-3What is the content of this course ?ThemeElementsIntroduction(Lectures 1-2)Definition and importance of bio-imagingUltrasound imagingBasis of x-ray imagingX-ray imaging(Lectures 3-7)Interactions of photons with matter/RadioprotectionX-ray imaging (computed tomography)Emission computed tomographyPositron emission tomographyTracer dynamicsMagnetic resonance I Basics(Lectures 8-10)Basis of magnetic resonance effectT1 and T2 relaxationSpectroscopy Echo formationMagnetic resonance IIAdvanced topics and contrast mechanisms(Lectures 11-13)Elements of image formationBiophysics of BOLD Contrast agentsDiffusion tensor imagingLinksLife science @ EPFLSystems and signalsImage processingMathematical and computational models in biologyPhysicsNeural networks and biological modelingClassical electrodynamics3Fund BioImag 20131-4Course text:Andrew Webb Introduction to biomedical imaging(250p. ~EUR 110, available as ebook at the library EPFL)USD 60+ on amazon.comIs more complete on MRIExcellent reference text for later useWhat supplemental reading/material is recommended ?Other Text booksZhang-Hee Cho, Joie J. Jones, Manbir Singh Foundations of Medical ImagingWilliam R. Hendee, E. Russel Ritenour Medical Imaging PhysicsJerrold T. Bushberg, J. Anthony Seibert, Edwin M. Leidholt, John M. Boone The Essential Physics of Medical Imaging For a shorter text: Penelope Allisy-Roberts, Jerry Williams Farrs Physics for Medical Imaging (200p., small, ~EUR 50)USD 30+ on amazon.comA lot of focus on simple x-ray (not covered in the course)

I will provide pdf versions of the lecture on moodleHandouts without your personal notes will not be complete. To complete the Handoutspersonal notes during courseincorporate insights gained during exos4Fund BioImag 20131-5What do these images represent ?

Data: Rosalind FranklynX-ray diffraction image of DNA crystalsWatson, Crick, Wilkins (Nobel 1962)MRI of a headLauterbur / Mansfield (2003)X-ray image of the handRntgen (1901) / Cormack & Hounsfield (1979)Electron microscopy of red blood cellsRuska (1986)5Fund BioImag 20131-61-2. What is Biomedical Imaging ?What is Contrast ? Ability to distinguish tissue features against noiseContrast = difference in signal between tissues one wishes to distinguishIn reality one needs to deal with Contrast-to-noiseLocalized measurement of a contrast generating biophysical effect in body/organ of living systemWhat is measured (some useful definitions)Image=nxm matrix of pixels Pixel = picture element 3D image=kxnxm matrix of voxelsVoxel = volume elementImportant:Contrast between voxels/pixelsDefinition of bio-imagingSTOP!Is there a free lunch for imaging ?In principle n,m,k can be unlimitedResolutionSensitivity/Contrast6Fund BioImag 20131-7What is the difference between signal-to-noise and contrast-to-noise ratio ?To obtain good measurements (not only in imaging) we need good signal to noise ratio

Definition Signal-to-noise ratio (SNR)S: signal (or measurement variable)s: standard deviation of its measurement (either determined experimentally (how?) or estimated quantitatively)

SNR provides a means to estimate the precision with which the signal S is measured

To discriminate two signals S1 and S2 we need more than just good signal to noise ratio. The ability to discriminate the two is assessed using the contrast to noise ratio

Definition Contrast-to-noise ratio (CNR)S1 and S2 : two signals (or measurement variable) of two different tissues,s : standard deviation of their measurement (see left, assumed here to be identical and statistically independent)

CNR provides a means to estimate the precision with which the signal S1 can be discriminated from S2

It is possible to have excellent SNR but no CNR (when?)7Fund BioImag 20131-8How can we optimize SNR ?It is possible to optimize SNR by performing N repeated measurements Si. The precision of the average =Si/N depends on the square root law (4 measurements improve the precision by twofold): Si=S+ei

where =s2, =0.

S is the true signal (unknown)

=Si/N=S+ ei/N

This is well-known from statistics (SEM) results in increased measurement time

=0, ij

8Fund BioImag 20131-9How can we optimize CNR ?Optimizing contrast = choice of experimental parameters (e.g. protocol) to maximize the difference in two tissue signals S1 and S2. complex and empirical procedure some effects can be predicted/calculated, if the signal behavior can be modeled.

Maximum is where derivative with respect to t is zero

t0=1/kFor an exponentially decaying signal, the optimal time of measurement is equal to 1/decay rateHow critical is the choice of t0 ?t0=0Error propagation calculation Let the signal S be a function S(k,t) k is a tissue property (signal decay rate) t an experimental parameter (such as time). Approach:Determine dS/dkFind t0 where dS/dk is maximal by taking derivative rel. to tExample:9Fund BioImag 20131-101-3. What is the importance of Bio-Imaging ? Life Sciences are unthinkable without Bio-Imaging Assessment of biological processes with minimal perturbation of the systemExamples: Humans, animals, cell/organ preparationsModalities: x-raycomputed tomographypositron emission tomographymagnetic resonanceultrasoundelectrical imaging (EEG, MEG)optical imagingDevelopment of Bio-Imaging capabilities, modalities and effects unthinkable without physics 10Fund BioImag 20131-11What are essential ingredients of bio-imaging ? Life Sciences PhysicsEngineering/Good instrumentationMathematicsChemistryMathematicsCancerElectricalMechanicalBio- & organic chemistryElectrodynamicsQuantum mechanicsThermodynamicsClassical MechanicsNeuroscienceMulti-disciplinarity is important !Biomedical engineering

11Fund BioImag 20131-12What is the perfect imaging modality ?Easy to usePortableHighly sensitive/good contrast

Does this exist ?

In this course you will learn to appreciate these and the reasons behindIn reality, every imaging method/modality has its strengths and limitations

12Fund BioImag 20131-131-4. ExamplesAutoradiography

Autoradiography of a brain sliceAutoradiography of a gelAutoradiography of a monkey brain (visual cortex)13Fund BioImag 20131-14What are the distinct advantages of Bio-imaging compared to tissue analysis ?Imaging advantages relative to histology or invasive tissue analysisRapid acquisition of the informationNon-destructive, i.e. minimal perturbationIn situ or in vivoRepetitive (longitudinal) studies possible

Mice subjected to 30 min of strokeassessed using MRI before and 3-24h afterHistology: Tissue is fixed, cut into slices, then subjected to a dye. The resulting sections are then analyzed.

Ultrasound of mouse heart14Fund BioImag 20131-15Examples: Biomedical Imaginghttp://nobelprize.org/educational_games/physics/imaginglife/narratives.html

3D rendering of tumor for surgical planning (MRI)Metastasis localization (PET)fMRI of whole brain activation15Whats next today ?Fund BioImag 20131-161. Tour of CIBMIf you would like to volunteer for a brief (15min) scan of your brain let us know

2. Exercise (~45min)

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