Advanced Imaging in Biology and Medicine: Technology, Software Environments, Applications PDF
Preview Advanced Imaging in Biology and Medicine: Technology, Software Environments, Applications
Christoph W. Sensen · Benedikt Hallgrímsson Editors Technology, Software Environments, Applications Advanced Imaging in Biology and Medicine Christoph W. Sensen • Benedikt Hallgrímsson Editors Advanced Imaging in Biology and Medicine Technology, Software Environments, Applications Editors Dr.rer.nat.ChristophW.Sensen BenediktHallgrímsson,Ph.D. SunCenterofExcellenceforVisualGenomics DepartmentofCellBiologyandAnatomy DepartmentofBiochemistry UniversityofCalgary andMolecularBiology 3330HospitalDriveNW UniversityofCalgary CalgaryABT2N4N1 3330HospitalDriveNW G503HealthSciencesCtr. CalgaryABT2N4N1 Canada Canada [email protected] [email protected] Marjan Eggermont is a senior instructor in The Schulich School of Engineering at the University of Calgary,teachingintheareaofengineeringdesign.SheusedtoteachintheFineArtsdepartmentinthe areasofdrawing,artfundamentals,andprintmaking.MarjanhasdegreesinMilitaryHistory(BA)and FineArts(BFA,MFA)andstudiedbrieflyatTheRoyalCollegeofArt(UK).Asanartistshehasbeenin numerousartexhibitionsnationallyandinternationally. Shewasin2004oneoftherecipientsofTheAllanBlizzardAward,anationalteachingawardforcollab- orativeprojectsthatimprovestudentlearning.In2005shewaspartoftheteamthatwontheAmerican SocietyforMechanicalEngineeringCurriculumInnovationAward.Sherecentlyappearedin‘Printmak- ingat TheEdge’as one of45international print artists. Marjan is represented bytheHerringer Kiss galleryinCalgaryandtheElissaCristallgalleryinVancouver. Theimage“TheOriginofThought” isanabstraction oftheMRI(Acetazo- lamidestimulation/Restingcondition)ontheleft.Artistsareoftentryingtoget totheessenceofanimage-theultimateabstraction.Insciencethegoalseems tobeextremerealism,especiallyindigitalimaging-forgoodreasonsImight add.Thisabstractioncanalsobereadasanextremeclose-up.Iamalwaysin- terestedinthesimilaritiesbetweenmacroandmicroscaleimages.AndifItry toimaginewherethoughtisformed,perhapsitis-today-onthemicroand macroscale. ISBN978-3-540-68992-8 e-ISBN978-3-540-68993-5 LibraryofCongressControlNumber:2008934400 (cid:2)c 2009Springer-VerlagBerlinHeidelberg Thisworkissubjecttocopyright. Allrightsarereserved,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting, reproductiononmicrofilmorinanyotherway,andstorageindatabanks.Duplicationofthispublication orpartsthereofispermitted onlyundertheprovisions oftheGermanCopyrightLawofSeptember9, 1965,initscurrentversion,andpermissionforusemustalwaysbeobtainedfromSpringer.Violationsare liabletoprosecutionundertheGermanCopyrightLaw. Theuseofgeneraldescriptivenames,registerednames,trademarks,etc.inthispublicationdoesnotimply, evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelaws andregulationsandthereforefreeforgeneraluse. Printedonacid-freepaper springer.com Preface A picture says more than a thousand words. This is something that we all know to be true. Imaginghas been importantsince the early daysof medicineand biol- ogy,as seen in the anatomicalstudies of LeonardoDa Vincior AndreasVesalius. Morethan100yearsago,thefirstnoninvasiveimagingtechnologies,suchasKon- radRoentgen’sX-raytechnology,wereappliedtothemedicalfield—andwhilestill crude—revolutionizedmedical diagnosis. Today, every patient will be exposed to some kind of advanced imaging technology such as medical resonance imaging, computedtomographyor four-dimensionalultrasoundduringtheirlifetime. Many diseases,suchasbraintumors,areinitiallydiagnosedsolelybyimaging,andmost ofthesurgicalplanningreliesonthepatientimagery.4Dultrasoundisavailableto expectingparentswhowishtocreateuniqueearlymemoriesofthenewbaby,and