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Publications sur Deconvolution
Résultat de la recherche dans la liste des publications :
Article |
1 - Richardson-Lucy Algorithm with Total Variation Regularization for 3D Confocal Microscope Deconvolution.
N. Dey et L. Blanc-Féraud et C. Zimmer et Z. Kam et P. Roux et J.C. Olivo-Marin et J. Zerubia. Microscopy Research Technique, 69: pages 260-266, avril 2006.
Mots-clés : Microscopie confocale, Methodes variationnelles, Variation totale, Deconvolution.
@ARTICLE{dey_mrt_05,
|
| author |
= |
{Dey, N. and Blanc-Féraud, L. and Zimmer, C. and Kam, Z. and Roux, P. and Olivo-Marin, J.C. and Zerubia, J.}, |
| title |
= |
{Richardson-Lucy Algorithm with Total Variation Regularization for 3D Confocal Microscope Deconvolution}, |
| year |
= |
{2006}, |
| month |
= |
{avril}, |
| journal |
= |
{Microscopy Research Technique}, |
| volume |
= |
{69}, |
| pages |
= |
{260-266}, |
| url |
= |
{http://dx.doi.org/10.1002/jemt.20294}, |
| keyword |
= |
{Microscopie confocale, Methodes variationnelles, Variation totale, Deconvolution} |
| } |
Abstract :
Confocal laser scanning microscopy is a powerful and popular technique for 3D imaging of biological specimens. Although confocal microscopy images are much sharper than standard epifluorescence ones, they are still degraded by residual out-of-focus light and by Poisson noise due to photon-limited
detection. Several deconvolution methods have been proposed to reduce these degradations, including the Richardson-Lucy iterative algorithm, which computes a maximum likelihood estimation adapted to Poisson statistics. As this algorithm tends to amplify noise, regularization constraints based on some prior knowledge on the data have to be applied to stabilize the solution. Here, we propose to combine the Richardson-Lucy algorithm with a regularization constraint based on Total Variation, which suppresses unstable oscillations while preserving object edges. We
show on simulated and real images that this constraint improves the deconvolution results as compared to the unregularized Richardson-Lucy algorithm, both visually and quantitatively. |
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Thèse de Doctorat et Habilitation |
1 - Détection de Filaments dans des images 2D et 3D; modélisation, étude mathématique et algorithmes..
A. Baudour. Thèse de Doctorat, Universite de Nice Sophia Antipolis, mai 2009.
Mots-clés : imagerie 3D, Segmentation, filaments, Deconvolution, Methodes variationnelles, mocroscopie confocale.
@PHDTHESIS{baudour2009,
|
| author |
= |
{Baudour, A.}, |
| title |
= |
{Détection de Filaments dans des images 2D et 3D; modélisation, étude mathématique et algorithmes.}, |
| year |
= |
{2009}, |
| month |
= |
{mai}, |
| school |
= |
{Universite de Nice Sophia Antipolis}, |
| url |
= |
{https://hal.inria.fr/tel-00507520/}, |
| keyword |
= |
{imagerie 3D, Segmentation, filaments, Deconvolution, Methodes variationnelles, mocroscopie confocale} |
| } |
Résumé :
Cette thèse aborde le problème de la modélisation et de la détection des laments
dans des images 3D.
Nous avons développé des méthodes variationnelles pour quatre applications
spéci ques :
l'extraction de routes où nous avons introduit la notion de courbure totale
pour conserver les réseaux réguliers en tolérant les discontinuités de
direction.
la détection et la complétion de laments fortement bruités et présentant
des occultation. Nous avons utilisé la magnétostatique et la théorie
de Ginzburg-Landau pour représenter les laments comme ensemble de
singularités d'un champ vectoriel.
la détection de laments dans des images biologiques acquises en microscopie
confocale. On modélise les laments en tenant compte des spéci cité
de cette dernière. Les laments sont alors obtenus par une méthode de
maximum à posteriori.
la détection de cible dans des séquences d'images infrarouges. Dans cette
application, on cherche des trajectoires optimisant la diérence de luminosit
é moyenne entre la trajectoire et son voisinage en tenant compte des
capteurs utilisés.
Par ailleurs, nous avons démontré des résultats théoriques portant sur la
courbure totale et la convergence de la méthode d'Alouges associée aux systèmes
de Ginzburg-Landau. Ce travail réunit à la fois modélisation, résulats théoriques
et recherche d'algorithmes numériques performants permettant de traiter de
réelles applications. |
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5 Articles de conférence |
1 - Algorithme rapide pour la restauration d'image régularisée sur les coefficients d'ondelettes.
