GPU-Accelerated Optical Coherence Tomography Signal Processing and Visualization

152 Pages·2016·18.52 MB·English

GPU-Accelerated Optical Coherence
Tomography Signal Processing and
Visualization
Seyed Hamid Hosseiny Darbrazi
Department of Physics and Astronomy
University of Porto
This thesis is submitted for the degree of
Doctor of Philosophy
Porto 2016

Dedicated to my family

Preface
This thesis is the result of the work undertaken at the Center for Applied Photonics (CAP)
GroupofINESCTEC,situatedattheDepartmentofPhysicsandAstronomyoftheFaculty
ofScienceoftheUniversityofPorto,Porto,Portugal,andtheResearchLaboratoryofElec-
tronics (RLE) Laser Medicine and Medical Imaging Group, located at the Department of
Electrical Engineering and Computer Science of the Massachusetts Institute of Technology
(MIT),Cambridge,USA.
Exceptwherespecificreferenceismadetotheworkofothers,thecontentsofthisthesis
are original and have not been submitted in whole or in part for consideration for any other
degreeorqualificationinthis,oranyotherUniversity.
HamidHosseiny
Advisors:
Dr. Carla Carmelo Rosa, Assistant Professor, advisor at the University of Porto and the
thesisadvisor
Prof. James G. Fujimoto, Professor of Electrical Engineering and Computer Science,
advisorattheMassachusettsInstituteofTechnology
Dr. ZhaoWang,PostdoctoralAssociate,co-advisorattheMassachusettsInstituteofTech-
nology

Acknowledgements
This thesis would have not been possible without the support, time and dedication of many
people with whom I had the pleasure of working throughout my PhD journey. Therefore, I
wouldherebyliketoexpressmysinceregratitudetoallofthem.
Foremost,IwouldliketothankmyadvisorsDr. CarlaCarmeloRosa,Prof. JamesFuji-
moto, and Dr. Zhao Wang for sharing their knowledge, and for their guidance and support
duringmyPhDstudyattheirsites. Ithasbeenatrueprivilegetoconductmyresearchattwo
international institutes of Portugal and USA, where I had access to outstanding resources
andtheopportunitytoworkintheworld-classlaboratories.
I am deeply grateful to all my caring colleagues and friends at the Center for Applied
Photonics(CAP)GroupandtheResearchLaboratoryofElectronics(RLE)LaserMedicine
andMedicalImagingGroup. Allscientificdiscussionsduringtheweeklymeetings,journal
clubs and lab work are greatly appreciated. Not only did these scientific gatherings play an
importantroleforthesuccessofmywork,butalsotheoccasionalsocialgroupgatheringin
Porto,PortugalandtheseasonalsocialgroupmeetingsinCambridge,USA.
I would like to acknowledge the financial support of the national Portuguese funding
agency,FoundationforScienceandTechnology(FCT),throughthegrantSFRH/BD/72801/
2010fortheentirePhDstudy. Iwouldalsoacknowledgetheexternalsupplementsupportof
theNationalInstituteofHealthandAirForceOfficeofScientificResearchduringmystudy
at the RLE Laser Medicine and Medical Imaging Group of the Massachusetts Institute of
Technology(MIT).
Last, but not least, I am deeply thankful to my family to whom I dedicate this thesis.
My most heartfelt thanks to my wife Parisa for her understanding, unending support, and
unwaveringlove. WordscannotexpresshowthankfulIamtomyfatherandmotherfortheir
allsacrifices,endlessaffectionandunconditionallove.

Abstract
Opticalcoherencetomography(OCT)hasbeencontinuouslyevolvingoverthepast25years
since its advent in early 1990’s. Despite the advances in the development of ultrahigh-
resolution and -speed OCT imaging systems, real-time processing and 2D/3D/4D visual-
ization of acquired OCT volumes are required. The emergence of graphics processing unit
(GPU) and its highly optimization advantage for massive parallel processing have tremen-
dously assisted OCT technology to meet the aforementioned need. This thesis presents
highly optimized GPU-based signal processing algorithms to significantly shorten process-
ing time of spectral domain (SD) and swept source (SS) optical coherence tomography
imagingsystems. TheoptimizationtechniquesforefficientOCTdataprocessingand2D/3D
visualizationareexplainedindetail. Areal-timevideoratevolumetric4DSS-OCTimaging
system is developed. The potential applications of such a powerful optical imaging tool are
introduced.
Thus far, high speed GPU-based OCT data processing approaches have been shown for
processing and display of small OCT volumes because of GPU memory latency and some
other hardware limitations. Conversely, this thesis demonstrates the feasibility of real-time
processing and visualization of large OCT volumes (1024 A-scans×1024 B-scans) with
highefficiency(81%)byusingonlyasinglecommercial-gradeGPU.
The spectrometer design and optimization steps for SD-OCT imaging systems are de-
scribed. Some important considerations to choose appropriate spectrometer components to
improve the overall performance are explained. A spectral calibration method that can be
used for calibration of SD-OCT and SS-OCT imaging systems is proposed, and it is nu-
merically implemented. A real-time video rate SD-OCT imaging system is developed for
sensing and imaging applications. Such a developed system is employed for quantitative
evaluationofpolyethyleneterephthalate(PET)bottlepreformsinrealtime.
Keywords: OpticalCoherenceTomography,OCTSignalProcessing,SpectrometerDesign
andOptimization,SpectralCalibration,OpticalThicknessMeasurement,Intra-
operativeOpticalCoherenceTomography,GraphicsProcessingUnit