Collaboration with Colombia

Academic partners : Universidad de los Andes and Pontificia Universidad Javeriana

French coordinator: Maciej Orkisz.


Universidad de los Andes     Address : Carrera 1 N° 18A 10 Bogotá, Colombie

Partner teams: Imagine and Ingeniería Biomédica.

Colombian coordinator: Marcela Hernández Hoyos (MSc 1998 and PhD 2002 at CREATIS).

Pontificia Universidad Javeriana     Address: Carrera 7 No. 40 - 62 Bogotá, Colombie

Partner team: Takina.

Colombian coordinator: Leonardo Flórez Valencia (MSc 2002 and PhD 2006 at CREATIS).


Agreements

  • framework agreement between Universidad de los Andes and INSA-Lyon, signed for the first time on 2002/02/13, most recent renewal, extended to Groupe INSA, signed on 2016/12/06 for 5 years
  • framework agreement between Universidad de los Andes and Université Lyon 1, signed for the first time on 2009/12/03, most recent renewal signed on 2015/06/22 for 5 years
  • MSc double diploma agreement, attached to the framwork agreement: signed on 2012/03/30 between Master EEAP, parcours Images et Systèmes and Maestría en Ingeniería de Sistemas y Computación
  • framework agreement between Pontificia Universidad Javeriana and Groupe INSA, signed on 2012/09/14 for 5 years

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Projects

ECOS Nord programme (each year, reciprocal mobility of one senior and one junior researcher from each side) :

2003-2004 : C03S02 (Interactive analysis and distributed storage of 3D medical images),

2007-2009 : C07M04 (Generation of vascular patient-specific phantoms from 3D medical images),

2011-2013 : C11S01 (Anomaly detection vascular trees).

2015-2017 : C15M04 (Quantification of pulmonary aeration in patients with the acute respiratory distress syndrom (ARDS) from CT images).

Involvement of CREATIS in projects supported by Colombian institutions CIFI and Colciencias.


Training through research

PhD

  1. Duván Alberto Gómez Betancur (ongoing UniAndes thesis, cosupervised by Maciej Orkisz, distinction at ICCVG 2016 conference),
  2. Alfredo Morales Pinzón (cotutorship UCBL/UniAndes, defended in 2016),
  3. Juan Carlos Prieto Bernal (defended in 2014),
  4. Maria Alejandra Zuluaga Valencia (cotutorship UCBL/UniAndes, defended in 2011),
  5. Leonardo Flórez Valencia (defended in 2006),
  6. Hector Duque (defended in 2005),
  7. Marcela Hernández Hoyos (defended in 2002).

MSc / DEA

  1. Leslie Evelyn Solórzano Vargas (double diploma UCBL/UniAndes, 2015),
  2. Diego Hernando Cáceres Herrera (2015),
  3. Juan Gabriel Riveros Reyes (double diploma INSA/Javeriana, 2014),
  4. Juan Sebastián Torres González (double diploma UCBL/UniAndes, 2013),
  5. Esteban Mauricio Correa Agudelo (double diploma UCBL/UniAndes, 2013),
  6. Diana Carolina Ortega Muñoz (double diploma UCBL/UniAndes, 2012),
  7. Ricardo Alberto Corredor Jerez (double diploma UCBL/UniAndes, 2012),
  8. Fabián Andrés Gutiérrez Ossa (2012),
  9. Edgar José Fernando Delgado Leyton (2011),
  10. Juan Carlos Prieto Bernal (2010),
  11. Fernando Yepez Calderon (2008),
  12. Juan Francisco Carrillo (double diploma INSA/UniAndes, 2005),
  13. Leonardo Flórez Valencia (double diploma INSA/UniAndes, 2002),
  14. Eduardo Enrique Dávila Serrano (2002),
  15. Marcela Hernández Hoyos (1998).

Maestría (Colombian MSc diploma, projects co-supervised by Maciej Orkisz)

  1. Carolina Pérez Romanello (2013),
  2. Vanessa Pérez Romanello (2013),
  3. Catalina María Rodríguez Useche (2012),
  4. Alfredo Morales Pinzón (2010),
  5. Diego Hernando Cantor Rivera (2007).

Post-docs

  1. Carolina Vallecilla Erazo (2011-2013),
  2. Maria Alejandra Zuluaga Valencia (2011-12),
  3. Marcela Hernández Hoyos (2002-3).

