Signal and Image Analysis for Biomedical and Life Sciences PDF
Preview Signal and Image Analysis for Biomedical and Life Sciences
Advances in Experimental Medicine and Biology 823 Changming Sun Tomasz Bednarz Tuan D. Pham Pascal Vallotton Dadong Wang Editors Signal and Image Analysis for Biomedical and Life Sciences Advances in Experimental Medicine and Biology Volume 823 EditorialBoard IrunR.Cohen,TheWeizmannInstituteofScience,Rehovot,Israel N.S.AbelLajtha,KlineInstituteforPsychiatricResearch,Orangeburg,NY,USA JohnD.Lambris,UniversityofPennsylvania,Philadelphia,PA,USA RodolfoPaoletti,UniversityofMilan,Milan,Italy Moreinformationaboutthisseriesathttp://www.springer.com/series/5584 Changming Sun • Tomasz Bednarz (cid:129) Tuan D. Pham Pascal Vallotton (cid:129) Dadong Wang Editors Signal and Image Analysis for Biomedical and Life Sciences 123 Editors ChangmingSun TuanD.Pham TomaszBednarz TheUniversityofAizu PascalVallotton Fukushima,Japan DadongWang DigitalProductivityFlagship,CSIRO Sydney,NSW,Australia ISSN0065-2598 ISSN2214-8019(electronic) ISBN978-3-319-10983-1 ISBN978-3-319-10984-8(eBook) DOI10.1007/978-3-319-10984-8 SpringerChamHeidelbergNewYorkDordrechtLondon LibraryofCongressControlNumber:2014955163 ©SpringerInternationalPublishingSwitzerland2015 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartof thematerialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation, broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformation storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology nowknownorhereafterdeveloped.Exemptedfromthislegalreservationarebriefexcerptsinconnection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’slocation,initscurrentversion,andpermissionforusemustalwaysbeobtainedfromSpringer. PermissionsforusemaybeobtainedthroughRightsLinkattheCopyrightClearanceCenter.Violations areliabletoprosecutionundertherespectiveCopyrightLaw. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant protectivelawsandregulationsandthereforefreeforgeneraluse. While the advice and information in this book are believed to be true and accurate at the date of publication,neithertheauthorsnortheeditorsnorthepublishercanacceptanylegalresponsibilityfor anyerrorsoromissionsthatmaybemade.Thepublishermakesnowarranty,expressorimplied,with respecttothematerialcontainedherein. Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface With an emphasis on applications of computational models for solving modern challengingproblemsinbiomedicalandlifesciences,thisbookaimstobringcollec- tionsofarticlesfrombiologists,medical/biomedicalandhealthscienceresearchers together with computational scientists to focus on problems at the frontier of biomedical and life sciences. The goals of this book are to build interactions of scientistsacrossseveraldisciplinesandtohelpindustrialusersapplyadvancedcom- putationaltechniquesforsolvingpracticalbiomedicalandlifescienceproblems. This book is for users in the fields of biomedical and life sciences who wish to keep abreast with the latest techniques in signal and image analysis. The book presents a detailed description to each of the applications. It can be used by those bothatgraduateandspecialistlevels. Wehaveincluded14chaptersinthisbook.Someofthechaptersareextensively revised versions of papers that were presented at the International Symposium on ComputationalModelsforLifeSciencesheldon27–29November2013inSydney, Australia. There are two main parts in the book: signal and image analysis issues withinthesubjectsofthebook. In the first part of the book, Chap.1 presents a novel visualisation strategy tailoredforproteomicsdata.Adatasetisvisualisedshowingphosphorylationevents inresponsetoinsulinthatleadstonewinsightsintotheinsulinresponsepathway. Astrategyforweb-basedpresentationofdataisalsodescribed.Chapter2proposes a new approach for the modelling of testosterone regulation to identify all model parameters from the hormone concentrations