My new website is located here: http://sites.google.com/site/pierrickcoupe/

I received the M. Eng degree in Biomedical engineering from University of Technology of Compiègne, France in 2003 and the M.Sc in Image and Signal processing degree from University of Rennes I, France in 2004. I obtained the Ph. D degree in Image processing from University of Rennes I, France in 2008. My Ph. D received the prize of the best thesis (innovation prize) from the Section France of IEEE - Chapter EMBS - SFGBM - and AGBM. I am currently a postdoctoral researcher at Brain Imaging Center of Montreal Neurological Institute.

I am working under the supervision of Prof. D. Louis Collins. Mainly focused on nonlocal modeling of images, my research deals with denoising, super-resolution and segmentation of medical and biological images.

  • Click on to get the pdf of author manuscripts.
  • Click on to get the Matlab codes of the methods.
  • Click on to get the C++ source codes of the methods.
  • Click on to go to the websites describing the methods.


Thesis:

  1. P. Coupé. Méthode de compensation des déformations cérébrales par imagerie ultrasonore intraopératoire pour la neurochirurgie guidée par l’image. (Ph.D) Thèse de l’Université Rennes I, Janvier 2008.
    Innovation prize IEEE France - Chapter EMBS - SFGBM - and AGBM
  2. P. Coupé. Segmentation multimodale d’IRM cérébrales par approche markovienne. (Master Thesis) Master de l’Université de Rennes I, Juin 2004.


Journal Papers:

  • 2011
  1. P. Coupé, S. F. Eskildsen, J. V. Manjon, V. Fonov, D. L. Collins and ADNI. Simultaneous Segmentation and Grading of Anatomical Structures for Patient’s Classification: Application to Alzheimer’s Disease. Neuroimage, Accepted, 2011.
  2. S. F. Eskildsen, P. Coupé, K. K. Leung, V. Fonov, J. V. Manjon, N. Guizard, S. Wassef, L.R. Østergaard, D. L. Collins and ADNI. BEaST: Brain Extraction based on nonlocal Segmentation Technique. Neuroimage, Accepted, 2011.
  3. P. Coupé, J. V Manjon, M. Robles, D. L. Collins. Adaptive Multiresolution Non-Local Means Filter for 3D MR Image Denoising. IET Image Processing, Accepted, 2011.
  4. P. Coupé, P. Hellier, X. Morandi, C. Barillot. 3D Rigid Registration of Intraoperative Ultrasound and Preoperative MR Brain Images based on Hyperechogenic Structures. International Journal of Biomedical Imaging, Accepted 2011.
  5. J. V. Manjon, P. Coupé, A. Buades, D. L. Collins, M. Robles. New Methods for MRI Denoising based on Sparseness and Self-Similarity. Medical Image Analysis, 2011. In press.
  6. S. Hu, P. Coupé, J. Pruessner, D. L. Collins. Appearance-based Modeling for Segmentation of Hippocampus and Amygdala using Multi-contrast MR Imaging. NeuroImage, 58(2):549–559, 2011.
  7. P. Coupé, J. V Manjon, V. Fonov, J. Pruessner, M. Robles, D. L. Collins. Patch-based Segmentation using Expert Priors: Application to Hippocampus and Ventricle Segmentation. NeuroImage, 54(2): 940–954, 2011.
  8. F. P. Xavier de Fontes, G. A. Barroso, P. Coupé, Pierre Hellier. Real time ultrasound image denoising. Journal of Real-Time Image Processing, 6(1): 15–22, 2011.
    • 2010
  9. J. V. Manjon, P. Coupé, A. Buades, V. Fonov, D. L. Collins, M. Robles. Non-Local MRI Upsampling. Medical Image Analysis, 14(6): 784–792, 2010.
  10. P. Coupé, J. V. Manjon, E. Gedamu, D. Arnold, M. Robles, D. L. Collins. Robust Rician Noise Estimation for MR Images. Medical Image Analysis, 14(4) : 483–493, 2010.
  11. P. Hellier, P. Coupé, X. Morandi and D. L. Collins. An automatic geometrical and statistical method to detect acoustic shadows in intraoperative ultrasound brain images. Medical Image Analysis, 14(2) : 195–204, 2010.
  12. J. V. Manjon, P. Coupé, L. Martí-Bonmatí, D. L. Collins, M. Robles. Adaptive Non-Local Means Denoising of MR Images with Spatially Varying Noise Levels. Journal of Magnetic Resonance Imaging, 31(1):192–203, 2010.
  13. J. V Manjon, P. Coupé, A. Buades, D. L. Collins, M. Robles. MRI Superresolution Using Self Similarity and Image Priors. Article ID 425891, International Journal of Biomedical Imaging 2010.
    • 2009
  14. P. Coupé, P. Hellier, C. Kervrann, C. Barillot. NonLocal Means-based Speckle Filtering for Ultrasound Images. IEEE Transactions on Image Processing, 18(10):2221–9, 2009.
    • 2008
  15. P. Coupé, P. Yger, S. Prima, P. Hellier, C. Kervrann, C. Barillot. An Optimized Blockwise NonLocal Means Denoising Filter for 3-D Magnetic Resonance Images. IEEE Transactions on Medical Imaging, 27(4):425–441, 2008.
  16. P. Coupé, P. Hellier, S. Prima, C. Kervrann, C. Barillot. 3D Wavelet Subbands Mixing for Image Denoising. International Journal of Biomedical Imaging, 2008.
    • 2007
  17. P. Coupé, P. Hellier, X. Morandi, C. Barillot. Probe Trajectory Interpolation for 3D Reconstruction of Freehand Ultrasound. Medical Image Analysis, 11(6):604–15, 2007.
  18. M. Kretowski, J. Bezy-Wendling, P. Coupé. Simulation of Biphasic CT Findings in Hepatic Cellular Carcinoma by a Two-level Physiological Model. IEEE Transactions on Biomedical Engineering, 54(3):538–542, 2007.


