1. D.S. Lopes, M.T. Silva, J.A. Ambrósio, and P. Flores, A mathematical framework for contact detection between quadric and superquadric surfaces, Multibody System Dynamics, 24(3): 255 - 280, 2010. DOI: 10.1007/s11044-010-9220-0
  2. D.S. Lopes, M.T. Silva, and J.A. Ambrósio, Tangent vectors to a 3-D surface normal: A geometric tool to find orthogonal vectors based on the Householder transformation, Computer-Aided Design, 45(3): 683 - 694, 2013. DOI: 10.1016/j.cad.2012.11.003
  3. D.S. Lopes, D. Mendes, M. Sousa, J. Jorge, Expeditious Illustration of Layer-Cake Models On and Above a Tactile Surface, Computers & Geosciences, 90, Part A, Pages 1–9, 2016. DOI: 10.1016/j.cageo.2016.02.009
  4. D.S. Lopes, R.R. Neptune, J.A. Ambrósio, and M.T. Silva, A superellipsoid-plane model for simulating foot-ground contact during human gait, Computer Methods in Biomechanics and Biomedical Engineering, 19 (9): 954-963, 2016. DOI: 10.1080/10255842.2015.1081181
  5. D.S. Lopes, R.R. Neptune, A.A. Gonçalves, J.A. Ambrósio, and M.T. Silva, Shape Analysis of the Femoral Head: A Comparative Study between Spherical, (Super)Ellipsoidal and (Super)Ovoidal Shapes, ASME Journal of Biomechanical Engineering, 137(11), 114504(1-8), 2015. DOI: 10.1115/1.4031650
  6. N.S. Ribeiro, P.C.R. Fernandes, D.S. Lopes, J. Folgado, and P.R. Fernandes, 3-D Solid and Finite Element Modeling of Biomechanical Structures - A Software Pipeline, ESMC2009 7th Euromech Solid Mechanics Conference, Lisboa, Portugal, September 2009.
  7. J.P. Jorge, F.M.F. Simões, E.B. Pires, P.A. Rego, D.G. Tavares, D.S. Lopes, and A. Gaspar, Finite element simulations of a hip joint with femoroacetabular impingement, Computer Methods in Biomechanics and Biomedical Engineering, 17(11): 1275 - 1284, 2012. DOI: 10.1080/10255842.2012.744398
  8. M.P.M. Pato, N.G.S. Santos, E.B. Pires, P. Areias, M. de Carvalho, S. Pinto, and D.S. Lopes, Finite element studies of the mechanical behaviour of the diaphragm in normal and pathological cases, Computer Methods in Biomechanics and Biomedical Engineering, 14(6): 505 - 513, 2011. DOI: 10.1080/10255842.2010.483683

About Me

Dr. Daniel Simões Lopes has a degree in biomedical engineering from the University of Lisbon and graduated in computational engineering under the framework of the UT Austin|Portugal Program. During his doctoral studies he formulated an efficient contact detection methodology for smooth convex surfaces based on an analytical formulation of surface tangent vectors. In addition, his doctoral studies aimed at modeling anatomical structures with smooth convex contact geometries, namely, synovial joints such as the shoulder, hip, and knee joints.

He was a visiting scholar at the Neuromuscular Biomechanics Laboratory of the University of Texas at Austin where, under the supervision of Dr. Richard Neptune, he focused his research on integrating detailed contact models and musculoskeletal modeling techniques to estimate joint loading during human gait. He was also a visiting scholar at INRIA - Lille where he contributed to the development of an application to interactively visualize and explore volume data in real-time.

Currently, he is a postdoc researcher and Head of Biomedical Research at the Visualization and Intelligent Multimodal Interfaces Group at INESC-ID Lisboa, where he carries research and development in several topics, namely, computational geometry, contact detection, sketch-based interfaces and modeling, spatial interfaces, computational biomechanics, image-based anatomical modeling, and interactive visualization of 3D medical images.

