CreaTools

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 08/03/10
  • Minor correction: 04/12/13
Keywords

CreaTools : development framework for medical image-processing software

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System: UNIX-like, Windows, MacOS X
  • Current version: 2.2.3 - November 7, 2013
  • License(s): CeCILL - APP: IDDN.FR.001.250014.000.S.P.2010.000.20700
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Eduardo Enrique Dávila Serrano, Claire Mouton, Frédéric Cervenansky Laurent Guigues, Jean-Pierre Roux
  • Contact designer(s): info-dev[at]creatis.insa-lyon.fr
  • Laboratory, service: CREATIS, Departamento de Sistemas y Computación, Universidad de los Andes, Bogota, Colombie

 

General software features

The CreaTools are a software suite for medical image processing. They have been developed in C++ and are cross-platform (Linux, Windows and MacOS). The main element of the suite is BBTK (black-box tootkit), a flexible framework for the design, programming, testing and prototyping of applications. It provides the user with libraries of high-level components for: the construction of graphical interfaces, input/output (file management), display, interaction… These components (black-boxes) can be heterogeneous. Currently, they are mainly based on the following libraries: VTK, ITK and wxWidgets. The black-boxes can be assembled into pipelines, by use a very intuitive script language (bbs), in order to realize either stand-alone applications or meta-widgets, reusable in other applications. Script edition and testing are made easy by a user-friendly graphical environment (bbStudio) providing several forms of on-line help.
Scripts can also be automatically generated by a graphical editor that permits to assembly the pipelines. Another very useful utility is creaNewProject that generates the whole structure of a new C++ project, including the necessary third-party libraries (ITK, VTK...). The structure is based on CMake and permits to generate projects for Windows, Linux et Mac OS platforms. The suite also provides several tools for end-users:

  • 3D image viewer,
  • interactive rigid registration (alignment) of 2D and 3D images ,
  • interactive contour tracing in N-dimensional images, permitting to calculate a number of statistics on the contours and on the delineated regions.
Context in which the software is used
  • Mutualization of developments : sharing of processing algorithms and complex graphical widgets, wrapped as black-boxes with standardized interface.
  • Prototyping and fast realization of customized applications for researchers or by the researchers themselves. These applications are mainly processing pipelines provided with a GUI for algorithms testing and demonstration. The components of validated workflows are then assembled, by use of the same mechanisms, to form end-user applications.
Publications related to the software
  1. F. Varray, C. Cachard, P. Tortoli, and O. Basset, "Nonlinear Radio Frequency Image Simulation for Harmonic Imaging - CREANUIS", IEEE Int Ultrasonics Symp, San Diego, USA, pp. 2179-2182, 2010.
  2. S. Bernhardt, J. Boutet, F. Duboeuf, A. Laidevant, J. M. Dinten, and D. Vray,  "Bimodality Ultrasound/Optical Imaging: Registration and 2D/3D Visualization",  IEEE Int Ultrasonics Symp, San Diego, USA, pp. 2127-2130, 2010.
  3. E. Bannier, K. Cieslar, K. Mosbah, F. Aubert, F. Duboeuf, Z. Salhi, S. Gaillard, Y. Berthezène, Y. Crémillieux, P. Reix, "Hyperpolarized 3He MR for sensitive imaging of ventilation function and treatment efficiency in young cystic fibrosis patients with normal lung function", Radiology, 255(1):225-232, April 2010.
  4. M. Sigovan, A. Bessaad, H. Alsaid, E. Lancelot, C.Corot, B. Neyran, N. Provost, Z. Majd, M. Breisse, E. Canet-Soulas, "Assessment of Age Modulated Vascular Inflammation in ApoE-/- Mice by USPIO-Enhanced Magnetic Resonance Imaging", Invest Radiol, 45(11):702-707, November 2010.
  5. R. Sablong, A. Rengle, A. Pouzin, O. Beuf. "IRM cardiaque du petit animal : Comparaison de synchronisations prospectives fondées sur un signal optique et ECG avec une technique retrospective". Journées Thématiques GDR « Imagerie in vivo » (IMAGIV), Marseille, 29/09-1/10 2010.
  6. M. A. Zuluaga, M. Orkisz, E. J. F. Delgado Leyton, V. Doré, A. Morales Pinzón, and M. Hernández Hoyos,  "Adaptación del algoritmo MARACAS para la segmentación de la bifurcación de la arteria carótida y cuantificación de estenosis en imágenes TAC",  Actas Biol Colombianas, vol. 15(3), pp. 195 - 210, 2010.
  7. M. A. Zuluaga, E. J. F. Delgado Leyton, M. Hernández Hoyos, and M. Orkisz,  "Can the coronary artery centerline extraction in computed tomography images be improved by use of a partial volume model?",  Int Conf Comput Vision Graphics, vol. LNCS 6375, no. 2, Warsaw, Poland, Springer, Heidelberg, pp. 385-392, September, 2010.
  8. A. Morales Pinzón, M. Orkisz, S. Teillaud, J. A. Sánchez, and M. Hernández Hoyos,  "Extracción semi-automática de ejes de canales de corales",  Sexto Seminario Internacional de Procesamiento de y Análisis de Imágenes Médicas, Bogotá, Colombia, pp. 10 pages in electronic proceedings, November 2010.
  9. M. A. Zuluaga, M. Orkisz, E. J. F. Delgado Leyton, V. Doré, A. Morales Pinzón, and M. Hernández Hoyos,  "Adaptación del algoritmo MARACAS para la segmentación de la bifurcación de la arteria carótida y cuantificación de estenosis en imágenes TAC",  Quinto Seminario de Ingeniería Biomédica y Quinto Seminario Internacional de Procesamiento de y Análisis de Imágenes Médicas, Bogota, Colombia, pp. 5 in electronic proc., November, 2009.
  10. M. A. Zuluaga, M. Orkisz, E. J. F. Delgado Leyton, V. Doré, A. Morales Pinzón, and M. Hernández Hoyos,  "Adaptations of MARACAS algorithm to the segmentation of the carotid bifurcation and stenosis quantification in CTA images",  MICCAI Workshop - 3D Segmentation in the Clinic: A Grand Challenge III, London, GB, Midas Journal, pp. 7 on-line: http://hdl.handle.net/10380/3102, September, 2009.