International Conference Papers:

  • 2011
  1. P. Coupé, S. F. Eskildsen, J. V. Manjon, V. Fonov, D. L. Collins and ADNI. Simultaneous Segmentation and Grading of Hippocampus for Patient Classification with Alzheimer’s Disease. MICCAI 2011.
  2. S. F. Eskildsen, P. Coupé, K. K. Leung, V. Fonov, N Guizard, S. Wassef, L. R. Østergaard, D. L. Collins and the ADNI. BEaST: Brain extraction using multiresolution nonlocal segmentation. MICCAI Workshop on Multi-Atlas Labeling and Statistical Fusion, pages 97–108, 2011.
    Oral presentation
  3. S. Hu, P. Coupé, J. Pruessner, D. L. Collins. Validation of appearance-model based segmentation with patch-based refinement on medial temporal lobe structures. MICCAI Workshop on Multi-Atlas Labeling and Statistical Fusion, pages 28–37, 2011.
    Oral presentation
  4. P. Coupé, V. Fonov, S. F. Eskildsen, J. V. Manjon, D. Arnold, D. L. Collins. Influence of the Training Library Composition on a Patch-based label fusion method: Application to Hippocampus Segmentation on ADNI dataset. Alzheimer’s and Dementia, Volume 7, Issue 4, Supplement 1, July 2011, Page S24, 2011.
  5. V. Fonov, P. Coupé, S. F. Eskildsen, D. L. Collins. Atrophy specific MRI brain template for Alzheimer’s disease and Mild Cognitive Impairment. Alzheimer’s and Dementia, Volume 7, Issue 4, Supplement 1, July 2011, Page S58, 2011.
  6. S.F. Eskildsen, V. Fonov, P. Coupé, L.R. Østergaard, D. L. Collins. Prediction of MCI converters in the ADNI cohort using patterns of cortical thinning. Alzheimer’s and Dementia, Volume 7, Issue 4, Supplement 1, July 2011, Page S211, 2011.
  7. S.F. Eskildsen, V. Fonov, P. Coupé, L.R. Østergaard, D. L. Collins. Prediction of Alzheimer’s disease in subjects with mild cognitive impairment using structural patterns of cortical thinning. 15th Nordic - Baltic Conference on Biomedical Engineering and Medical Physics, Volume 34, pages 156–159, 2011.
    2st place of the Young Investigators Award
  8. S.F. Eskildsen, P. Coupé, V. Fonov, L.R. Østergaard, D. L. Collins. Effect of non-local means denoising on cortical segmentation accuracy. Organization for Human Brain Mapping 2011 Annual Meeting, 2011.
  9. J. V. Manjón, P. Coupé, A. Buades, D. L. Collins, M. Robles. MRI denoising based on Sparseness and Self-Similarity. Organization for Human Brain Mapping’11, 2011.
  10. N. Guizard, P. Coupé, V. Fonov, D. Arnold, D. L. Collins. Robust fusion of Jacobian maps for Deformation-Based Morphometry. Organization for Human Brain Mapping’11, 2011.
  11. C. Haegelen, N. Guizard, P. Coupé, P. Jannin, X. Morandi, D. L. Collins. Validation of basal ganglia segmentation on a 3T MRI template. Organization for Human Brain Mapping’11, 2011.
    • 2010
  12. P. Coupé, J. V. Manjón, V. Fonov, J. Pruessner, M. Robles, D. L. Collins. Nonlocal Patch-based label fusion for Hippocampus Segmentation. MICCAI’10, pages 129–136, vol 3, 2010.
  13. N. Guizard, P. Coupé, N. Stifani, S. Stifani, D. L. Collins. Robust 3D Reconstruction and Mean-Shift Clustering of Motoneurons from Serial Histological Images. MIAR’10, pages 191–199, 2010.
    MIAR Best Paper Award
  14. P. Coupé, P. Hellier, X. Morandi, C. Barillot. Intraoperative ultrasonography for the correction of brainshift based on the matching of hyperechogenic structures. IEEE ISBI’10, pages 1405–1408, 2010.
    Oral presentation
  15. P. Coupé, V. Fonov, J. V. Manjon, D. L. Collins. Template Construction using a Patch-based Robust Estimator. Organization for Human Brain Mapping’10, 2010.
