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Editedby EmmanuelG.Reynaud ImagingMarineLife RelatedTitles Speight,M.,Henderson,P. Kubitscheck,U.(ed.) MarineEcology-Conceptsand FluorescenceMicroscopy Applications FromPrinciplestoBiologicalApplications 2010 2013 PrintISBN:978-1-444-33545-3, PrintISBN:978-3-527-32922-9, alsoavailableasdigitalformat alsoavailableasdigitalformat Eleftheriou,A.(ed.) Miller,C.,Wheeler,P. MethodsforStudyofMarine Biological Oceanography Benthos 2ndEdition 2012 4thEdition PrintISBN:978-1-444-33301-5, 2013 alsoavailableasdigitalformat PrintISBN:978-0-470-67086-6, alsoavailableasdigitalformat Biotechnology Journal www.biotechnology-journal.com Edited by Emmanuel G. Reynaud Imaging Marine Life Macrophotography and Microscopy Approaches for Marine Biology TheEditor LimitofLiability/DisclaimerofWarranty:While thepublisherandauthorhaveusedtheirbest effortsinpreparingthisbook,theymakeno Dr.EmmanuelG.Reynaud representationsorwarrantieswithrespectto SchoolofBiology&EnvironmentalScience theaccuracyorcompletenessofthecontentsof ScienceCentreWest thisbookandspecificallydisclaimanyimplied UniversityCollegeDublin warrantiesofmerchantabilityorfitnessfora Belfield particularpurpose.Nowarrantycanbecreated Dublin4 orextendedbysalesrepresentativesorwritten Ireland salesmaterials.TheAdviceandstrategiescon- tainedhereinmaynotbesuitableforyoursit- Cover uation.Youshouldconsultwithaprofessional Planktonorganisms(diatoms(rows1–2), whereappropriate.Neitherthepublishernor hydroid(row3)andradiolarian(row4)can authorsshallbeliableforanylossofprofitor beimagedusingdifferenttechniquesand anyothercommercialdamages,includingbut differentimageprocessingschemes.Thecover notlimitedtospecial,incidental,consequential, showsfourdifferentorganisms:Planktoniella orotherdamages. sol(Schu¨tt,1892;MarquesasArchipelago,Tara Oceans),Coscinodiscussp.(Azoresislands, LibraryofCongressCardNo.:appliedfor TaraOceans),Porpitaporpita(Linnaeus, 1758;NorthPacificOcean;LuisGutierrez- BritishLibraryCataloguing-in-PublicationData Heredia,TaraOceans)andaradiolarian Acataloguerecordforthisbookisavailable (Actinommasp.;MediterraneanSea,Tara fromtheBritishLibrary. Oceans).Alloriginalcolourimageswere convertedto8-bitthenprocessedusingdif- Bibliographicinformationpublishedbythe ferentLookupTables(LUT)tohighlight DeutscheNationalbibliothek specificcharacteristicsusingNIHImageJ. TheDeutscheNationalbibliothekliststhispub- Backgroundunderwaterscene©adimas, licationintheDeutscheNationalbibliografie; fotolia.com detailedbibliographicdataareavailableonthe Internetat<http://dnb.d-nb.de>. ©2014Wiley-VCHVerlagGmbH&Co.KGaA, Boschstr.12,69469Weinheim, Germany Wiley-BlackwellisanimprintofJohnWiley& Sons,formedbythemergerofWiley’sglobal Scientific,Technical,andMedicalbusinesswith BlackwellPublishing. Allrightsreserved(includingthoseof