  11. F. Benmansour, L.D. Cohen, E.E. Dávila-Serrano, P. Douek, M. Orkisz, and M.A. Zuluaga. 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, May 2009.
  12. M. Sigovan, L. Boussel, A. Sulaiman, D. Sappey-Marinier, H. Alsaid, C. Desbleds-Mansard, D. Ibarrola, D. Gamondès, C. Corot, E. Lancelot, et al.,  "Rapid-Clearance Iron Nanoparticles for Inflammation Imaging in Atherosclerotic Plaque: Initial Experience in Animal Model",  Radiology, vol. 252, no. 2, pp. (401-409), 2009.
  13. H. Alsaid, G. De Souza, M. C. Bourdillon, F. Chaubet, A. Sulaiman, C. Desbleds-Mansard, L. Chaabane, C. Zahir, E.Lancelot, O. Rousseaux, et al.,  "Biomimetic MRI Contrast Agent for Imaging of Inflammation in Atherosclerotic Plaque of ApoE-/- Mice: A Pilot Study",  Invest Radiol, 44(3):151-158, March 2009.
  14. A. Rengle, R. Sablong, and O. Beuf, "Prospective synchronization of small animal heart MRI: a quantitative comparison of an optical device, pressure sensor and ECG", Int. Soc. Magn. Reson. Med. 17th Annual Meeting, Hawai, USA, pp. 1794, April, 2009.
  15. A. Marion, J. Porée, and D. Vray,  "CREASIMUS: a fast simulator of ultrasound image sequence using 3D tissue motion",  IEEE Int Ultrasonics Symp, Roma, Italy, pp. 2308-2311, 2009.
  16. E. Bannier, "Développements méthodologiques pour l’IRM de l’hélium 3 hyperpolarisé et applications", PhD thesis, Université Claude
    Bernard Lyon 1, 2009.
  17. E. Bannier, B. Neyran, K. Cieslar, J. Rivoire, R.M. Heidemann, S. Gaillard, A.R. Sulaiman, E. Canet-Soulas, Y. Cremillieux, "Free breathing hyperpolarized 3He lung ventilation spiral MR imaging", Invest Radiol, 44(4):185-191, April 2009.
  18. A. Rengle, L. Baboi, H. Saint-Jalmes, R. Sablong, and O. Beuf, "An optical fiber-based gating device for cardiac and abdominal MRI of small animals", Int. Soc. Magn. Reson. Med. Annual Meeting, Toronto, Canada, pp. 1028, April, 2008.
  19. M. Hernández Hoyos, M. A. Zuluaga, M. Lozano, J. C. Prieto, P. Douek, I. E. Magnin, and M. Orkisz,  "Coronary centerline tracking in CT images with use of an elastic model and image moments",  MICCAI Workshop - Grand Challenge Coronary Artery Tracking, New York City, USA, Midas Journal, pp. 8 on-line: http://hdl.handle.net/10380/1401, September, 2008.
  20. D. Charpigny, F. Duboeuf, C. Odet, and H. Benoit-Cattin,  "Echo Time (TE) Influence on the statistical parameters of Molecular MRI Images",  12ème Congrès du GRAMM, Lyon, France, pp. 210, 2008.
  21. S. Moreno Trillos, S. L. Caicedo, T. Strulovic, J. C. Briceño Triana, F. Briceño Rincón, S. I. Gómez Ramírez, M. Hernández Hoyos. "Inferior Maxillary Bone Tissue Classification in 3D CT Images". Int Conf Comput Vision Graphics, vol. LNCS 6375, no. 2, Warsaw, Poland, Springer, Heidelberg, September, 2010.
  22. S. Moreno Trillos, T. Strulovic, S. I. Gómez Ramírez, J. C. Briceño Triana, F. Briceño Rincón, M. Hernández Hoyos. "Segmentación del tejido óseo en el hueso maxilar inferior en imágenes TAC 3D". Quinto Congreso Colombiano de Computación. ISBN: 978-958-8387-40-6. Cartagena, Colombia, 2010.
  23. L. Caicedo. "Segmentación y diferenciación de tejidos de las cavidades de las órbitas en imágenes CT". VI Semin Ingeniería Biomédica. Universidad de los Andes. 2012.
  24. A. Morales Pinzón, J. A. Sánchez, C. E. Gómez, S. Teillaud, M. Hernández Hoyos, "Medición automática de la tasa de calcificación de corales en imágenes de microscopía confocal" In: XXXV Conferencia Latinoamericana de Informática, Brasil, 1:1, p.33 (abstract), 2009.