Research Interests

  • Computational Geometry
  • Contact / Collision Detection
  • Sketch-Based Interfaces & Modeling
  • Spatial User Interaction
  • Input Devices
  • Interactive Computer-Aided Design
  • Image-Based Anatomical Modeling
  • Computational Biomechanics
  • Interactive Visualization
  • Computer-Assisted Tools in Healthcare

Research Projects

Position Name/Reference Budget (€)
Principal Investigator STREAKER - Skeletal TRacking Enhanced with Anatomically Correct Kinematics for Exergames and Rehabilitation, UTAP-EXPL/CA/0065/2017 tbd
Principal Investigator IT-MEDEX - Interactive Tablets for Collaborative Scenarios Related to 3D Medical Image Exploration, PTDC/EEI-SII/6038/2014 €173.882,00
Project Coordinator A-MOP - Algorithms for Macro-Molecular Pocket Detection, UTAP-EXPL/QEQ-COM/0019/2014 €29.870,00
Research Member TECTON3D - Digital Mockup: Touching the 3rd dimension, PTDC/EEI-SII/3154/2012 €137.036,00
Research Member DACHOR - Multibody Dynamics and Control of Hybrid Active Orthoses, MIT-Pt/BS-HHMS/0042/2008 €192,620.00
Research Member PROPAFE - Design and Development of a Patello-Femoral Prosthesis, PTDC/EME-PME/67687/2006 €140.000,00

Selected Publications


D.S. Lopes, P.F. Parreira, A.R. Mendes, V.M. Pires, S.F. Paulo, C.S. Sousa, J.A. Jorge, Explicit design of transfer functions for volume-rendered images by combining histograms, thumbnails and sketch-based interaction, The Visual Computer, ...(...), Pages ...–..., 2017. DOI: 10.1007/s00371-017-1448-8

D.S. Lopes, P.F. Parreira, S.F. Paulo, V. Nunes, P.A. Rego, M.C. Neves, P.S. Rodrigues, J.A. Jorge, On the utility of 3D hand cursors to explore medical volume datasets with a touchless interface, Journal of Biomedical Informatics, 72, Pages 140–149, 2017. DOI: 10.1016/j.jbi.2017.07.009

R.K. dos Anjos, C.S. Ribeiro, D.S. Lopes, J.M. Pereira, Stroke-based splatting: an efficient multi-resolution pointcloud visualization technique, The Visual Computer, 33(9), Pages 1–15, 2017. DOI: 10.1007/s00371-017-1420-7

A.A. Gonçalves, A. Bernardino, J.A. Jorge, D.S. Lopes, A benchmark study on accuracy-controlled distance calculation between superellipsoid and superovoid contact geometries, Mechanism and Machine Theory, 115, Pages 77–96, 2017. DOI: 10.1016/j.mechmachtheory.2017.04.008

T. Simões, D.S. Lopes, S. Dias, F. Fernandes, J. Pereira, J. Jorge, C. Bajaj, A. Gomes, Geometric detection algorithms for cavities on protein surfaces in molecular graphics: a survey, Computer Graphics Forum, 36, Pages 643–683, 2017. DOI: 10.1111/cgf.13158

M. Sousa, D. Mendes, S. Paulo, N. Matela, J. Jorge, D.S. Lopes, VRRRRoom: Virtual Reality for radiologists in the reading room, Proceedings of the 35th Annual ACM Conference on Human Factors in Computing Systems (CHI 2017), New York: ACM Press, 2017. DOI: 10.1145/3025453.3025566  [website]

D.S. Lopes, D. Mendes, M. Sousa, J. Jorge, Expeditious Illustration of Layer-Cake Models On and Above a Tactile Surface, Computers & Geosciences, 90, Part A, Pages 1–9, 2016. DOI: 10.1016/j.cageo.2016.02.009

D.S. Lopes, R.R. Neptune, J.A. Ambrósio, and M.T. Silva, A superellipsoid-plane model for simulating foot-ground contact during human gait, Computer Methods in Biomechanics and Biomedical Engineering, 19 (9): 954-963, 2016. DOI:10.1080/10255842.2015.1081181

D.S. Lopes, R.R. Neptune, A.A. Gonçalves, J.A. Ambrósio, and M.T. Silva, Shape Analysis of the Femoral Head: A Comparative Study between Spherical, (Super)Ellipsoidal and (Super)Ovoidal Shapes, Journal of Biomechanical Engineering, 137(11): 114504(1-8), 2015. DOI:10.1115/1.4031650