M. Carlavan et P. Weiss et L. Blanc-Féraud et J. Zerubia. Dans Proc. Symposium on Signal and Image Processing (GRETSI), Dijon, France, septembre 2009.
Mots-clés : Deconvolution, nesterov scheme, Ondelettes, l1 norm.
@INPROCEEDINGS{GRETSICarlavan09,
|
| author |
= |
{Carlavan, M. and Weiss, P. and Blanc-Féraud, L. and Zerubia, J.}, |
| title |
= |
{Algorithme rapide pour la restauration d'image régularisée sur les coefficients d'ondelettes}, |
| year |
= |
{2009}, |
| month |
= |
{septembre}, |
| booktitle |
= |
{Proc. Symposium on Signal and Image Processing (GRETSI)}, |
| address |
= |
{Dijon, France}, |
| url |
= |
{http://www.math.univ-toulouse.fr/~weiss/Publis/Conferences/CarlavanGretsi09.pdf}, |
| pdf |
= |
{http://www.math.univ-toulouse.fr/~weiss/Publis/Conferences/CarlavanGretsi09.pdf}, |
| keyword |
= |
{Deconvolution, nesterov scheme, Ondelettes, l1 norm} |
| } |
Résumé :
De nombreuses méthodes de restauration d'images consistent à minimiser une énergie convexe. Nous nous focalisons sur l'utilisation de ces méthodes et considérons la minimisation de deux critères contenant une norme l1 des coefficients en ondelettes. La plupart des travaux publiés récemment proposent un critère à minimiser dans le domaine des coefficients en ondelettes, utilisant ainsi un a priori de parcimonie. Nous proposons un algorithme rapide et des résultats de déconvolution par minimisation d'un critère dans le domaine image, avec un a priori de régularité exprimé dans le domaine image utilisant une décomposition redondante sur une trame. L'algorithme et le modèle proposés semblent originaux pour ce problème en traitement d'images et sont performants en terme de temps de calculs et de qualité de restauration. Nous montrons des comparaisons entre les deux types d' a priori. |
Abstract :
Many image restoration techniques are based on convex energy minimization. We focus on the use of these techniques and consider the minimization of two criteria holding a l1-norm of wavelet coefficients. Most of the recent research works are based on the minimization of a criterion in the wavelet coefficients domain, namely as a sparse prior. We propose a fast algorithm and deconvolution results obtained by minimizing a criterion in the image domain using a redundant decomposition on a frame. The algorithm and model proposed are unusual for this problem and very efficient in term of computing time and quality of restoration results. We show comparisons between the two different priors. |
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2 - Complex wavelet regularization for solving inverse problems in remote sensing.
M. Carlavan et P. Weiss et L. Blanc-Féraud et J. Zerubia. Dans Proc. IEEE International Geoscience and Remote Sensing Symposium (IGARSS), Cape Town, South Africa, juillet 2009.
Mots-clés : Deconvolution, Dual smoothing, nesterov scheme, remote sensing, wavelet.
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3 - Point-spread function retrieval for fluorescence microscopy.
P. Pankajakshan et L. Blanc-Féraud et Z. Kam et J. Zerubia. Dans Proc. IEEE International Symposium on Biomedical Imaging (ISBI), Publ. IEEE, Org. IEEE, Boston, USA, juin 2009.
Mots-clés : fluorescence microscopy, point spread function, Algorithme EM, Deconvolution.
Copyright : Copyright 2009 IEEE. Published in the 2009 International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2009), scheduled for June 28 - July 1, 2009 in Boston, Massachusetts, U.S.A. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works, must be obtained from the IEEE. Contact: Manager, Copyrights and Permissions / IEEE Service Center / 445 Hoes Lane / P.O. Box 1331 / Piscataway, NJ 08855-1331, USA. Telephone: + Intl. 908-562-3966.
@INPROCEEDINGS{ppankajakshan09a,
|
| author |
= |
{Pankajakshan, P. and Blanc-Féraud, L. and Kam, Z. and Zerubia, J.}, |
| title |
= |
{Point-spread function retrieval for fluorescence microscopy}, |
| year |
= |
{2009}, |
| month |
= |
{juin}, |
| booktitle |
= |
{Proc. IEEE International Symposium on Biomedical Imaging (ISBI)}, |
| publisher |
= |
{IEEE}, |
| organization |
= |
{IEEE}, |
| address |
= |
{Boston, USA}, |
| pdf |
= |
{http://hal.inria.fr/docs/00/39/55/34/PDF/pankajakshan.pdf}, |
| keyword |
= |
{fluorescence microscopy, point spread function, Algorithme EM, Deconvolution} |
| } |
Abstract :
In this paper we propose a method for retrieving the Point-Spread Function (PSF) of an imaging system given the observed images of fluorescent microspheres. Theoretically calculated PSFs often lack the experimental or microscope specific signatures while empirically obtained data are either over sized or (and) too noisy. The effect of noise and the influence of the microsphere size can be mitigated from the experimental data by using a Maximum Likelihood Expectation Maximization (MLEM) algorithm. The true experimental parameters can then be estimated by fitting the result to a model based on the scalar diffraction theory. The algorithm was tested on some simulated data and the results obtained validate the usefulness of the approach for retrieving the PSF from measured data. |
|
4 - Image deconvolution using a stochastic differential equation approach.
