Advances in Bio-Imaging: From Physics to Signal Understanding Issues: State-of-the-Art and Challenges

250 Pages·2012·13.7 MB·English

by  Jo Keeble, Chi Ching Goh, Yilin Wang, Wolfgang Weninger, Lai Guan Ng (auth.), Nicolas Loménie, Daniel Racoceanu, Alexandre Gouaillard (eds.)

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ISBN978-3-642-25193-1 ISBN978-3-642-25546-5
Nicolas Loménie, Daniel Racoceanu,
and Alexandre Gouaillard (Eds.)
Advances in Bio-Imaging:
From Physics to Signal
Understanding Issues
State-of-the-Art and Challenges
ABC
Editors
Dr.NicolasLoménie Dr.AlexandreGouaillard
SilesianUniversityofTechnology SingaporeImmunology
IPAL,I2R&CNRS, Network(SIgN),
RepublicofSingapore RepublicofSingapore
Dr.DanielRacoceanu
IPAL,I2R&CNRS,
RepublicofSingapore
ISSN1867-5662 e-ISSN1867-5670
ISBN978-3-642-25546-5 e-ISBN978-3-642-25547-2
DOI10.1007/978-3-642-25547-2
SpringerHeidelbergNewYorkDordrechtLondon
LibraryofCongressControlNumber:2011941759
(cid:2)c Springer-VerlagBerlinHeidelberg2012
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Thisbookisdedicated tothe
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technologicalcollaborationandfriendship.
Foreword
Wearedelightedtohaveco-organizedthe2011editionoftheSingaporean-French
BioimagingWorkshoptogetherwith IPAL. Thiseditionwas heldin Biopolis, and
attracted200scientistsmainlyfromthefieldsofimageprocessingandbiology.This
interdisciplinaryapproachisdeartoourheartformanyreasons:firstofallwebe-
lievethatscientificinnovationsanddiscoveriescomefrombridgingdisciplines,as
shownmanyyearsagobyLeonardodaVinci.Second,thiseventhasbeenanillus-
trationofhowsuccessfulajointBMRC-SERCinitiativecanbeincatalyzingshared
interestsinbio-imaging,fromimagingtoimmunology,includingimageprocessing,
physicsetc.Thecomplexityofthehumanimmunesystemcanonlybeaddressedby
amultidisciplinaryapproach.SIgNisplanningtomakemoreofsucheventshappen
in the future in order to foster communication between the two communities and
enhanceknowledgecreation.
Singapore,September2011 PaolaCastagnoli,AlexGouaillard,
PhilippeKourilsky
Preface
After more than ten years of passionate research work between Singaporean and
FrenchscientistswithintheImageandPervasiveAccessLaboratory1,ajointwork-
shopaboutbio-imagingtechnologieshasbeenheldatBiopolis,SingaporeinFebru-
ary 2011 in which the long-term scientific collaboration about computer vision
issues and medical image analysis applications has been shaped again for the
next couple of decades. This workshop was aimed at detecting the key techno-
logical partnerships to be promoted within the broad topic of bio-imaging. The
workshop followed a multidisciplinary approach by sharing researchers’ experi-
ence from the physics of acquisition [Athanasiou et al. 2008] to the numerical
handlingoftheacquireddatathroughcutting-edgeresearchinbiologyandlifesci-
ences[Lutzetal.2008].
As the currentseriesis historicallymostly orientedtowardsthe numericalhan-
dling of visual data, we highlighted the image analysis challenges related to each
contributed topic. However, this book is targeting an audience of students or re-
searchers in the field of bio-imaging that are willing to get the big picture of the
multi-(if possible trans-)disciplinary aspects of bio-imaging. Subsequently, con-
tributions from physics and chemistry are given a large share of exposure while
emerging research works in bio-engineeringrelated to high-contentscreening are
broached.
The workshophas been a greatsuccess with more than one hundredregistered
attendees mostly local Singaporeans working either within the Biopolis facilities
or the NationalUniversity of Singaporeresearch units. A few collaborationshave
beensetupsofarbetweenaFrenchandaSingaporeanteam.Forinstance,aFrench
researchworkaboutinnovativechemicalprobesasdescribedinthisbook(seep.37,
infra)hasbeenfosteredbyacollaborationwithaSingaporeanphysicsteamexpert