itmaysoonbeusedforthemorphometricdiagnosisofmalformationsthatmayone daybetreatable—inutero! Light and electron microscopy are unequal brethren, which have contributed to most of our knowledge about the existence and organization of cells, tissues and microorganisms. Every student of biology or medicine is introduced to the fascinating images of the microcosm. New advances have converted these imag- ing technologies,which were consideredby manyto be antiquated,into powerful tools for research in systems biologyand related fields. The developmentof laser technologyandadvancesinthedevelopmentofcomputersystemshavebeeninstru- mentalintheimprovementofimagingtechnologies,whichwillbeutilizedformany generationstogainnewinsightintocomplexbiologicalandmedicalphenomena. Withthecompletionofthehumangenome,hopeswerehighthatwewouldnow beabletoreadthe“blueprint”oflifeandunderstandhowthehumanbodyworks. Unfortunately,as is quite commonin science, the complete genome has triggered more questions than it has helped to answer at this point. A simple approach to understanding how the body functions by reading the “blueprint” is not possible, as almost all of the bodily functions are spatiotemporal in nature. In addition, a protein modification which causes curled wings in Drosophila melanogaster will naturallyhaveacompletelydifferentfunctioninhumans,andsoa1:1transposition ofknowledgefromoneorganismtoanotherisimpossible.Genomeresearchersare v vi Preface now forced to conduct additional large-scale experiments, including gene expres- sion,proteomicandmetabolomicstudies.Integratingthedatafromthesecomplex experimentsis an extremelydifficulttask, and displayingthe results requiresnew approachestoimaginginordertoallowawideaudiencetomakesenseofthefacts. Imaging technologies will be especially useful for the creation of spatiotemporal models,whichcanbeusedfortheintegrationof“omics”data. Aswecanseefromtheabovethreeparagraphs,advancedimaginginmedicine andbiologyisaverywidefield.Whenwestartedtoplanthisbook,wewereunable tofindapublicationthatprovidedabroadsamplingofthisrapidlyexpandingfield. We hope that our readers will appreciate and benefit from the diversity of topics presentedhere. We would like to thank Dr. Andrea Pillmann and Anne Clauss from Springer Verlag,Heidelberg,fortheirendlesspatiencewiththeauthorsandeditors.Without theirconstantsupport,thisbookwouldhavebeenimpossibletocreate. Calgary, BenediktHallgr´ımsson December2008 ChristophW.Sensen Contents PartI ImagingTechnologies 1 Micro-ComputedTomography ................................ 3 StevenK.Boyd 2 AdvancedExperimentalMagneticResonanceImaging ............ 27 UrsulaI.Tuor 3 Freehand3DUltrasoundCalibration:AReview ................. 47 Po-WeiHsu,RichardW.Prager,AndrewH.Gee, andGrahamM.Treece 4 LaserScanning:3DAnalysisofBiologicalSurfaces............... 85 MatthewW.Tocheri 5 OpticalCoherenceTomography:TechniqueandApplications ...... 103 J.B.Thomsen,B.Sander,M.Mogensen,L.Thrane,T.M.Jørgensen, G.B.E.Jemec,andP.E.Andersen 6 MassSpectrometry-BasedTissueImaging....................... 131 CarolE.Parker,DerekSmith,DetlevSuckau, andChristophH.Borchers 7 ImagingandEvaluatingLiveTissuesattheMicroscopicLevel ..... 147 JohnRobertMatyas 8 UltrastructureImaging:ImagingandProbingtheStructure andMolecularMake-UpofCellsandTissues .................... 171 M.Amrein 9 OpticalProjectionTomography ............................... 199 JamesSharpe vii viii Contents 10 MedicalImagingModalities–AnIntroduction................... 225 Jo¨rgPeter PartII Software 11 VolumeVisualizationUsingVirtualReality...................... 257 AntonH.J.Koning 12 SurfaceModeling ........................................... 271 AndreiL.Turinsky 13 CAVEman,AnObject-OrientedModeloftheHumanBody ........ 