translationintootherlanguages).Nopart ofthisbookmaybereproducedinany form–byphotoprinting,microfilm,orany othermeans–nortransmittedortranslated intoamachinelanguagewithoutwrittenper- missionfromthepublishers.Registerednames, trademarks,etc.usedinthisbook,evenwhen notspecificallymarkedassuch,arenottobe consideredunprotectedbylaw. PrintISBN:978-3-527-32744-7 ePDFISBN:978-3-527-66420-7 ePubISBN:978-3-527-67542-5 MobiISBN:978-3-527-67543-2 oBookISBN:978-3-527-67541-8 CoverDesign AdamDesign,Weinheim, Germany Typesetting LaserwordsPrivateLimited, Chennai,India PrintingandBinding MarkonoPrintMedia PteLtd,Singapore Printedonacid-freepaper. V Contents Preface XIII ListofContributors XVII 1 UndertheEyeofNeptune:AnHistoricalPerspectiveofMarine CreatureImagery 3 EmmanuelG.Reynaud 1.1 Introduction 3 1.2 AncientUsesoftheOceans 5 1.2.1 Seafarers 5 1.2.2 TheMediterraneanSea:thecradleofmarinebiology 6 1.2.2.1 AristotleandPlinytheElder,theFoundingFathers 6 1.2.2.2 UnderstandingtheOceans 7 1.3 FromNeptunetoAnimalcules 8 1.3.1 AgeofEuropeanDiscoveryandExploration 8 1.3.2 VoyagesofExplorationandfinallyScience 9 1.3.3 AGlimpseattheInvisible 9 1.4 TheBirthofOceanography(TheNineteenthCentury) 10 1.4.1 DrawingtheJellyfish 10 1.4.2 TheH.M.S.ChallengerExpedition 11 1.4.3 StationsandInstitutions 14 1.5 TheTwentiethCentury:Institutionsandmovingimages 15 1.5.1 Newtools – newimages: 15 1.5.2 JeanPainleve 16 1.5.3 TheWritersandtheExplorers 16 1.5.4 TheFuture 18 1.6 TimeLineofOceanImagery 18 FurtherReading 20 BasicTexts 20 SourceBooks 20 ShipsandExpeditions 21 Institutions 21 VI Contents 2 NewSolutionsinUnderwaterImagingandVisionSystems 23 FranciscoBonin-Font,AntoniBurguera,andGabrielOliver 2.1 Introduction 23 2.2 UnderwaterOpticalImageFormation 25 2.3 IlluminationTechniques 27 2.3.1 IlluminationSources 27 2.3.2 SelectionoftheLightSourcePosition 28 2.3.3 IlluminatingSystems 30 2.4 Laser-BasedTechniques 32 2.4.1 LaserRange-Gating(LRG)Methods 32 2.4.2 LaserLineScan(LLS)Methods 33 2.4.3 ScatteredLightRejectionUsingModulation/Demodulation Techniques 33 2.5 UnderwaterImagingInfrastructures 34 2.6 ImageImprovementviaPolarization 35 2.6.1 ExtendedRangeUsingPolarization 36 2.6.2 Housing 36 2.6.3 ExperimentalEvaluation 37 2.7 AVisionSystemforUnderwaterApplications 39 2.7.1 TheFuguVisionSystem 40 2.8 Conclusion 42 Acknowledgements 44 References 44 3 HolographicMicroscopyofMarineOrganisms 49 StefanK.Jericho,ManfredH.Jericho,andHansJ.Kreuzer 3.1 Introduction 49 3.2 AdvantagesofHolographicMicroscopy 50 3.3 PastAttemptstoImageMicroplankton 51 3.4 PointSourceDigitalIn-LineHolographicMicroscopy 54 3.4.1 Instruments 55 3.4.2 ImageReconstruction 56 3.4.3 ImageExamples 58 3.4.4 Resolution 60 3.4.5 VolumeImagingChallenges 63 3.5 FutureOutlook 64 References 65 4 ConfocalLaserScanningMicroscopy – DetailedThree-Dimensional MorphologicalImagingofMarineOrganisms 69 