B.R. de Araújo, D.S. Lopes, P. Jepp, J.A. Jorge, and B. Wyvill, A Survey on Implicit Surface Polygonization, ACM Computing Surveys, 47(4): Article 60, 39 pages, 2015. DOI:10.1145/2732197

D.S. Lopes, M.T. Silva, and J.A. Ambrósio, Tangent vectors to a 3-D surface normal: A geometric tool to find orthogonal vectors based on the Householder transformation, Computer-Aided Design, 45(3): 683 - 694, 2013. DOI: 10.1016/j.cad.2012.11.003

D.S. Lopes, M.T. Silva, J.A. Ambrósio, and P. Flores, A mathematical framework for contact detection between quadric and superquadric surfaces, Multibody System Dynamics, 24(3): 255 - 280, 2010. DOI: 10.1007/s11044-010-9220-0

J.P. Jorge, F.M.F. Simões, E.B. Pires, P.A. Rego, D.G. Tavares, D.S. Lopes, and A. Gaspar, Finite element simulations of a hip joint with femoroacetabular impingement, Computer Methods in Biomechanics and Biomedical Engineering, 17(11): 1275 - 1284, 2012. DOI: 10.1080/10255842.2012.744398

M.P.M. Pato, N.G.S. Santos, E.B. Pires, P. Areias, M. de Carvalho, S. Pinto, and D.S. Lopes, Finite element studies of the mechanical behaviour of the diaphragm in normal and pathological cases, Computer Methods in Biomechanics and Biomedical Engineering, 14(6): 505— - 513, 2011. DOI: 10.1080/10255842.2010.483683

L. B. Rodrigues, D.S. Lopes, J. Folgado, P.R. Fernandes, E.B. Pires, E.B. Las Casas, and R.R. Faleiros, Bone remodelling analysis of a bovine femur for a veterinary implant design, Computer Methods in Biomechanics and Biomedical Engineering, 12(6): 683 - 690, 2009. DOI: 10.1080/10255840902865641

L.B. Rodrigues, E.B. Las Casas, D.S. Lopes, J. Folgado, P.R. Fernandes, E.B. Pires, G.E.S. Alves, and R.R. Faleiros, A finite element model to simulate femoral fractures in calves: testing different polymers for intramedullary interlocking nails, Veterinary Surgery, 41(7): 838 - 844, 2012. DOI: 10.1111/j.1532-950X.2012.01032.x

Thesis

D.S. Lopes, Smooth convex surfaces for modeling and simulating multibody systems with compliant contact elements, Ph.D. Thesis, Instituto Superior Técnico, Universidade de Lisboa, 2013. [PDF (3.64MB)]

D.S. Lopes, Geometric Modeling of Human Structures Based on CT Data-a Software Pipeline, Final Course Project Thesis, Instituto Superior Técnico, Universidade Técnica de Lisboa, 2006. [PDF (5.70MB)]

Magazine Articles

D.S. Lopes, Medical interfaces of the future, Impact, Volume 2017, Number 10, November 2017, pp. 76-77(2). DOI: 0.21820/23987073.2017.10.76.

Paden Shorey, Audrey Girouard, Sang Ho Yoon, Yunbo Zhang, Ke Huo, Karthik Ramani, Mauricio Sousa, Daniel Mendes, Soraia Paulo, Nuno Matela, Joaquim Jorge, Daniel Simões Lopes, Dirk Wenig, Johannes Schöxning, Alex Olwal, Mathias Oben, and Rainer Malaka, Demo hour, interactions 24, 6 (October 2017), 8-11. DOI: 10.1145/31433182013

D.S. Lopes, Virtualmente Real: O Futuro do Radiodiagnóstico, Entrevista concedida à Revista Frontal sobre Realidade Virtual aplicada a cenários médicos, Revista Frontal, Associação de Estudantes da NOVA Medical School, edição 47, Ano 31, Dezembro 2017. [PDF]

Software

Apps

A homage to the classic video game Pong (Credits: Artur A. Gonçalves, Daniel Simões Lopes).

