Manuel JorgeM. MarquesCurriculum Vitae

107 Canterbury RoadHerne Bay CT6 5SA

Kent, United Kingdom

T +44(0)1227 823772 (office)H +44(0)7501 323646

B manuel@mjmarques.euÍ mjmarques.eu

mjmarques@manuelmarque

Last updated: 10th February 2019

“Live this day as if it will be your last.” (Og Mandino)

QualificationsOctober 2012 toNovember 2016

PhD in Physics, School of Physical Sciences, University of Kent, Canterbury, UnitedKingdom.Thesis title: “Spectrometer-based Optical Coherence Tomography Systems with ExtendedFunctionality”, under the supervision of Prof Adrian Podoleanu, submitted in April 2016,viva-voce examination took place in August 2016, graduated November 2016.Examiners: Prof Christoph Hitzenberger (Medical University of Vienna), Dr Stuart Gibson(University of Kent).

September 2007to September

2012

BSc+MSc in Engineering Physics, Faculdade de Ciências da Universidade doPorto, Porto, Portugal.Integrated Masters Programme (BSc+MSc).Level 16.8 in a numerical scale of 20.

EmploymentMay 2017 topresent day

Research Associate, Applied Optics Group, University of Kent, Canterbury, UnitedKingdom.Post-doctoral researcher in the EPSRC-funded project “Robotic Endobronchial Optical Tomog-raphy” (REBOT ), jointly with Hamlyn Robotics Centre (Imperial College London).The purpose of the REBOT project is to develop a robot-guided endobronchial probe thatwill allow access to the deepest reaches of the lung. It will be introduced through a workingchannel of a bronchoscope, making it highly compatible with current procedures. This probewill incorporate several imaging modalities such as OCT and fluorescence imaging.

May 2016 to April2017

Research Associate, Applied Optics Group, University of Kent, Canterbury, UnitedKingdom.Post-doctoral researcher in the European Research Council Proof of Concept project “Add-onmodule for optical coherence tomography with en-face view option” (AMEFOCT ).Developing Optical Coherence Tomography systems utilising a new signal processing technol-ogy invented at the AOG, Complex Master-Slave Interferometry.

September2010–2016

Project Instructor, Physics and Astronomy Department, Faculdade de Ciências daUniversidade do Porto, Porto, Portugal.Tutoring of high school students in the annual department-organised week-long PhysicsSummer School (Escola de Verão de Física) project on robotics and control systems (pro-gramming PID controllers in LEGO Mindstorms systems using LabVIEW). Also managing andsupervising the on-line registration and feedback process.

Manuel J. M. Marques’ CV Page 1 of 8

April 2015 toOctober 2015

Research Assistant in Photonics/Optical Coherence Tomography, Applied Op-tics Group, University of Kent, Canterbury, Kent, United Kingdom.Pre-doctoral Researcher in the project titled "Combined time domain and spectral domaincoherence gating for imaging and biosensing", funded by the European Research Council(ERC), grant number 249889.

October 2012 toApril 2015

Graduate Teaching Assistant, School of Physical Sciences, University of Kent, Can-terbury, Kent, United Kingdom.Performing laboratory demonstrations and marking as part of the Graduate Teaching AssistantStudentship programme, which funded my PhD studies.

October 2009 toOctober 2012

Researcher, INESC Porto, Optoelectronics and Electronic Systems Unit, Porto,Portugal.Researching in the area of White Light Interferometry and Optical Coherence Tomography(Applied Optics).

February 2012 toAugust 2012

Visiting MSc exchange (Erasmus) Student, Applied Optics Group, School of Phys-ical Sciences, University of Kent, Canterbury, Kent, United Kingdom.Researching in the area of White Light Interferometry and Optical Coherence Tomography(Applied Optics) as part of my Master’s degree in Physical Engineering, supported by theErasmus Placement programme.

July 2009 to June2010

Translator, Calouste Gulbenkian Foundation, Project “Casa das Ciências” , Porto,Portugal.Translating educational/formative texts and applets from English/French to Portuguese, so thatthey could be distributed among high school teachers.