X. Descombes et M. Lebellego et E. Zhizhina. Dans Proc. nternational Conference on Computer Vision Theory
and Applications, Barcelona, Spain, mars 2007.
Mots-clés : Deconvolution, Stochastic Differential Equation.
@INPROCEEDINGS{xavBarca2,
|
| author |
= |
{Descombes, X. and Lebellego, M. and Zhizhina, E.}, |
| title |
= |
{Image deconvolution using a stochastic differential equation approach}, |
| year |
= |
{2007}, |
| month |
= |
{mars}, |
| booktitle |
= |
{Proc. nternational Conference on Computer Vision Theory
and Applications}, |
| address |
= |
{Barcelona, Spain}, |
| pdf |
= |
{ftp://ftp-sop.inria.fr/ariana/Articles/2007_xavBarca2.pdf}, |
| keyword |
= |
{Deconvolution, Stochastic Differential Equation} |
| } |
|
5 - Wavelet-based restoration methods: application to 3D confocal microscopy images.
C. Chaux et L. Blanc-Féraud et J. Zerubia. Dans Proc. SPIE Conference on Wavelets, 2007.
Mots-clés : Restauration, Deconvolution, 3D images, Microscopie confocale, Poisson noise, Ondelettes.
Copyright : Copyright 2007 Society of Photo-Optical Instrumentation Engineers.
This paper was published in Proc. SPIE Conference on Wavelets and is made available as an electronic reprint (preprint) with permission of SPIE. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper are prohibited.
@INPROCEEDINGS{chaux2007,
|
| author |
= |
{Chaux, C. and Blanc-Féraud, L. and Zerubia, J.}, |
| title |
= |
{Wavelet-based restoration methods: application to 3D confocal microscopy images}, |
| year |
= |
{2007}, |
| booktitle |
= |
{Proc. SPIE Conference on Wavelets}, |
| pdf |
= |
{ftp://ftp-sop.inria.fr/ariana/Articles/2007_chaux2007.pdf}, |
| keyword |
= |
{Restauration, Deconvolution, 3D images, Microscopie confocale, Poisson noise, Ondelettes} |
| } |
|
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8 Rapports de recherche et Rapports techniques |
1 - Restoration mehod for spatially variant blurred images.
S. Ben Hadj et L. Blanc-Féraud. Rapport de Recherche 7654, INRIA, juin 2011.
Mots-clés : Deconvolution, energy minimization, spatially-variant PSF, Variation totale.
@TECHREPORT{RR_SBH_11,
|
| author |
= |
{Ben Hadj, S. and Blanc-Féraud, L.}, |
| title |
= |
{Restoration mehod for spatially variant blurred images}, |
| year |
= |
{2011}, |
| month |
= |
{juin}, |
| institution |
= |
{INRIA}, |
| type |
= |
{Research Report}, |
| number |
= |
{7654}, |
| url |
= |
{ http://hal.inria.fr/inria-00602650/fr/}, |
| keyword |
= |
{Deconvolution, energy minimization, spatially-variant PSF, Variation totale} |
| } |
|
2 - Complex wavelet regularization for 3D confocal microscopy deconvolution.
M. Carlavan et L. Blanc-Féraud. Rapport de Recherche 7366, INRIA, août 2010.
Mots-clés : 3D confocal microscopy, Deconvolution, complex wavelet regularization, discrepancy principle, Alternating Direction technique.