Free & Opensource Software

Tangent vectors to a surface normal - Application of the Householder formula to compute tangent vector fields given the surface normals. Lopes et al. Comp Aid Design, 45(3): 683 - 694, 2013. DOI: 10.1016/j.cad.2012.11.003

Algebraic Separation Condition for Ellipsoids - A proximity query that is expressed as an algebraic condition for realtime continuous contact detection for ellipsoids moving under rigid body transformations. Wang et al. Comp Aid Geo Design, 18(6):531-539, 2001.

MDC-ELLIPSOIDs v1.0 - MATLAB® code to calculate the minimum distance between two ellipsoidal surfaces in a non-conformal rigid contact situation.

Anisotropic Diffusion (Perona & Malik): 1,2,3-D signal filter that performs image enhancement and restoration based on the PDE of heat transfer.

Tutorials

Contact Modeling with OpenSim: a User's Approach - SimTK project consisting of tutorials on how to integrate contact elements within a OpenSim model. Musculoskeletal modelers that wish to incorporate surface contact elements within a multibody model will find this project of their interest.

Manual Segmentation of Radial MRA Images - a tutorial on how to manually extract anatomical information of hip joint structures given a set of radial MRA images. Also feel free to explore the accompanying *blend file.

Awards & Honors

  • 2013 FCT Post-Doctoral Fellowship, SFRH/BPD/97449/2013
  • 2008 UT Austin | Portugal Program Doctoral Scholarship, SFRH/BD/47750/2008
  • Nominee for the Best INESC-ID Junior Researcher Prize 2017, Lisboa, Portugal, INESC-ID Lisboa
  • Nominee for the Best INESC-ID Junior Researcher Prize 2016, Lisboa, Portugal, INESC-ID Lisboa
  • Inaugural OpenSim Virtual Workshop, Coolest Video: Contact for Tackle Simulations, Stanford University, California, April 25 to May 6, 2016, NIH National Center for Simulation in Rehabilitation Research
  • 2014 NCSRR Visiting Scholars Travel Award, Stanford University, California, August 25 to August 27, 2014, NIH National Center for Simulation in Rehabilitation Research
  • Fraunhofer Portugal Challenge 2013 (finalist), Porto, Portugal, 2013, Fraunhofer Portugal
  • 2012 OpenSim Developer's Week Travel Award, Stanford University, California, July 16 to July 20, 2012, NIH National Center for Simulation in Rehabilitation Research
  • CIME Grant to participate in the CIME course on IsoGeometric Analysis: a New Paradigm in the Numerical Approximation of PDEs, CIME-EMS Summer School in Applied Mathematics, Cetraro, Italy, June 18 to June 22, 2012, CIME Foundation
  • Carlos Lima Award (honorable mention) attributed to the work intitled: "Pressão de contacto intra-articular no conflito femuro-acetabular, estudo tridimensional por elementos finitos" by P. Rego, J.P. Jorge, F.M. Simões, E.B. Pires, D.S. Lopes, P. Pinto, A. Spranger, F. Oliveira, A. Gaspar, J. Monteiro, Portuguese Society of Orthopaedics and Traumatology