  16. C. Clouchoux, P. Coupé, J.V. Manjón, N. Guizard, M. Bouyssi-Kobar, M. Lefebvre, A. du Plessis, A.C. Evans, C. Limperopoulos. A novel approach for high-resolution image reconstruction for in-vivo fetal brain MRI. Organization for Human Brain Mapping’10, 2010.
  17. C. Gaser, P. Coupé. Impact of Non-local Means filtering on Brain Tissue Segmentation. Organization for Human Brain Mapping’10, 2010.
    • 2009
  18. P. Coupé, J. V. Manjon, E. Gedamu, D. Arnold, M. Robles, D. L. Collins. An Object-based Method for Rician Noise Estimation in MR Images. MICCAI’09, pages 601–608, 2009.
  19. P. Coupé, J. V. Manjon, M. Robles, D. L. Collins. Adaptive Multiresolution Denoising Filter for 3D MR Images. NeuroImage, Volume 47, Supplement 1, Organization for Human Brain Mapping’09, July 2009, Page S50.
  20. J. V. Manjon, P. Coupé, L Marti-Bonmati, D. L. Collins, M. Robles. Spatially Adaptive Non-local MRI Denoising. NeuroImage, Volume 47, Supplement 1, Organization for Human Brain Mapping’09, July 2009, Page S72.
  21. P. Coupé, J. V. Manjon, E. Gedamu, D. Arnold, M. Robles, D. L. Collins. Object-based Rician Noise Estimation for MR Images. NeuroImage, Volume 47, Supplement 1, Organization for Human Brain Mapping’09, July 2009, Page S81.
    • 2008
  22. N. Wiest-Daesslé, S. Prima, P. Coupé, S.P. Morrissey, C. Barillot. Rician noise removal by non-Local Means filtering for low signal-to-noise ratio MRI: applications to DT-MRI. In MICCAI’08, pages 171–179, 2008.
  23. P. Coupé, P. Hellier, C. Kervrann, C. Barillot. Bayesian Non Local Means-based speckle filtering. In IEEE ISBI’08, pages 1291–1294. 2008.
    Oral presentation
  24. P. Hellier, P. Coupé, P. Meyer, X. Morandi, L. Collins. Acoustic shadows detection, application to accurate reconstruction of 3D intraoperative ultrasound. In IEEE ISBI’08. pages 1569–1572, 2008.
    • 2007
  25. P. Coupé, P. Hellier, X. Morandi, C. Barillot. A probabilistic objective function for 3D rigid registration of intraoperative US and preoperative MR brain images. In IEEE ISBI’07, pages 1320–1323, 2007.
    Oral presentation
  26. N. Wiest-Daesslé, S. Prima, P. Coupé, S.P. Morrissey, C. Barillot. Non-local means variants for denoising of diffusion-weighted and diffusion tensor MRI. In MICCAI’07, Volume 4792, pages 344–351, 2007.
  27. C. Kervrann, J. Boulanger, P. Coupé. Bayesian non-local means filter, image redundancy and adaptive dictionaries for noise removal. In SSVM’ 07, Volume 4485, pages 520–532, 2007.
  28. C. Barillot, P. Coupé, O. El Ganaoui, B. Gibaud, P. Hellier, P. Jannin, Paul P., Prima S., Wiest-Daessle N., Morandi X. Image Guidance in neurosurgical procedures, the “VISAGES” point of view. In IEEE ISBI’2007, pages 1056–1059, 2007.
    Invited paper
    • 2006
  29. P. Coupé, P. Yger, C. Barillot. Fast Non Local Means Denoising for 3D MR Images. In MICCAI’2006, Volume 4191, pages 33–40, 2006.
    • 2005
  30. P. Coupé, P. Hellier, N. Azzabou, C. Barillot. 3D Freehand Ultrasound Reconstruction based on Probe Trajectory. In MICCAI’2005, Volume 3749, pages 597–604, 2005.
    • 2004
  31. F. Ossant, R. Libgot, P. Coupé, P. Lermusiaux, F. Patat. High frequency ultrasound characterization of the coagulation process of whole blood. In IEEE International Ultrasonics, Ferroelectrics, and Frequency Control 50th Anniversary Joint Conference, Pages 846–849, 2004.
  32. J. Bezy-Wendling, M. Kretowski, P Coupé. Modeling of tumor conspicuity in hepatic CT images: combined compartment and vascular models. In IEEE ISBI’2004, Pages 444–447, 2004.