Research engineers

  1. Ricardo Alberto Corredor Jerez (2012-14) – IT, contractual
  2. William Alberto Romero Ramírez (2011-16) – IT, contractual
  3. Eduardo Enrique Dávila Serrano– IT, IE CNRS

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Other exchanges

Researcher mobility

The ECOS Nord programme supports each year 2-weeks stays of one senior researcher from both Colombia and France and 2-months stays of one PhD student from each country. Thus, more than thirty missions have been carried out in this framework. Additionally, Leonardo Flórez Valencia stayed at CREATIS for 4 months, from september to december 2014, as researcher invited by INSA-Lyon.

Undergraduate trainee program (Colombian students at INSA-Lyon)

devised to provide R&D training to students who are in their last year of Computer Engineering. The trainees develop software tools for medical image processing applicationsand their graduation project is supervised by one of the CREATIS IT team members (info-dev).

Pontificia Universidad Javeriana

  1. Monica Lizeth Espinosa Rodríguez (2014-15),
  2. Carlos Felipe Torres Jiménez (2013-14),
  3. Daniel Felipe González Obando (2012-13), engineer diploma with honors,
  4. Juan Gabriel Riveros Reyes (2011-12), Otto de Greiff 3rd prize winner
  5. José Luis Guzmán Rodríguez (2011-12),
  6. Diego Hernando Cáceres Herrera (2010-11).

Universidad de los Andes

  1. Margarita María Gómez Ballén (2017),
  2. María Camila Ángel Flórez (2015-16),
  3. Johann Felipe González Ávila (2014-15),
  4. Juan Pablo Reyes Gómez (2010-11),
  5. José Felipe Vargas Casadiego (2009-10),
  6. Ricardo Alberto Corredor Jerez (2009-10),
  7. Carolina Pérez Romanello (2009-10),
  8. Vanessa Pérez Romanello (2009-10),
  9. José Nicolas Trillos Uribe (2009-10),
  10. Juan Carlos Prieto Bernal (2008-9),
  11. John Harvey Casallas León (2008-9),
  12. Andrés Eugenio Donadio Galvis (2008-9),
  13. Juan Sebastián Caballero (2008-9),
  14. Juan Sebastián Torres González (2007-8),
  15. Silvia Lorena de la Torre Díaz (2007-8),
  16. Mónica María Lozano Romero (2007-8).

Graduation projects (co-supervision of Colombian students in Bogotá by Maciej Orkisz)

  1. Michael Baltaxe Milwer (2007) – Otto de Greiff 2nd prize winner

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Scientific results

Software

MARACAS : analysis of medical vascular images

CreaTools : software suite underlying the research work in common.

Publications

Thesis

[MORA-16]A. Morales Pinzón, Lung segmentation and airway tree matching : Application to aeration quantification in CT images of subjects with ARDS, Université Claude Bernard Lyon 1; Universidad de los Andes, Lyon, Bogotá, 2016.
Jury: Anna Fabijanska, Łódz University of Technology, Rapporteur Isabelle Bloch, Telecom ParisTech, Rapporteur Fraçoise Prêteux, École des Ponts ParisTech Examinateur Jean-Christophe Richard, Université Lyon 1, Hôpital de la Croix Rousse, Examinateur José Tiberio Hernández, Universidad de los Andes, Examinateur Leonardo Flórez Valencia, Pontificia Universidad Javeriana, Examinateur Maciej Orkisz, Université Lyon 1, Directeur de thèse Marcela Hernández Hoyos, Universidad de los Andes, Directeur de thèse
PDF icon Alfredo MORALES PINZON.pdf (20.9 MB)
[PRIE-14]J. C. Prieto, Multiparametric organ modeling for shape statistics and simulation procedures, INSA Lyon, Lyon, 2014.
Jury : Martin Styner (rapporteur), Christian Germain (rapporteur), François Cotton, David Rousseau, Charles Guttmann, Stephen Pizer, Christophe Odet (directeur), Chantal Muller (co-directeur)
[ZULU-11d]M. A. Zuluaga, Methods for the automation of vascular lesions detection in computed tomography images, Université Claude Bernard Lyon 1, Lyon, 2011.
Bloch I. (rap.), Hernández J.T. (Pdt), Hernández Hoyos M.(co-Dir.), Magnin I.E., Orkisz M. (co-Dir.), Romero E.E. et Salvado O. (rap.)
[FLOR-06]L. Flórez-Valencia, Modèle d'état de cylindre généralisé et la quantification de sténoses artérielles en imagerie 3D, INSA Lyon, 2006.
Jacques Demongeot (rap.), Philippe Douek, José Tiberio Hernández, Isabelle Magnin (prés.), Maciej Orkisz, Jean Sequeira (rap.)
[DUQU-05b]H. Duque, Conception et mise en oeuvre d'un environnement logiciel de manipulation et d'accès à des données réparties. Application aux grilles d'images médicales: le système DSEM/DM2, Université Claude-Bernard Lyon I, 2005.
L. Brunie (dir.), I.E. Magnin (dir), J. Montagnat, J.F. Mehaut, V. Breton (rap.), R Namyst (rap.)
[HERN-02d]M. Hernández Hoyos, Segmentation anisotrope 3D pour la quantification en imagerie vasculaire par résonnance magnétique, INSA-Lyon, 2002.
Bloch I. (rap.), Douek P., Hernandez J.T., Magnin I.E., Nahum R., Orkisz M. et Sequeira J. (rap.)