Volunteering workSince 2017 Reviewer for IEEE’s Photonics Technology Letters journal.Since 2016 Reviewer for MDPI’s Sensors and Applied Sciences journals.Since 2015 Reviewer for Optical Society of America’s Applied Optics journal.

June 2014 toOctober 2016

President of the University of Kent OSA Student Chapter (http://osakent.osahost.org/)

November 2013 toJune 2014

Vice-president of the University of Kent OSA Student Chapter (http://osakent.osahost.org/)

June 2013 to June2014

Treasurer of the Portuguese Association of Researchers and Students in the UnitedKingdom - PARSUK (http://www.parsuk.pt/)

July 2012 toNovember 2013

Treasurer and web-designer of the University of Porto SPIE Student Chapter (http://upspiechapter.inescporto.pt/)

February 2009 toJanuary 2012

Member of the administration and web-designer of the Portuguese Association ofPhysics Students - Physis (http://physis.org.pt/)

Teaching and mentoring experience{ Mentoring (i) 2 PhD students (European Industrial Doctorate), whose projects

involved Optical Angiography with OCT and multi-modal imaging with OCT andphoto-acoustic microscopy; (ii) 2 MSc students (line-field OCT, dispersion mea-surements with white light interferometry); (iii) 1 UG student (assembly of a visiblespectrometer for OCT).

{ Teaching assistant at the School of Physical Sciences’ PS370 module, “Skills forPhysicists” for the academic years 2012-13, 2013-14 and 2014-15 (∼ 200 hours peryear).- lab demonstrator role: answering student queries, addressing issues with the experimentalset-ups and protocols.- marking lab reports (3 lab reports along the year), providing comprehensive feedback onthem.- training new PS370 lab demonstrators for the 2015-16 academic year.

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Public engagementDecember 14th,

2018Participant in the Hamlyn Centre Christmas Showcase (Imperial College London)with an endoscopic optical coherence tomography probe demonstration done incollaboration with the REBOT project researchers.

November 24th,2015

Invited talk (repeat from the one in December 2014) titled “Optical Coherence To-mography: from a Michelson interferometer to 3-D biomedical imaging (and beyond!)”for a Physics undergraduate audience (Physics students’ society - Physoc - at theUniversity of Kent).

April 23rd, 2015 Joint invited talk (with Dr Adrian Bradu) titled “Seeing the Unseen: A talk about novelbiomedical imaging techniques” for the public (IOP / CSES lecture) at Chelmsford,Essex, United Kingdom.

March 14th, 2015 Volunteer and part-organiser for the “Light Up Your Life - Day of Discovery ” communityoutreach event at The Beaney House of Art of Knowledge (Canterbury).

December 9th,2014

Invited talk (repeat from the one in February 2014) titled “Optical Coherence Tomogra-phy: from a Michelson interferometer to 3-D biomedical imaging (and beyond!)” for aPhysics undergraduate audience (Physics students’ society - Physoc - at the Universityof Kent).

October 4th, 2014 Student Guide and Physics Lab Demonstrator (School of Physical Sciences) at theUniversity of Kent Open Days.

July 18th, 2014 Presented poster showcasing current research at an Institute of Physics Updatesession (for Physics teachers), which took place in the School of Physical Sciences,University of Kent.

July 12th, 2014 Student Guide (School of Physical Sciences) at the University of Kent Open Days.

February 18th,2014

Invited talk titled “Optical Coherence Tomography: from a Michelson interferometerto 3-D biomedical imaging (and beyond!)” for a Physics undergraduate audience(Physics students’ society - Physoc - at the University of Kent).

Personal skills and competencesLanguages{ Portuguese: Native. { English: Highly fluent.

{ French: Basic understanding and ex-pression (elementary school level).

{ Spanish: Basic understanding and ex-pression.

Social skills and competences{ Experience in team work and mentoring from previous work and volunteering posi-

tions, and also from sport-related activities, in particular from rowing and athletics.Also holds a UKCC Level 2 Award in Coaching Sessions, awarded by British Rowingin November 2016.