  25. C. Revol-Muller, T. Grenier, J. L. Rose, A. Pacureanu, F. Peyrin and C. Odet, Region Growing: Adolescence and adulthood; Two visions of region growing: in feature space and variational framework, VISAPP 2012. Int Conf Computer Vision Theory Appl, Roma, Italy, pp. 286-297, 24-26 February 2012.
  26. J. C. Prieto, C. Revol-Muller, F. Peyrin, P. Camelitti and C. Odet, 3D Texture synthesis for modeling realistic organic tissues, VISAPP 2012. International Conference on Computer Vision Theory and Applications, Rome, Italy, 24-26 February 2012, pp.60-65.
  27. E. E. Dávila-Serrano, L. Guigues, F. Cervenansky, S. Pop, J. G. Riveros Reyes, L. Flórez-Valencia, M. Hernández Hoyos, and M. Orkisz, CreaTools: a framework to develop medical image processing software. Application to simulate pipeline stent deployment in intracranial vessels with aneurysms, Int. Conf. Comput. Vision. Graphics.http://dx.doi.org/10.1007/978-3-642-33564-8.
  28.   J. C. Prieto, C. Revol-Muller, C. Odet, M. Orkisz, and M. Hernández Hoyos, "CreaLungs: a variational region growing method to segment pulmonary vascular trees", ISBI VESSEL12 Challenge, Barcelona, Spain, May 2, 2012.
  29.   E. E. Dávila-Serrano, L. Guigues, J. P. Roux, F. Cervenansky, S. Pop, J. G. Riveros Reyes, L. Flórez-Valencia, M. Hernández Hoyos, and M. Orkisz, "CreaTools: applications and development framework for medical image-processing software", ISBI Workshop on Open Source Medical Image Analysis Software, Barcelona, Spain, Apr. 30 - May 1, 2012
  30. M. Hernández Hoyos, E. E. Dávila-Serrano, E. M. Correa Agudelo, J. S. Torres González, R. A. Corredor Jérez, F. A. Gutiérrez Ossa, L. Flórez-Valencia, C. Mouton, and M. Orkisz, "CreaTools: una plataforma para desarrollo de software de procesamiento de imágenes médicas. Aplicación a la segmentación de arterias coronarias y a la detección automática de lesiones en imágenes de angioTAC", Revista Colombiana de Radiología. 23(3), pp. 3521-3528, 2012.
  31. E. E. Dávila-Serrano, L. Guigues, J.-P. Roux, F. Cervenansky, C. Mouton, S. Pop, L. Flórez-Valencia, M. Hernández Hoyos, and M. Orkisz, "CreaTools: applications and development framework for medical image-processing software", Libre Software Meeting, Geneva, Switzerland, July 2012.
  32. L. Flórez-Valencia, E. E. Dávila Serrano, J. G. Riveros Reyes, O. Bernard, J. Latt, O. Malaspinas, B. Chopard, G. Courbebaisse, and M. Orkisz, "Virtual deployment of pipeline flow diverters in cerebral vessels with aneurysms to understand thrombosis", MICCAI-Workshop on Computer Assisted Stenting, Nice, France, pp. 49-56 (electronic proc.), 10/2012.
  33. C. Mouton, E. E. Dávila Serrano, F. Cervenansky, S. Camarasu-Pop, E. Correa, L. Flórez-Valencia, M. Hernández Hoyos, and M. Orkisz, "CreaTools: A development framework for medical image processing software ; an application to segmentation, anomaly detection and quantification for coronary arteries", European BioImage Analysis Symposium 2013, IRB Barcelona, Spain, 10/2013.
  34. F. Varray, O. Basset, P. Tortoli, and C. Cachard, "CREANUIS: A Nonlinear Radio Frequency Ultrasound Image Simulator", Ultrasound in Medicine and Biology, pp. 1915-1924, 2013.
  35. F. Varray, L. H. Wang, L. Fanton, Y. M. Zhu, and I. E. Magnin, "High resolution extraction of local human cardiac fibre orientations", International Conference on Functional Imaging and Modeling of the Heart, London, England, LNCS 7945, pp. 150-157, 2013.
  36. R. Sablong, A. Rengle, A. Ramgolam, H. Saint Jalmes, and O. Beuf, "An optical fiber-based gating device for prospective mouse cardiac MRI", IEEE Transactions on Biomedical Engineering , 2013. In press.
  37. A. Morales Pinzón, M. Orkisz, C. M. Rodríguez Useche, J. S. Torres González, S. Teillaud, J. A. Sanchez, and M. Hernández Hoyos, "A semi-automatic method to extract canal pathways in 3D micro-CT images of octocorals", PLoS ONE, 2013. In Press.