inspecificmeasuredevices.
Aspecificrangeofpapersdealswiththeemergingfieldofdigitizedhistopathol-
ogy building up a bridge between two communities: the one that handles real
1IPAL CNRS UMI France-Singapore 2955 (I2R/A*STAR, NUS, UJF, TELECOM,
UPMC/Sorbonne).
X Preface
matterandtheonethatdealswithinformationalmatter.Bybringingtogethercogni-
tive,mathematical,algorithmicandtechnologicalissues, thisnewfield constitutes
aperfectcandidatetobecomeafavouriteplaygroundforinnovativeintegratedap-
proaches for high-content, distributed monitoring of physiologicalbiologicalpro-
cessesasenvisionedbytheVirtualPhysiologicalHumanproject2.
Webelievethatthisintroductiontothelatestdevelopmentsinthebroadfieldof
bio-imagingwill deliver as much as inspiration and willingness for the upcoming
generationofresearcherstotacklethenewchallengesofbiologysystems.
References
[Athanasiouetal.2008] Athanasiou, A., Deffieux, T., Gennisson, J.L., Montaldo, G.,
Muller,M.,Tardivon,A.,Fink,M.:Quantitativeassessment ofbreastlesionviscoelas-
ticity:initialclinicalresultsusingSuperSonicImagineshearimaging.UltrasoundMed.
Biol.(April4,2008)
[Lutzetal.2008] Lutz, C., Otis, T., DeSars, V., Charpak, S., DiGregorio, D.A., Emiliani,
V.:Holographic photolysis of caged neurotransmitters. NatureMethods 5(9), 821–827
(2008)
Singapore, NicolasLome´nie
May2011, AlexandreGouaillard
DanielRacoceanu
2http://www.vph-noe.eu/
Acknowledgments
We are verygratefulto theSingaporeanresearchagencieswithin A*STARandin
particulartheJointCouncilOrganization(JCO)thatfundedtheworkshoptofoster
collaborationsbetweentheBiopolisandFusionopolisresearchteams3inSingapore.
TheFrenchEmbassyviatheMERLIONgrantandUniversityParisDescartes4made
it possible to invite outstanding speakers from French research top institutes. The
FrenchNationalCenter forResearch (CNRS5) gavethe firstimpulseto set upthe
eventandbeitearnestlyacknowledgedfortheconstantefforttowardstheFrench-
Singaporeancollaborationsuccessovertheyears.ManythankstotheIPALteam6
andI2R7fortheorganizationandabovealltotheSIgN8teamforthestrongsupport:
PeggyandCheryl,executiveassistant managersandPaolaCastagnoli,headofthe
department.
3http://www.a-star.edu.sg/tabid/860/default.aspx
4http://www.sorbonne-paris-cite.fr/index.php/en
5http://www.cnrs.fr/
6http://ipal.i2r.a-star.edu.sg/
7http://www.i2r.a-star.edu.sg/
8http://www.sign.a-star.edu.sg/
Contents
PartI Biology
IntravitalMultiphotonImagingofImmuneCells..................... 3
JoKeeble,ChiChingGoh,YilinWang,WolfgangWeninger,
andLaiGuanNg
1 Introduction.............................................. 3
2 MultiphotonMicroscopy ................................... 4
3 IntravitalSkinImagingModel .............................. 5
3.1 TheSkin:AnImportantImmunologicalSite ........... 5
3.2 TheMouseEarSkinModel ......................... 6
3.3 VisualizingImmuneCellsintheVasculatureandSkin... 6
3.4 DataProcessingandPresentation .................... 9
3.5 IntravitalMultiphotonImagingConsiderations......... 10
4 The Missing Link in MultiphotonMicroscopy:Software
Development............................................. 11
4.1 ImageAcquisitionandDataManagement ............. 11
4.2 SpectralUnmixing ................................ 11
4.3 ImageAnalysis ................................... 12
4.4 TowardsStandardizedImaging ...................... 12
4.5 DataInterpretationandPresentation.................. 13
5 ConcludingRemarks ...................................... 13
FunctionalMRIofNeuralPlasticityandDrugEffectintheBrain....... 17
Kai-HsiangChuangandFatimaA.Nasrallah
1 Introduction.............................................. 17
2 MRIofNeuralPlasticityafterNerveAmputation............... 18
3 MRIofNeuralPlasticityafterLearning....................... 20
4 MRIofDrugEffect ....................................... 22
5 ConcludingRemarks ...................................... 23