Journal Article

[ZULU-11d]M. A. Zuluaga, Ibañez, L., and Peyrin, F., Large Image Streaming using ITKv4, The Insight Journal, vol. January-June, 2011.

Invited Conference

[COUR-15]G. Courbebaisse, Déploiement virtuel interactif d’un stent à dérivation de flux. SFNR 2015 (42 ème Congrès de la Société Française de Neuroradilogie), Paris, France, 2015.
[COUR-14b]G. Courbebaisse, Corredor Jerez, R. A., and Flórez-Valencia, L., Modelling of flow diverter & CFD. ICS 14 (Interdisciplinary Cerebrovascular Symposium - Intracranial Stent Meeting), Zurich, Switzerland, 2014.
[ORKI-09a]M. Orkisz, Medical imaging in CREATIS-LRMN, Inauguration de COLIVRI, Universidad de los Andes. Bogota, Colombia, 2009.
[ORKI-02b]M. Orkisz and Hernández Hoyos, M., From inertia matrix to the analysis of vascular pathologies, Int Conf Computer Vision and Graphics. Zakopane, Poland, pp. 6-15, 2002.
[ORKI-01f]M. Orkisz and Hernández Hoyos, M., Models for 3D Vascular Image Analysis, Computer Graphics, Image Processing and Recognition. Warsaw, Poland, 2001.
[ORKI-01b]M. Orkisz and Hernández Hoyos, M., Models for 3D vascular image analysis, Med. Informatics and Technologies, vol. 2. Jaszowiec, Poland, pp. IP13-IP22, 2001.
[ORKI-98d]M. Orkisz and Hernández Hoyos, M., Développements récents dans le traitement d'images : principes des techniques de segmentation d'images vasculaires 3D, 2-èmes Journées du Groupe de Recherche et de Réflexion en Angiographie par Résonance Magnétique. Paris, France, pp. 94-103, 1998.