Computer skills{ Operating Systems: GNU/Linux (ma-

jor distributions only, Fedora andUbuntu); Mac OS (pre- and post-OSX); Microsoft Windows/DOS.

{ Programming: Python and LabVIEW(used regularly); C/C++, PHP (basicknowledge).

{ Scientific and Engineering: WolframMathematica; AutoCAD; OpenSCAD;OriginLab; scipy and matplotlib.

{ Typography and Design: LATEX2e;Inkscape; The GIMP; Scribus; AdobePhotoshop.

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{ Web Design: XHTML, CSS. Experiencein setting up on-line content manage-ment systems (CMS) such as Plone,Drupal, and WordPress.

Scientific societies membershipsSPIE (the international society for optics and photonics, formerly the Society ofPhoto-Optical Instrumentation Engineers), since June 2012; OSA (Optical Societyof America), since November 2012; Sociedade Portuguesa de Física (PortuguesePhysics Society), since January 2013.

FundingFebruary 2018 Secured funding from the University of Kent Faculty of Sciences Research Fund to

cover the refurbishment costs of the lab’s Vytran GPX-3600 glass processing machine(totalling £1,300).

November 2015 Awarded SPIE Travel Scholarship ($1,500) for attending Photonics West 2016 (SanFrancisco, California, United States of America).

September 2014 Awarded Incubic/Milton Chang Travel Grant ($500) for attending Frontiers in Optics2014/Laser Science (Tucson, Arizona, United States of America).

Prizes and awardsJune 2016 Outstanding Postgraduate Research Student in Physical Sciences, awarded by the

School of Physical Sciences, University of Kent (Canterbury, United Kingdom).

June 2014 Best poster award - SEPnet Graduate Network Summer School (National PhysicalLaboratory, Teddington, United Kingdom).

June 2013 Best poster award (Faculty of Sciences) - 3rd Annual University of Kent Post-graduateResearch Festival (Canterbury, United Kingdom).

March 2006 toSeptember 2007

Participant on the 2006-2007 edition of the Portuguese Physics Olympiads, wherequalified for the Ibero-American Physics Olympiads.

Peer-reviewed publications and conference proceedingsManuel J. Marques, Sylvain Rivet, Adrian Bradu, and Adrian Podoleanu. Complexmaster-slave for long axial range swept-source optical coherence tomography. OSAContinuum, 1:1251–1259, December 2018.

Adrian Bradu, Niels Møller Israelsen, Michael Maria, Manuel J. Marques, SylvainRivet, Thomas Feuchter, Ole Bang, and Adrian Podoleanu. Recovering distanceinformation in spectral domain interferometry. Scientific Reports, 8:15445, October2018.

Fangliang Bai, Stuart J. Gibson, Manuel J. Marques, and Adrian Podoleanu. Super-pixel guided active contour segmentation of retinal layers in OCT volumes. In Proc. ofSPIE, volume 10591, page 1059106. International Society for Optics and Photonics,March 2018.

Sophie Caujolle, Ramona Cernat, Giuseppe Silvestri, Manuel J. Marques, AdrianBradu, Thomas Feuchter, Gary Robinson, Darren K. Griffin, and Adrian Podoleanu.Assessing embryo development using swept source optical coherence tomography. InProc. of SPIE, volume 10591, pages 1059108–1, 2018.

Adrian Podoleanu, Ole Bang, Sophie Bojesen, Magalie Bondu, Adrian Bradu, SophieCaujolle, Catherine Chin, Mark Denninger, Thomas Feuchter, Felix Fleischhauer,Merete Hædersdal, Niels Møller Israelsen, Mikkel Jensen, Ivan B. Gonzalo, Michael

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Maria, Manuel J. Marques, Lasse Leick, Mette Mogensen, and Peter M. Moselund.Supercontinuum applications in high resolution non invasive optical imaging. In CLEO:Applications and Technology, pages AW3S–1. Optical Society of America, 2018.

Manuel J. Marques, Sylvain Rivet, Adrian Bradu, and Adrian Podoleanu. Snapshotpolarization-sensitive plug-in optical module for a fourier-domain optical coherencetomography system. In Proc. of SPIE, volume 10483, pages 10483 – 10483 – 5,2018.