JanMichels 4.1 Introduction 69 4.2 TechnicalandMethodologicalAspectsofConfocalLaserScanning Microscopy 69 Contents VII 4.3 PrerequisitesforGeneratingHigh-QualityConfocalLaserScanning Micrographs 73 4.4 UsingAutofluorescencesforDetailedThree-Dimensional MorphologicalImaging 76 4.5 ApplicationofFluorescenceDyes 80 4.6 SurfaceTopographyAnalyses 85 4.7 FuturePerspectives 88 Acknowledgements 89 References 89 5 OpticalProjectionTomography 93 KarlGaff,LukeMcCormacParker,DeeLawlor,and EmmanuelG.Reynaud 5.1 Introduction 93 5.2 WhatIsOpticalProjectionTomography? 94 5.2.1 AssemblyofanOPTSystem 98 5.2.1.1 DetectionUnit 98 5.2.1.2 IlluminationUnits 98 5.2.1.3 SampleManipulationUnit 98 5.2.2 IlluminationSources 99 5.2.3 SystemCapabilitiesandLimitations 99 5.3 ComparisonwithOther3DMicroscopyTechniques 100 5.3.1 ConfocalMicroscopy 101 5.3.2 Two-PhotonMicroscopy 102 5.4 SamplePreparation 102 5.5 ImageProcessingandAnalysis 104 5.6 MarineBiologyApplications 104 Acknowledgments 108 References 108 6 ElectronMicroscopyTechniquesforImagingMarine Phytoplankton 111 GustaafHallegraeff 6.1 Introduction 111 6.2 CollectingandProcessingSpecimens 112 6.3 LightMicroscopy 113 6.4 SedimentCystSurveys 113 6.5 TransmissionElectronMicroscopy 114 6.6 ScanningElectronMicroscopy 116 Acknowledgements 121 References 121 VIII Contents 7 LookingInsideMarineOrganismswithMagneticResonanceandX-ray Imaging 123 IreneZanette,GheylenDaghfous,TimmWeitkamp,BrigitteGillet, DominiqueAdriaens,MaxLanger,PeterCloetens,LukasHelfen, AlbertoBravin,Fran¸coisePeyrin,TiloBaumbach,Jean-MichelDischler, DenisVanLoo,TomasPraet,MariePoirier-Quinot,andRenaudBoistel 7.1 Introduction 123 7.2 MagneticResonanceImaging 124 7.2.1 ExperimentalSetup 124 7.2.2 HardwareImprovements 128 7.2.3 Contrast 128 7.2.4 Applications 129 7.2.4.1 AnatomicalMRI 129 7.2.4.2 FunctionalMRI 129 7.2.4.3 DiffusionTensorImagingorDiffusionMRI(DTI) 129 7.2.4.4 MEMRIorManganese-EnhancedMagneticResonance Imaging 131 7.3 X-RayMicrotomography 132 7.3.1 Sources 133 7.3.1.1 Laboratory-BasedSetups 133 7.3.1.2 Synchrotron-BasedSetups 135 7.3.2 SampleStage 138 7.3.3 Detector 138 7.3.4 ForwardProblem(ContrastFormation) 140 7.3.5 TomographicReconstruction 142 7.3.5.1 2DFilteredBack-Projection 142 7.3.5.2 ImageQualityandArtifacts 144 7.3.5.3 3DImageReconstruction 145 7.4 Synchrotronlaminography 146 7.4.1 Introduction 146 7.4.2 ImageReconstruction 149 7.4.3 ExampleApplications 151 7.5 AbsorptionImaging 151 7.5.1 NaturalContrast 151 7.5.2 StainingContrast 152 7.6 Phase-ContrastImaging 155 7.6.1 Introduction 155 7.6.2 Free-SpacePropagationMethods(Holotomography) 157 7.6.3 Analyzer-BasedImaging 160 7.6.3.1 Applications 161 7.6.4 X-RayGratingInterferometry 162 7.6.4.1 Introduction 162 7.6.4.2 PerformanceCharacteristicsandApplications 165 7.7 Applications(Post-treatment) 166 7.7.1 Segmentation – VisualizationMethods 166