Conference Paper

[RIVE-14]J. G. Riveros Reyes, Flórez-Valencia, L., Corredor Jerez, R. A., and Courbebaisse, G., Virtual Stent Deployment, in ICFD 2014, Eleventh International Conference on Flow Dynamics, Sendai, Japon, 2014.
[COUR-13]G. Courbebaisse, Ohta, M., Chen, Y., Vallecilla, C., and Kuze, M., Flow Analysis for Coiled Intracranial Aneurysms, in ICFD 2013, Tenth International Conference on Flow Dynamics, Sendai, Japon, 2013.
[DONG-12a]P. Dong, Pacureanu, A., Zuluaga, M. A., and Peyrin, F., Quantification of Bone Cell Connections from 3D Nano-CT Images, in TOPIM - Hot Topics in Molecular Imaging, Les Houches, France, 2012.
[PRIE-12e]J. C. Prieto, Pérez Romanello, C., Pérez Romanello, V., Revol-Muller, C., Odet, C., Orkisz, M., and Hernández Hoyos, M., Segmentación del árbol vascular pulmonar, in XXXVIII Conferencia Latinoamericana en Informática (CLEI), Medellín, Colombia, 2012, pp. 1-7.
[ZULU-11b]M. A. Zuluaga, Hush, D., Delgado Leyton, E. J. F., Hernández Hoyos, M., and Orkisz, M., Learning from Only Positive and Unlabeled Data to Detect Lesions in Vascular CT Images, in Medical Image Computing and Computer Assisted Interventions - MICCAI , Toronto, Canada, 2011, vol. LNCS 6893, Part III, pp. 9-16.
[GUTI-11]F. A. Gutiérrez Ossa, Ortega, D. C., Orkisz, M., Uriza, L. F., and Hernández Hoyos, M., Automatic segmentation of pulmonary arterial tree in Computed Tomography images, in Sexto Congreso Colombiano de Computación (6CCC), Manizales, Colombia, 2011, p. 6 in electronic proc.
[ZULU-10b]M. A. Zuluaga, Orkisz, M., Hernández Hoyos, M., Lozano Martínez, F., and Magnin, I. E., Towards vascular abnormality detection: an SVM approach, in 24rth CARS - Comput Assisted Radiol Surg, Geneva, Switzerland, 2010, vol. 5-suppl.1, pp. S355-6 (abstract).
[FLOR-10c]L. Flórez-Valencia, Azencot, J., and Orkisz, M., Carotid arteries segmentation in CT images with use of a right generalized cylinder model, in Quinto Congreso Colombiano de Computación (5CCC), Cartagena de Indias, Colombia, 2010, p. 6 in electronic proc.
[ZULU-10e]M. A. Zuluaga, Delgado Leyton, E. J. F., Hernández Hoyos, M., and Orkisz, M., Feature selection for SVM-based vascular anomaly detection, in MICCAI Workshop on Medical Computer Vision, Beijing, China, 2010, vol. LNCS 6533, pp. 141-152.
[MORA-10]A. Morales Pinzón, Orkisz, M., Teillaud, S., Sánchez, J. A., and Hernández Hoyos, M., Extracción semi-automática de ejes de canales de corales, in Sexto Seminario Internacional de Procesamiento de y Análisis de Imágenes Médicas, Bogotá, Colombia, 2010, p. 10 pages in electronic proceedings.
[ZULU-09a]M. A. Zuluaga, Hernández Hoyos, M., and Orkisz, M., Evaluation of partial volume effects in computer tomography for the improvement of coronary artery segmentation, in 23rd CARS - Comput Assisted Radiol Surg, Berlin, Germany, 2009, vol. 4-suppl.1, pp. S40-1 (abstract).
[ZULU-09d]M. A. Zuluaga, Hernández Hoyos, M., and Orkisz, M., Evaluación del efecto de volumen parcial en imágenes TAC para el mejoramiento de la segmentación arterial coronaria, in Quinto Seminario de Ingeniería Biomédica y Quinto Seminario Internacional de Procesamiento de y Análisis de Imágenes Médicas, Bogota, Colombia, 2009, p. 4 in electronic proc.
[FLOR-09]L. Flórez-Valencia, Azencot, J., and Orkisz, M., Carotid arteries segmentation in CT images with use of a right generalized cylinder model, in MICCAI Workshop - 3D Segmentation in the Clinic: A Grand Challenge III, London, GB, 2009, p. 8 on-line.
[ZULU-09c]M. A. Zuluaga, Orkisz, M., Delgado Leyton, E. J. F., Doré, V., Morales Pinzón, A., and Hernández Hoyos, M., Adaptación del algoritmo MARACAS para la segmentación de la bifurcación de la arteria carótida y cuantificación de estenosis en imágenes TAC, in Quinto Seminario de Ingeniería Biomédica y Quinto Seminario Internacional de Procesamiento de y Análisis de Imágenes Médicas, Bogota, Colombia, 2009, p. 5 in electronic proc.