Participation in Academic Juries

  • MSc Theses
  • November 22nd 2017, Instituto Superior Técnico, Universidade de Lisboa, Participation in the panel for the appreciation of the thesis intitled "CAVE COLON: Cave-like Virtual Reality Environments for CT Colonography", written by Pedro Brasil Borges for his Master's Dissertation in Biomedical Engineering.
    November 10th 2017, Instituto Superior Técnico, Universidade de Lisboa, Participation in the panel for the appreciation of the thesis intitled "Flow-Z: A Flow-based Adaptable Game to Maintain Optimal Challenge", written by Tomá s Alves for his Master's Dissertation in Engineering Systems and Computer Engineering.
    January 18th 2017, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Participation in the panel for the appreciation of the thesis intitled "Development of a neurofeedback-based virtual reality environment", written by Jorge Miguel Ribeiro Dias for his Master's Dissertation in Biomedical Engineering.
    November 25th 2016, Instituto Superior Técnico, Universidade de Lisboa, Participation in the panel for the appreciation of the thesis intitled "Understanding the Hip Joint: a Morphological Study of the Articular Surfaces in Asymptomatic and Pathologic Conditions", written by Sara Pires for her Master's Dissertation in Biomedical Engineering.
    November 22nd 2016, Instituto Superior Técnico, Universidade de Lisboa, Participation in the panel for the appreciation of the thesis intitled "Precise Extraction of Anatomical Segment Orientations from the Kinect One Sensor", written by Nuno Matias for his Master's Dissertation in Biomedical Engineering.
    November 22nd 2016, Instituto Superior Técnico, Universidade de Lisboa, Participation in the panel for the appreciation of the thesis intitled "Sketching in Virtual Space with Voxels: A CAD tool for the Early Stages of Architectural Design", written by André Duarte for his Master's Dissertation in Electrical and Computers Engineering.
  • Preparatory MSc Theses Proposals
  • February 3rd 2017, Instituto Superior Técnico, Universidade de Lisboa, Participation in the jury for the appreciation of the report intitled "Flow-Z: A Real-Time Flow-based Adaptable Game to Maintain Optimal Challenge", written by Tomás Alves, for the chair of Master Project in Information and Software Engineering.
    February 2nd 2017, Instituto Superior Técnico, Universidade de Lisboa, Participation in the jury for the appreciation of the report intitled "Exploration of Unknown Places by Blind People Using Mobile Virtual Reality", written by João Sequeira, for the chair of Master Project in Information and Software Engineering.
    June 23rd 2016, Instituto Superior Técnico, Universidade de Lisboa, Participation in the jury for the appreciation of the report intitled "GyroGlove: Natural Interactions in Virtual Reality Environments", written by Filipe Costa, for the chair of Introduction to the Research in Electrical and Computer Engineering.

Teaching

  • MIT-Portugal Graduate Program
    Lecture on Image-Based Anatomical Modeling for the Biomedical Devices and Technologies Course (2015 and 2016) [Lecture slides of Part I and Part II]
    Teaching Assistant of the Biomedical Devices and Technologies Course Module, 3rd Edition, 2010
  • Fall 2016
    Computer Graphics, LEIC-T, IST / University of Lisbon
    Master Project in Information and Software Engineering, MEIC-T, IST / University of Lisbon
    Master Thesis - Information and Software Engineering, MEIC-A, IST / University of Lisbon
    Introduction to the Research in Electrical and Computer Engineering, MEEC, IST / University of Lisbon
    Master Dissertation in Electrical and Computers Engineering, MEEC, IST / University of Lisbon
    Master's Dissertation in Biomedical Engineering, MEBiom, IST / University of Lisbon
  • Spring 2016
    Lecture on Introduction to Biomedical Engineering, Engenharia Biomédica e Biofísica, FCUL / University of Lisbon
    Master Project in Information and Software Engineering, MEIC-T, IST / University of Lisbon
    Master Thesis - Information and Software Engineering, MEIC-A, IST / University of Lisbon
    Introduction to the Research in Electrical and Computer Engineering, MEEC, IST / University of Lisbon
    Master Dissertation in Electrical and Computers Engineering, MEEC, IST / University of Lisbon
    Master's Dissertation in Biomedical Engineering, MEBiom, IST / University of Lisbon
  • Fall 2015
    Computer Graphics for Games, MEIC-T, IST / University of Lisbon
    Master Project in Information and Software Engineering, MEIC-A, IST / University of Lisbon
    Master Dissertation in Electrical and Computers Engineering, MEEC, IST / University of Lisbon
    Master's Dissertation in Biomedical Engineering, MEBiom, IST / University of Lisbon
  • Spring 2015
    Master Project in Information and Software Engineering, MEIC-A, IST / University of Lisbon
    Introduction to the Research in Electrical and Computer Engineering, MEEC, IST / University of Lisbon
    Master Dissertation in Electrical and Computers Engineering, MEEC, IST / University of Lisbon
    Master's Dissertation in Biomedical Engineering, MEBiom, IST / University of Lisbon
  • Fall 2014
    Master Thesis - Information and Software Engineering, MEIC-T, IST / University of Lisbon
    Introduction to the Research in Electrical and Computer Engineering, MEEC, IST / University of Lisbon
  • Spring 2014
    Master Thesis - Information and Software Engineering, MEIC-T, IST / University of Lisbon