of testosterone and luteinizing hor- mone.Simulationresultsaredescribedtorevealbehavioursimilartoclinicaldata. Chapter3proposestwodistincthybridalgorithmsthatcombineefficientsequential change-point detection procedures with the Cross-Entropy method. Results show effectiveness of the described method. In Chap.4, two methods for distinguishing betweenhealthycontrolsandpatientsdiagnosedwithParkinson’sdiseasebymeans ofrecordedsmoothpursuiteyemovementsarepresentedandevaluated.Theresults are indicative of the potential of the presented methods as diagnosing or staging v vi Preface toolsforParkinson’sdisease.Chapter5presentsanapproachfortheidentification oftheReichardtelementarymotiondetectormodel.Apoolofspatiallydistributed elementarymotiondetectorsisconsidered,andawayofdesigningthevisualstimuli for a certain order of spatial resolution is suggested. Chapter 6 discusses on the complexityensemblemeasuresforgaittimeseriesanalysisthatcouldhaveasignifi- cantlywiderapplicationscoperangingfromdiagnosticsandearlydetectionofphys- iological regime change to gait-based biometrics. Chapter 7 presents the develop- mentofamotioncapturingandloadanalyzingsystemforcaregiversaidingapatient tositupinbed.Thedifferencebetweentheperformancesofthetwotypesofcare- giverswerefound:theprofessionaladoptedaposturethatwassafeanddidnotstress the lumbar vertebrae, whereas the layperson tended to adopt an unsafe posture. Chapter 8 proposes an unsupervised multi-scale K-means algorithm to distinguish epilepticEEGsignalsandidentifyepilepticzones.Theexperimentalresultsdemon- strate that identifying seizure with multi-scale K-means algorithm and delay per- mutationentropyachieveshigheraccuracythanthatofK-meansandsupportvector machine.Chapter9presentsamethodforthetrackingofEEGactivityusingmotion estimationinbraintopomapstounderstandthemechanismofbrainwiring.Authors demonstratethatitispossibletotrackthepathofasignalacrossvariouslobes. Inthesecondpartofthebook,Chap.10presentsanapproachtoprocessingultra high-resolution, large-size biomedical imaging data for the purposes of detecting andquantifyingvasculatureandmicrovasculature.Theresultsoncerebralandliver vasculatures of a mouse captured at the Shanghai Synchrotron Radiation Facility are presented. Chapter 11 describes a novel way of carrying out image analysis, reconstruction and processing tasks using cloud based service provided on the Australian National eResearch Collaboration Tools and Resources infrastructure. Thetoolboxisavailableontheweb.Chapter12presentsaninvestigationintohow MasseyUniversity’sPollenClassifyndercanacceleratetheunderstandingofpollen and its role in nature. Chapter 13 presents a digital image processing and analysis approachforactivatedsludgewastewatertreatment.Chapter14presentsacomplete systemfor3Dreconstructionofrootsgrowninatransparentgelmediumorwashed andsuspendedinwater. Wethankalltheauthorsfortheircontributionstothiseditedbook.Wealsothank DanHillsandSusanMcMasterfromCSIROContractsandLegalfortheirhelpwith the Publishing Agreement between Springer and CSIRO. We are grateful to Dr. Thijs van Vlijmen, Sara Germans-Huisman, Magesh Kaarthick Sundaramoorthy, and other editors at Springer and S. Madhuriba at SPi Technologies India Private Ltd. for their help and great support from the beginning to the production of this book. Materials from the American Institute of Physics (AIP) Publishing that are used by some authors are acknowledged and credits are given in the respective chapterswithinthisbook. Sydney,Australia ChangmingSun TomaszBednarz Aizu,Japan TuanD.Pham Sydney,Australia PascalVallotton DadongWang July2014 Contents PartI SignalAnalysis 1 VisualAnalyticsofSignallingPathwaysUsingTimeProfiles ......... 3 DavidK.G.Ma,ChristianStolte,SandeepKaur,MichaelBain, andSeánI.O’Donoghue 2 ModelingofTestosteroneRegulationbyPulse-Modulated Feedback..................................................................... 