Magalie Bondu, Manuel J. Marques, Peter M. Moselund, Gurprit Lall, Adrian Bradu,and Adrian Podoleanu. Multispectral photoacoustic microscopy and optical coherencetomography using a single supercontinuum source. Photoacoustics, 9:21–30, Nov2017.

Sophie Caujolle, Ramona Cernat, Giuseppe Silvestri, Manuel J. Marques, AdrianBradu, Thomas Feuchter, Gary Robinson, Darren K. Griffin, and Adrian Podoleanu.Speckle variance OCT for depth resolved assessment of the viability of bovine em-bryos. Biomed. Opt. Express, 8(11):5139–5150, Nov 2017.

Sylvain Rivet, Manuel J. Marques, Adrian Bradu, and Adrian Podoleanu. Passiveoptical module for polarization-sensitive optical coherence tomography systems. Opt.Express, 25(13):14533–14544, Jun 2017.

Manuel J. Marques, Sylvain Rivet, Adrian Bradu, and Adrian Podoleanu. Novelsoftware package to facilitate operation of any spectral (Fourier) OCT system. InOptical Coherence Imaging Techniques and Imaging in Scattering Media II, page104160B. Optical Society of America, Jun 2017.

Manuel J. Marques, Sylvain Rivet, Adrian Bradu, and Adrian Podoleanu. Polarization-sensitive plug-in optical module for a fourier-domain optical coherence tomographysystem. In Proc. of SPIE, volume 10053, pages 100531B–1, 2017.

Sylvain Rivet, Manuel J. Marques, Adrian Bradu, and Adrian Podoleanu. Opticalmodule to extend any Fourier-domain optical coherence tomography system into apolarisation-sensitive system. Journal of Optics, 18(6):5607, May 2016.

Manuel J. Marques, Sylvain Rivet, Adrian Bradu, and Adrian Podoleanu. Spectral-domain, polarization-sensitive optical coherence tomography system insensitive tofiber disturbances. In SPIE BiOS, pages 96971K–96971K. International Society forOptics and Photonics, 03 2016.

Michael Maria, Manuel J. Marques, Christopher Costa, Adrian Bradu, ThomasFeuchter, Lasse Leick, and Adrian GH Podoleanu. Broadband master-slave inter-ferometry using a super-continuum source. In SPIE BiOS, pages 96972R–96972R.International Society for Optics and Photonics, 03 2016.

Manuel J. Marques, Adrian Bradu, and Adrian Podoleanu. Two-grating Talbot bandsspectral-domain interferometer. Optics Letters, 40(17):4014–4017, September 2015.

Manuel J. Marques, Sylvain Rivet, Adrian Bradu, and Adrian Podoleanu. Polarization-sensitive optical coherence tomography system tolerant to fiber disturbances using aline camera. Optics Letters, 40(16):3858–3861, August 2015.

Manuel J. Marques, Adrian Bradu, and Adrian G. Podoleanu. Optical CoherenceTomography and Scanning Laser Ophthalmoscopy: approaches to dual-channelretinal tissue imaging. In Frontiers in Optics 2014, page FTu2F.3. Optical Society ofAmerica, October 2014.

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Manuel J. Marques, Adrian Bradu, and Adrian Gh. Podoleanu. Towards simultane-ous Talbot bands based optical coherence tomography and scanning laser ophthal-moscopy imaging. Biomed. Opt. Express, 5(5):1428–1444, April 2014.

Mohammadreza RN Avanaki, Manuel J. Marques, Adrian Bradu, Ali Hojjatoleslami,and Adrian G Podoleanu. A new algorithm for speckle reduction of optical coherencetomography images. In SPIE BiOS, pages 893437–893437. International Society forOptics and Photonics, 2014.

Manuel J. Marques, Adrian Bradu, and Adrian Gh. Podoleanu. Tuning a fast linearcamera used within a Talbot bands spectrometer-based optical coherence tomographyset-up. In Manuel Filipe P. C. Martins Costa, editor, 8th Iberoamerican Optics Meetingand 11th Latin American Meeting on Optics, Lasers, and Applications, volume 8785,pages 8785E1–8785E1–7, July 2013.