Patents

  1. P. Coupé, P. Hellier, X. Morandi, C. Barillot. Dispositif de traitement d’images pour la mise en correspondance d’images d’une même portion d’un corps obtenues par résonances magnétique et par ultrasons. INRIA, Patent: 07/02386, 2007. Publication No. WO/2008/135668. International Application No.: PCT/FR2008/000394.
  2. P. Coupé, P. Hellier, C. Kervrann, C. Barillot. Dispositif de traitement d’images amélioré. INRIA, Patent: 08/02206, 2008. Publication No. : WO/2009/133307. International Application No. : PCT/FR2009/000445.


National Conference Papers:

  • 2011
  1. C. Haegelen, V. Fonov, P. Coupé, F. Lalys, P. Jannin, X. Morandi, D.L. Collins. Validation de la segmentation des ganglions de la base d’un template Parkinson. Congres de la Societe Francaise de Neurochirurgie, 2011.
    • 2009
  2. P-L Henaux, P. Hellier, P. Jannin, P. Coupé, C. Haegelen, S. Diabara, X. Morandi. Évaluation de la précision d’une méthode de recalage automatique échographie 3D intraopératoire – IRM préopératoire en neurochirurgie. Neurochirurgie, Volume 55, numéro 4–5, pages 499–500, 2009.


Protected Softwares

  1. P. Coupé, P. Hellier, C. Barillot.. INRIABrainshift. Dépôt à l’agence pour la Protection des Programmes, numéro IDDN.FR.001.110024.000.S.P.2008.000.21000.
  2. P. Coupé, P. Yger, S. Prima, P. Hellier, C Kervrann, C. Barillot. MONADE: Multimodal and Optimized Non local meAns DEnoising. Dépôt à l’Agence pour la Protection des Programmes, numéro IDDN.FR.001.070033.000.S.P.2007.000.21000, Février 2007.
  3. P. Coupé, P. Hellier, C. Barillot. TULIPE : Three-dimensional ULtrasound reconstruction Incorporating ProbE trajectory. Dépôt à l’Agence pour la Protection des Programmes, numéro IDDN.FR.001.120034.000.A.2006.000.21000, Janvier 2006.


Technical report

  1. P. Coupé, P. Hellier, C. Barillot. État de l’art des méthodes de correction des déformations cérébrales per-opératoires. Rapport de Recherche INRIA, n°5589, 2005.


Online service and source codes

  • Optimized nonlocal means filter for 3D MRI (see for details)
    • Online application :
    • Matlab C-MEX :
    • C++ implementation as MINC tool :
  • Robust rician noise estimation for 3D MRI (see for details)
    • Matlab code :
    • C++ implementation as MINC tool :
  • Spatially adaptive nonlocal means filter for 3D MRI (see for details)
    • Matlab C-MEX code :
  • Nonlocal MRI upsampling (see for details)
    • Matlab C-MEX code :
  • MRI Superresolution Using Self Similarity and Image Priors (see for details)
    • Matlab C-MEX code :
  • Bayesian nonlocal means filter for speckle reduction (see for details, Patent: 08/02206, 2008. Publication No. : WO/2009/133307 )
    • Matlab C-MEX code for 2D ultrasound images .
    • For demo webpage click here