289 ChristophW.SensenandJungSoh 14 Image-BasedFiniteElementAnalysis .......................... 301 StevenK.Boyd 15 GeometricMorphometricsandtheStudyofDevelopment ......... 319 Benedikt Hallgr´ımsson, Julia C. Boughner, Andrei Turinsky, TrishE.Parsons,CairineLogan,andChristophW.Sensen PartIII Applications 16 ImaginginAudiology ........................................ 339 JosJ.Eggermont 17 ApplicationsofMolecularImagingwithMR..................... 363 LindaB.AndersenandRichardFrayne 18 GenomicDataVisualization:TheBluejaySystem ................ 395 JungSoh,PaulM.K.Gordon,andChristophW.Sensen 19 AnatomicalImagingandPost-GenomicBiology.................. 411 BenediktHallgr´ımssonandNicholasJones 20 FunctionalMeasuresofTherapyBasedonRadiologicalImaging ... 427 David Dean, Nathan Cross, DavoodVarghai,NancyL. Oleinick, andChrisA.Flask Index .............................................................439 Contributors MatthiasAmrein Microscopyand ImagingFacility, Departmentof Cell Biology and Anatomy, FacultyofMedicine,UniversityofCalgary,3330HospitalDriveN.W.,Calgary, AB,CanadaT2N4N1,e-mail:[email protected] LindaBAndersen RadiologyandClinicalNeurosciences,HotchkissBrainInstitute,Universityof Calgary,Calgary,AB,CanadaT2N1N4 and Sea´manFamilyMRResearchCentre,FoothillsMedicalCentre,CalgaryHealth Region,Calgary,AB,CanadaT2N2T9,e-mail:[email protected] P.E.Andersen DepartmentofPhotonicsEngineering,TechnicalUniversityofDenmark, Frederiksborgvej399,Roskilde,DK-4000,Denmark, e-mail:[email protected] ChristophH.Borchers DepartmentofBiochemistry&Microbiology,UniversityofVictoria—Genome British ColumbiaProteinCentre,UniversityofVictoria,#3101-4464Markham Street,VancouverIslandtechnologyPark,Victoria,BC,CanadaV8Z7X8, e-mail:[email protected] JuliaC.Boughner DepartmentofCellBiologyandAnatomyandtheMcCaigBoneandJointInstitute, FacultyofMedicine,UniversityofCalgary,3330HospitalDriveNW,Calgary,AB, CanadaT2N4N1 StevenK.Boyd DepartmentofMechanicalandManufacturingEngineering,SchulichSchoolof Engineering,UniversityofCalgary,2500UniversityDrive,N.W.,Calgary,Alberta, CanadaT2N1N4,e-mail:[email protected] ix x Contributors NathanCross DepartmentofNeurologicalSurgery,CaseWesternReserveUniversity, 10900EuclidAvenue,Cleveland,OH44106,USA DavidDean DepartmentofNeurologicalSurgery,CaseComprehensiveCancerCenter,Case WesternReserveUniversity,10900EuclidAvenue,Cleveland,OH44106,USA, e-mail:[email protected] JosJ.Eggermont DepartmentofPsychology,2500UniversityDriveN.W, UniversityofCalgary, Calgary,AB,Canada,T2N1N4,e-mail:[email protected] ChrisA.Flask Case ComprehensiveCancer Center, Departmentof Radiology,Case Western ReserveUniversity,10900EuclidAvenue,Cleveland,OH44106,USA RichardFrayne RadiologyandClinicalNeurosciences,HotchkissBrainInstitute,Universityof Calgary,Calgary,AB,CanadaT2N1N4 and SeamanFamilyMRResearchCentre,FoothillsMedicalCentre,CalgaryHealth Region,Calgary,AB,CanadaT2N2T9,e-mail:[email protected] AndrewH.Gee Department of Engineering, University of Cambridge, Trumpington Street, CambridgeCB21PZ,UK PaulM.K.Gordon FacultyofMedicine,UniversityofCalgary,SunCenterofExcellenceforVisual Genomics,3330HospitalDriveNW,Calgary,AB,Canada,T2N4N1 BenediktHallgr´ımsson DepartmentofCellBiologyandAnatomyandtheMcCaigBoneandJointInstitute, FacultyofMedicine,UniversityofCalgary,3330HospitalDriveNW,Calgary,AB, CanadaT2N4N1,[email protected] Po-WeiHsu Department of Engineering, University of Cambridge, Trumpington Street, CambridgeCB21PZ,UK G.B.E.Jemec Department of Photonics Engineering, Technical University of Denmark, Frederiksborgvej399,Roskilde,DK-4000,Denmark NicholasJones McCaigBoneandJointInstitute,FacultyofMedicine,UniversityofCalgary,3330 HospitalDriveNW,Calgary,AB,CanadaT2N4N1,e-mail:[email protected]
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