Adrian Bradu, Manuel J. Marques, Petr Bouchal, and Adrian Gh. Podoleanu. Com-bining Gabor and Talbot bands techniques to enhance the sensitivity with depth inFourier domain optical coherence tomography. In James G. Fujimoto; Joseph A. Izatt;Valery V. Tuchin, editor, Optical Coherence Tomography and Coherence Domain Op-tical Methods in Biomedicine XVII, volume 8571, pages 857136–857136–6, February2013.

Attended Conferences and MeetingsFebruary 2 – 7,

2019SPIE Photonics West 2019 (SPIE BiOS conference) (San Francisco, CA,United States of America) (presented oral communication titled “Multi-modalOCT/fluorescence en-face surgical imaging using a robotic scanner” and posterstitled “Long axial range swept-source OCT instrument enhanced by ComplexMaster-Slave processing” and “Evaluation of a commercial-grade camera for line-fieldspectral-domain OCT”.)

June 28th, 2018 EPSRC UK Image Guided Therapies Network+ (IGT), Early-Career Researcherworkshop (St Thomas’ Hospital, London, UK) (presented oral communication titled“Custom-designed, side-viewing optical coherence tomography endoscopic probesfor less invasive bronchial imaging” and poster titled “Custom-built, miniaturisedside-viewing OCT probes for less invasive bronchial imaging”).

February 8, 2018 EPSRC UK Image Guided Therapies Network+, seventh event (Canterbury, UK)(presented oral communication titled “Development of OCT imaging and sensingtools for the lung” and poster titled “REBOT: Robotic Endobronchial Optical Tomogra-phy”).

January 27 –February 1, 2018

SPIE Photonics West 2018 (SPIE BiOS conference) (San Francisco, CA, UnitedStates of America) (presented oral communication titled “Interchangeable endo-scopic probes for optical coherence tomography set-ups” and poster titled “Snapshotpolarization-sensitive, plug-in optical module for a Fourier-domain OCT system”).

September 6 – 8,2017

2nd Canterbury Conference on OCT, emphasis on broadband optical sources (Can-terbury, United Kingdom). (presented oral communication, “Versatile hand-held/interfaceable Master-Slave optical coherence tomography instrument”).

June 25 – 29,2017

European Conferences on Biomedical Optics (Munich, Germany). (presented oralcommunication, “Novel software package to faciliate operation of any spectral (Fourier)OCT system”).

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May 19th, 2017 BMLA Laser and Aesthetics Conference 2017, 35th Annual British Medical Laser As-sociation meeting (Salford, Manchester, United Kingdom). (presented oral communi-cations, “Robust low coherence interferometry based proximity sensor for medicalrobotics” and “Versatile hand-held Master-Slave optical coherence tomography systemfor clinical diagnosis”).

Feburary 8th,2017

MedCity meeting, Assessing Research and Clinical Expertise in Cambridge, London,Oxford and Greater South East (London, United Kingdom).

January 27th –February 2nd,

2017

SPIE Photonics West 2017 (SPIE BiOS conference) (San Francisco, CA, UnitedStates of America) (presented oral communication titled “Polarization-sensitive plug-in optical module for a Fourier-domain optical coherence tomography system”).

November 29th,2016

NI Days 2016, National Instruments developers meeting (London, United Kingdom).

September29th–30th, 2016

Workshop on supercontinuum sources and bioimaging applications such as OCT(“UBAPHODESA” project) (Canterbury, Kent, UK). (presented oral communication,“Proof of concept for a handheld MS-OCT device”.)

June 24th, 2016 EPSRC UK Image Guided Therapies Network+, inaugural event (University CollegeLondon, UK) (presented poster, “Hand-held optical coherence tomography probes foreye imaging and ENT”.)

February13th–18th, 2016

SPIE Photonics West 2016 (SPIE BiOS conference) (San Francisco, CA, UnitedStates of America) (presented oral communication titled “Spectral-domain,polarization-sensitive optical coherence tomography system insensitive to fiber distur-bances”.)