23 PerMattssonandAlexanderMedvedev 3 HybridAlgorithmsforMultipleChange-PointDetection inBiologicalSequences .................................................... 41 Madawa Priyadarshana, Tatiana Polushina, and Georgy Sofronov 4 StochasticAnomalyDetectioninEye-TrackingDatafor QuantificationofMotorSymptomsinParkinson’sDisease ........... 63 DanielJansson,AlexanderMedvedev,HansAxelson,and DagNyholm 5 Identification of the Reichardt Elementary Motion DetectorModel.............................................................. 83 EgiHidayat,AlexanderMedvedev,andKarinNordström 6 Multi-complexity Ensemble Measures for Gait Time SeriesAnalysis:ApplicationtoDiagnostics,Monitoring andBiometrics.............................................................. 107 ValeriyGavrishchaka,OlgaSenyukova,andKristinaDavis vii viii Contents 7 DevelopmentofaMotionCapturingandLoadAnalyzing SystemforCaregiversAidingaPatienttoSitUpinBed .............. 127 Akemi Nomura, Yasuko Ando, Tomohiro Yano, Yosuke Takami,ShoichiroIto,TakakoSato,AkinobuNemoto,and HiroshiArisawa 8 ClassifyingEpilepticEEGSignalswithDelayPermutation EntropyandMulti-scaleK-Means ....................................... 143 GuohunZhu,YanLi,Peng(Paul)Wen,andShuaifangWang 9 TrackingofEEGActivityUsingMotionEstimationto UnderstandBrainWiring ................................................. 159 Humaira Nisar, Aamir Saeed Malik, Rafi Ullah, Seong-O Shim, Abdullah Bawakid, MuhammadBurhanKhan,andAhmadRaufSubhani PartII ImageAnalysis 10 Towards Automated Quantitative Vasculature UnderstandingviaUltraHigh-ResolutionImagery .................... 177 Rongxin Li, Dadong Wang, Changming Sun, Ryan Lagerstrom,HaiTan,YouHe,andTiqiaoXiao 11 CloudBasedToolboxforImageAnalysis,Processingand ReconstructionTasks....................................................... 191 Tomasz Bednarz, Dadong Wang, Yulia Arzhaeva, Ryan Lagerstrom,PascalVallotton,NeilBurdett,AlexKhassapov, PiotrSzul,ShipingChen,ChangmingSun,LukeDomanski, DarrenThompson,TimurGureyev,andJohnA.Taylor 12 Pollen Image Classification Using the Classifynder System:AlgorithmComparisonandaCaseStudyonNew ZealandHoney ............................................................. 207 Ryan Lagerstrom, Katherine Holt, Yulia Arzhaeva, Leanne Bischof, Simon Haberle, Felicitas Hopf, andDavidLovell 13 Digital Image Processing and Analysis for Activated SludgeWastewaterTreatment ............................................ 227 MuhammadBurhanKhan,XueYongLee,HumairaNisar, ChoonAunNg,KimHoYeap,andAamirSaeedMalik 14 ACompleteSystemfor3DReconstructionofRootsfor PhenotypicAnalysis........................................................ 249 PankajKumar,JinhaiCai,andStanleyJ.Miklavcic Index............................................................................... 271 Contributors YasukoAndoYokohamaCityUniversity,Yokohama,Japan HiroshiArisawaYokohamaNationalUniversity,Yokohama,Japan YuliaArzhaevaDigitalProductivityFlagship,CSIRO,NorthRyde,Sydney,NSW, Australia HansAxelsonDepartmentofNeuroscience,Neurophysiology,UppsalaUniversity, Uppsala,Sweden MichaelBainTheUniversityofNSW,Sydney,NSW,Australia Abdullah BawakidFaculty of Computing and Information Technology, King AbdulAzizUniversity,Jeddah,KingdomofSaudiArabia TomaszBednarzDigitalProductivityFlagship,CSIRO,Sydney,NSW,Australia LeanneBischofDigitalProductivityFlagship,CSIRO,NorthRyde,Sydney,NSW, Australia NeilBurdettDigitalProductivityFlagship,CSIRO,Brisbane,QLD,Australia Jinhai CaiSchool of Information Technology and Mathematical Sciences, Phenomics and Bioinformatics Research Centre, Australian Centre for Plant FunctionalGenomics,UniversityofSouthAustralia,MawsonLakes,SA,Australia ShipingChenDigitalProductivityFlagship,CSIRO,Sydney,NSW,Australia KristinaDavisDepartmentofPathology,UniversityofMichigan,AnnArbor,MI, USA LukeDomanskiCSIROIM&T,Sydney,NSW,Australia Valeriy GavrishchakaDepartment of Physics, West Virginia University, Morgantown,WV,USA ix
The list of books you might like