@TECHREPORT{RR-7366,
|
| author |
= |
{Carlavan, M. and Blanc-Féraud, L.}, |
| title |
= |
{Complex wavelet regularization for 3D confocal microscopy deconvolution}, |
| year |
= |
{2010}, |
| month |
= |
{août}, |
| institution |
= |
{INRIA}, |
| type |
= |
{Research Report}, |
| number |
= |
{7366}, |
| url |
= |
{http://hal.inria.fr/inria-00509447/fr/}, |
| keyword |
= |
{3D confocal microscopy, Deconvolution, complex wavelet regularization, discrepancy principle, Alternating Direction technique} |
| } |
Abstract :
Confocal microscopy is an increasingly popular technique for 3D
imaging of biological specimens which gives images with a very good resolution
(several tenths of micrometers), even though degraded by both blur and Poisson
noise. Deconvolution methods have been proposed to reduce these degradations,
some of them being regularized on a Total Variation prior, which gives
good results in image restoration but does not allow to retrieve the thin details
(including the textures) of the specimens. We rst propose here to use instead
a wavelet prior based on the Dual-Tree Complex Wavelet transform to retrieve
the thin details of the object. As the regularizing prior e ciency also depends
on the choice of its regularizing parameter, we secondly propose a method to
select the regularizing parameter following a discrepancy principle for Poisson
noise. Finally, in order to implement the proposed deconvolution method, we
introduce an algorithm based on the Alternating Direction technique which allows
to avoid inherent stability problems of the Richardson-Lucy multiplicative
algorithm which is widely used in 3D image restoration. We show some results
on real and synthetic data, and compare these results to the ones obtained with
the Total Variation and the Curvelets priors. We also give preliminary results
on a modi cation of the wavelet transform allowing to deal with the anisotropic
sampling of 3D confocal images. |
|
3 - Space non-invariant point-spread function and its estimation in fluorescence microscopy.
P. Pankajakshan et L. Blanc-Féraud et Z. Kam et J. Zerubia. Research Report 7157, INRIA, décembre 2009.
Mots-clés : Confocal Laser Scanning Microscopy, point spread function, Estimation bayesienne, Estimation MAP, Deconvolution, fluorescence microscopy.
@TECHREPORT{ppankajakshan09c,
|
| author |
= |
{Pankajakshan, P. and Blanc-Féraud, L. and Kam, Z. and Zerubia, J.}, |
| title |
= |
{Space non-invariant point-spread function and its estimation in fluorescence microscopy}, |
| year |
= |
{2009}, |
| month |
= |
{décembre}, |
| institution |
= |
{INRIA}, |
| type |
= |
{Research Report}, |
| number |
= |
{7157}, |
| url |
= |
{http://hal.archives-ouvertes.fr/inria-00438719/en/}, |
| keyword |
= |
{Confocal Laser Scanning Microscopy, point spread function, Estimation bayesienne, Estimation MAP, Deconvolution, fluorescence microscopy} |
| } |
Résumé :
Dans ce rapport de recherche, nous rappelons brièvement comment la nature limitée de diffraction de l'objectif d'un microscope optique, et le bruit
intrinsèque peuvent affecter la résolution d'une image observée. Un algorithme de déconvolution aveugle a été proposé en vue de restaurer les fréquences manquants au delà de la limite de diffraction. Cependant, sous d'autres conditions, l'approximation du systéme imageur l'imagerie sans aberration n'est plus valide et donc les aberrations de la phase du front d'onde émergeant d'un médium ne sont plus ignorées. Dans la deuxième partie de
ce rapport de recherche, nous montrons que la distribution d'intensité originelle et la localisation d'un objet peuvent être retrouvées uniquement en obtenant de la phase du front d'onde
réfracté, à partir d'images d'intensité observées. Nous démontrons cela par obtention de la fonction de ou a partir d'une microsphère imagée. Le bruit et l'infl uence de la taille de la
microsphère peuvent être diminués et parfois complètement supprimes des images observées en utilisant un estimateur maximum a posteriori. Néanmoins, a cause de l'incohérence du système d'acquisition, une récupération de phase a partir d'intensités observées n'est possible que si la restauration de la phase est contrainte. Nous avons utilisé l'optique géométrique
pour modéliser la phase du front d'onde réfracté, et nous avons teste l'algorithme sur des images simulées. |
Abstract :
In this research report, we recall briefly how the diffraction-limited nature of an optical microscope's objective, and the intrinsic noise can affect the observed images' resolution. A blind deconvolution algorithm can restore the lost frequencies beyond the diffraction limit. However, under other imaging conditions, the approximation of aberration-free imaging, is not applicable, and the phase aberrations of the emerging wavefront from a specimen immersion medium cannot be ignored any more. We show that an object's location and its original intensity distribution can be recovered by retrieving the refracted wavefront's phase from the observed intensity images. We demonstrate this by retrieving the point-spread function from an imaged microsphere. The noise and the influence of the microsphere size can be mitigated and sometimes completely removed from the observed images by using a maximum a posteriori estimate. However, due to the incoherent nature of the acquisition system, phase retrieval from the observed intensities will be possible only if the phase is constrained. We have used geometrical optics to model the phase of the refracted wavefront, and tested the algorithm on some simulated images. |
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Rapport d'activité 2011
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