December 28th,2015

GraPE 2015: 4th Annual Meeting of Portuguese Graduates living Abroad(“Graduados Portugueses no Estrangeiro”), "RE:Inventar Portugal" (Guimarães, Por-tugal).

November 3rd,2015

NI Days 2015, LabVIEW developers meeting (London, United Kingdom).

September24th–25th, 2015

Workshop on supercontinuum sources and bioimaging applications such as OCT(“UBAPHODESA” project) (NKT Photonics, Birkerød, Denmark). (presented oralcommunication, “Polarization-sensitive OCT tomography system immune to fibre-based influences”.)

June 11th–12th,2015

1st Doctoral Congress in Engineering – Symposium on Engineering Physics (Porto,Portugal). (part of the scientific committee, also presented oral communication, “Dual-imaging ophthalmic system using optical coherence tomography and scanning laserophthalmoscopy”.)

March 19th–20th,2015

”IMAGE 2015 - Workshop on Glaucoma and Imaging” (Canterbury, United Kingdom).

December 20th,2014

GraPE 2014: 3rd Annual Meeting of Portuguese Graduates living Abroad(“Graduados Portugueses no Estrangeiro”), “Portugueses sem Fronteiras :criatividade e inovação”. (Lisbon, Portugal)

November 4th,2014

”Imaging the Optical Frontier” joint Physical Sciences/Engineering/Computing collo-quium (Canterbury, United Kingdom). (part of the organising committee)

October19th–23rd, 2014

Frontiers in Optics/Laser Science 2014, Optical Society of America’s 98th AnnualMeeting (Tucson, AZ, United States of America). (presented oral communication,“Optical Coherence Tomography and Scanning Laser Ophthalmoscopy: approachesto dual-channel retinal tissue imaging” )

September 25th,2014

School of Physical Sciences’ Research Symposium (Canterbury, United Kingdom).(presented oral communication, “Spectral-domain Optical Coherence Tomographywith Talbot bands - further developments” )

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June 23rd, 2014 University of Kent’s 4th Post-Graduate Research Festival (Canterbury, United King-dom). (presented oral communication, “Imaging the eye with a dual-purpose in-strument: optical coherence tomography (OCT) and scanning laser ophthalmoscopy(SLO)” )

June 21st, 2014 LUSO 2014 - 8th Annual Meeting of Portuguese Researchers and Students in the UK(Bath, United Kingdom)

June 9th–12th,2014

SEPnet Graduate Network Summer School: “Modelling Today - Leading Tomorrow”(National Physical Laboratory, Teddington, United Kingdom). (presented poster )

June 5th, 2014 ISAT Institute of Physics (IoP) seminar: Test and Measurement using NationalInstruments Technology (Kingston upon Thames, United Kingdom). (presented oralcommunication, “NI-based solutions used in OCT: challenges”)

December 21st,2013

GraPE 2013: 2nd Annual Meeting of Portuguese Graduates living Abroad(“Graduados Portugueses no Estrangeiro”), “Migrações Científicas: Ir e Voltar”(Porto, Portugal)

November 20th,2013

NI Days 2013, LabVIEW developers meeting (London, United Kingdom).

July 22nd–26th,2013

RIAO/OPTILAS 2013 - VII Iberoamerican Conference on Optics, XI Latinamericanmeeting on Optics, Lasers and Applications (Porto, Portugal). (presented poster ).

June 22nd, 2013 LUSO 2013 - 7th Annual Meeting of Portuguese Researchers and Students in the UK(Cambridge, United Kingdom)

September6th–8th, 2012

Física 2012, XVIII national meeting of the Portuguese Physical Society (Aveiro, Portu-gal). (presented poster “Fourier-domain Optical Coherence Tomography imaging withmirror term attenuation using Talbot Bands”)

May 2nd–4th,2011

International Symposium on behalf of the 25th anniversary of Europhysics Letters -Frontiers of Physics (Munich, Germany).

September8th–10th, 2010

EWOFS 2010 - 4th European Workshop on Optical Fibre Sensors (Porto, Portugal).

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