Supervision

  • Internship supervision of graduated and undergraduate students from Instituto Superior Técnico at INESC-ID Lisboa.
    Carolina Barata (MEBiom, Summer 2017, 4 weeks)
    Rafaela Saraiva (MEBiom, Summer 2017, 4 weeks)
    André Manso (MEBiom, Summer 2016, 6 weeks)
    Bernardo Rodrigues (MEBiom, Summer 2016, 6 weeks)
    Felicia Negru (MEBiom, Summer 2016, 6 weeks)
    Filipe Marques (MEEC, Summer 2016, 6 weeks)
    Orlando Vaz (MEEC, Summer 2016, 6 weeks)
    João Pedro Pereira (MEIC, Summer 2016, 6 weeks)
    José Pedro Serrano (MEIC, Summer 2016, 6 weeks)
    Nuno Matias (MEBiom, Summer 2015, 6 weeks)
    Rui Garcia (MEBiom, Summer 2015, 6 weeks)
    Sara Pires (MEBiom, Summer 2015, 6 weeks)
    João Martins (MEBiom, Summer 2015, 6 weeks)
    David Dias (MEEC, Summer 2015, 6 weeks)
    Francisco Salgado (MEEC, Summer 2015, 6 weeks)
    Vicente Queiróz (MEEC, Summer 2015, 6 weeks)
    Artur Gonçalves (MEEC, Summer 2014, 6 weeks)
    André Duarte (MEEC, Summer 2014, 6 weeks)
    Oleksandr Galskyy (MEEC, Summer 2014, 6 weeks)
    Telmo Oliveira (MEEC, Summer 2014, 6 weeks)

Scientific Activities

Collaborations

  • International Academic Collaborations
    NIH National Center for Simulation in Rehabilitation Research, Stanford, California, USA
    Neuromuscular Biomechanics Lab at the University of Texas at Austin, USA
    College of Arts and Architecture, Pennsylvania State University, USA
    Applied Biomechanics Suite, Department for Health, University of Bath, United Kingdom
    INRIA Lille - Nord Europe, France
    The AnyBody Group, Department of Mechanical and Manufacturing Engineering, Aalborg University, Denmark
    SPiN - Study in Portugal Network
    DICAM, University of Bologna, Italy
    DEES/EE, DCCV/EV, Federal University of Minas Gerais, Belo Horizonte, Brazil
    State University of Bahia Southwest, Itapetinga, Brazil
  • National Academic Collaborations
    Champalimaud Foundation, Lisboa
    Serviço de Neurorradiologia - Centro Hospitalar de Lisboa Central, E.P.E.
    Centro de Imagiologia, Hospital da Luz, Lisboa
    Instituto da Próstata e Incontinência Urinária, Lisboa
    Unidade Funcional de Patologia Mamária - Centro Hospitalar de Lisboa Central, E.P.E.
    Ortopedia da Criança e do Adolescente, CUF Descobertas, Lisboa
    Serviço de Ortopedia, Hospital Beatriz Ângelo, Loures
    IBEB, Institute of Biophysics and Biomedical Engineering, University of Lisbon
    CiiEM, Centro de Investigação Interdisciplinar Egas Moniz, Monte da Caparica
    Clínica Dentária Egas Moniz, Monte da Caparica
    Escola Superior de Saúde Egas Moniz, Monte da Caparica
    CI2, Centro de Investigação e Criatividade em Informática, Hospital Prof. Dr. Fernando Fonseca, E.P.E., Amadora
    Departamento de Informática, Universidade da Beira Interior, Covilhã
    DCG, Design & Computation Group, Faculty of Architecture, University of Lisbon
    LCISA, Center for Image in Science and Art, University of Lisbon, Lisboa
    DeCivil, ICIST, and IDMEC, Instituto Superior Técnico, University of Lisbon, Lisboa
    Clínica Universitária de Ortopedia, Medical School, University of Lisbon, Lisboa
    CT2M/Mechanical Engineering Department, University of Minho, Guimarães

Knowledge Transfer

Contact

Address
Edificio IST
Av Prof Cavaco Silva, Room 2N9.1
2744-016 Porto Salvo
Portugal