[BENM-09]F. Benmansour, Cohen, L. D., Dávila Serrano, E. E., Douek, P., Orkisz, M., and Zuluaga, M. A., New Interactive Methods for Tubular Structure Segmentation on Medical Images, in 12th ISRACAS - Israeli Symposium on Computer-Aided Surgery, Medical Robotics, and Medical Imaging, Tel-Aviv, Israel, 2009, p. 10 in CD.
[CANT-07d]D. Cantor Rivera, Orkisz, M., Uriza Carrasco, L. F., and Hernández Hoyos, M., Generación de modelos vasculares específicos al paciente a partir de IRM 3D usando el algoritmo de fast-marching, in Cuarto Seminario de Ingeniería Biomédica y Quinto Seminario Internacional de Procesamiento de y Análisis de Imágenes Médicas, Bogota, Colombia, 2007, p. 2 in electronic proc.
[CARR-06a]J. F. Carrillo, Hernández Hoyos, M., and Orkisz, M., Automatic vascular tree segmentation, in XXXII Conferencia Latinoamericana de Informática CLEI, Santiago de Chile, Chile, 2006, p. 174 (abstract; 8 p. full paper on CD).
[CARR-06b]J. F. Carrillo, Dávila Serrano, E. E., Hernández Hoyos, M., and Orkisz, M., Vascular tree extraction from 3D images, in 20th CARS - Computer Assisted Radiology and Surgery, Osaka, Japan, 2006, p. 462 (abstract).
[CARR-06c]J. F. Carrillo, Hernández Hoyos, M., Dávila Serrano, E. E., and Orkisz, M., Segmentación y visualización arterial en ARM y TAC, in XXXI Congreso Colombiano de Radiología, Cartagena, Colombia, 2006, pp. 21-22 (abstract).
[PIER-05]J. M. Pierson, Seitz, L., Duque, H., and Montagnat, J., MetaData for Efficient, Secure and Extensible Access to Data in a Medical Grid, in Database and Expert System Applications (DEXA'04), Zaragoza, Spain, 2005, pp. 562-566.
[FLOR-04a]L. Flórez-Valencia, Vincent, F., and Orkisz, M., Fast 3D pre-segmentation of arteries in computed tomography angiograms, in Int Conf Comput Vision Graphics, Warsaw, Poland, 2004, Computational Imaging and Vision., vol. 32, pp. 361-366.
[DUQU-03]H. Duque, Montagnat, J., Pierson, J. M., Brunie, L., and Magnin, I. E., DM2: A Distributed Medical Data Manager for Grids, in Biogrid'03, proceedings of the IEEE CCGrid03, Tokyo, Japan, 2003, pp. 606-611.
[ORKI-02c]M. Orkisz and Hernández Hoyos, M., Suivi de vaisseaux sanguins dans des images 3D à l'aide d'un modèle de base de moments, in Mathématiques et Imagerie, Journée 'Application à la modélisation et l'imagerie en Cardio-Vasculaire', Lyon, France, 2002.
[FLOR-02]L. Flórez-Valencia, Montagnat, J., and Orkisz, M., 3D graphical models for vascular-stent pose simulation, in Int Conf Comput Vision Graphics, Zakopane, Poland, 2002, pp. 259-266.
[MONT-02]J. Montagnat, Dávila Serrano, E. E., and Magnin, I. E., 3D objects visualization for remote interactive medical applications, in 3D Data Visualization, Processing, and Transmission (3DPVT'02), Padova, Italy, 2002, pp. 75-48.
[ORKI-01c]M. Orkisz and Hernández Hoyos, M., Models for 3D Vascular Image Analysis, in Computer Graphics, Image Processing and Recognition, Warsaw, Poland, 2001.
[HERN-99]M. Hernández Hoyos, Orkisz, M., Roux, J. P., and Douek, P., Inertia-based vessel axis extraction and stenosis quantification in 3D MRA images, in Computer Assisted Radiology and Surgery (CARS'99), Paris, France, 1999, pp. 189-193.

Book Chapter

[FLOR-17a]Right generalized cylinder model for vascular segmentation, in Computing and Visualization for Intravascular Imaging and Computer-Assisted Stenting, 1st ed., Elsevier, 2017, pp. 131-156.
[ORKI-04]M. Orkisz and Hernández Hoyos, M., Podstawy technik segmentacji stosowanych w przetwarzaniu obrazow 3D naczyn krwionosnych, in Polska Akademia Nauk Biocybernetyka i Inzynieria Biomedyczna 2000, Obrazowanie biomedyczne, vol. 8, M. Nalecz, Chmielewski, L., Kulikowski, J. M., and Nowakowski, A. Warszawa, Poland: Akademicka Oficyna Wydawnicza EXIT, Publ., 2004, pp. 351–372.