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Publications about Blind Deconvolution
Result of the query in the list of publications :
Article |
1 - Blind deconvoltion for thin layered confocal imaging.
P. Pankajakshan and B. Zhang and L. Blanc-Féraud and Z. Kam and J.C. Olivo-Marin and J. Zerubia. Applied Optics, 48(22): pages 4437-4448, August 2009.
Keywords : Blind Deconvolution, Confocal microscopy, Inverse Problems.
Copyright : Optical Society of America
@ARTICLE{ppankajakshan09b,
|
| author |
= |
{Pankajakshan, P. and Zhang, B. and Blanc-Féraud, L. and Kam, Z. and Olivo-Marin, J.C. and Zerubia, J.}, |
| title |
= |
{Blind deconvoltion for thin layered confocal imaging}, |
| year |
= |
{2009}, |
| month |
= |
{August}, |
| journal |
= |
{Applied Optics}, |
| volume |
= |
{48}, |
| number |
= |
{22}, |
| pages |
= |
{4437-4448}, |
| pdf |
= |
{http://hal.inria.fr/docs/00/39/55/23/PDF/AppliedOpticsPaperTypesetting.pdf}, |
| keyword |
= |
{Blind Deconvolution, Confocal microscopy, Inverse Problems} |
| } |
Abstract :
We propose an alternate minimization algorithm for estimating the point-spread function (PSF) of a confocal laser scanning microscope and the specimen fluorescence distribution. A three-dimensional separable Gaussian model is used to restrict the PSF solution space and a constraint on the specimen is used so as to favor the stabilization and convergence of the algorithm. The results obtained from the simulation show that the PSF can be estimated to a high degree of accuracy, and those on real data show better deconvolution as compared to a full theoretical PSF model. |
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PhD Thesis and Habilitation |
1 - Blind Deconvolution for Confocal Laser Scanning Microscopy.
P. Pankajakshan. PhD Thesis, Universite de Nice Sophia Antipolis, December 2009.
Keywords : Confocal Laser Scanning Microscopy, Blind Deconvolution, point spread function, Maximum likelihood estimation , total variation regularization.
@PHDTHESIS{PankajakshanThesis09,
|
| author |
= |
{Pankajakshan, P.}, |
| title |
= |
{Blind Deconvolution for Confocal Laser Scanning Microscopy}, |
| year |
= |
{2009}, |
| month |
= |
{December}, |
| school |
= |
{Universite de Nice Sophia Antipolis}, |
| url |
= |
{http://tel.archives-ouvertes.fr/tel-00474264/fr/}, |
| keyword |
= |
{Confocal Laser Scanning Microscopy, Blind Deconvolution, point spread function, Maximum likelihood estimation , total variation regularization} |
| } |
Résumé :
La microscopie confocale à balayage laser, est une technique puissante pour
étudier les spécimens biologiques en trois dimensions (3D) par sectionnement
optique. Elle permet d’avoir des images de spécimen vivants à une résolution de
l’ordre de quelques centaines de nanomètres. Bien que très utilisée, il persiste
des incertitudes dans le procédé d’observation. Comme la réponse du système à
une impulsion, ou fonction de flou (PSF), est dépendante à la fois du spécimen
et des conditions d’acquisition, elle devrait être estimée à partir des images
observées du spécimen. Ce problème est mal posé et sous déterminé. Pour
obtenir une solution, il faut injecter des connaisances, c’est à dire, a priori dans le
problème. Pour cela, nous adoptons une approche bayésienne. L’état de l’art des
algorithmes concernant la déconvolution et la déconvolution aveugle est exposé
dans le cadre d’un travail bayésien. Dans la première partie, nous constatons
que la diffraction due à l’objectif et au bruit intrinsèque à l’acquisition, sont les
distorsions principales qui affectent les images d’un spécimen. Une approche
de minimisation alternée (AM), restaure les fréquences manquantes au-delà de
la limite de diffraction, en utilisant une régularisation par la variation totale
sur l’objet, et une contrainte de forme sur la PSF. En outre, des méthodes
sont proposées pour assurer la positivité des intensités estimées, conserver le
flux de l’objet, et bien estimer le paramètre de la régularisation. Quand il
s’agit d’imager des spécimens épais, la phase de la fonction pupille, due aux
aberrations sphériques (SA) ne peut être ignorée. Dans la seconde partie, il est
montré qu’elle dépend de la difference à l’index de réfraction entre l’objet et
le milieu d’immersion de l’objectif, et de la profondeur sous la lamelle. Les
paramètres d’imagerie et la distribution de l’intensité originelle de l’objet sont
calculés en modifiant l’algorithme AM. Due à la nature de la lumière incohérente
en microscopie à fluorescence, il est possible d’estimer la phase à partir des
intensités observées en utilisant un modèle d’optique géométrique. Ceci a été
mis en évidence sur des données simulées. Cette méthode pourrait être étendue
pour restituer des spécimens affectés par les aberrations sphériques. Comme la
PSF varie dans l’espace, un modèle de convolution par morceau est proposé, et la
PSF est approchée. Ainsi, en plus de l’objet, il suffit d’estimer un seul paramétre libre. |
Abstract :
Confocal laser scanning microscopy is a powerful technique for studying
biological specimens in three dimensions (3D) by optical sectioning. It permits
to visualize images of live specimens non-invasively with a resolution of few
hundred nanometers. Although ubiquitous, there are uncertainties in the
observation process. As the system’s impulse response, or point-spread function
(PSF), is dependent on both the specimen and imaging conditions, it should be
estimated from the observed images in addition to the specimen. This problem is
ill-posed, under-determined. To obtain a solution, it is necessary to insert some
knowledge in the form of a priori and adopt a Bayesian approach. The state of
the art deconvolution and blind deconvolution algorithms are reviewed within a
Bayesian framework. In the first part, we recognize that the diffraction-limited
nature of the objective lens and the intrinsic noise are the primary distortions
that affect specimen images. An alternative minimization (AM) approach
restores the lost frequencies beyond the diffraction limit by using total variation
regularization on the object, and a spatial constraint on the PSF. Additionally,
some methods are proposed to ensure positivity of estimated intensities, to
conserve the object’s flux, and to well handle the regularization parameter.
When imaging thick specimens, the phase of the pupil function due to spherical
aberration (SA) cannot be ignored. It is shown to be dependent on the refractive
index mismatch between the object and the objective immersion medium, and
the depth under the cover slip. The imaging parameters and the object’s original
intensity distribution are recovered by modifying the AM algorithm. Due to
the incoherent nature of the light in fluorescence microscopy, it is possible to
retrieve the phase from the observed intensities by using a model derived from
geometrical optics. This was verified on the simulated data. This method could
also be extended to restore specimens affected by SA. As the PSF is space varying,
a piecewise convolution model is proposed, and the PSF approximated so that,
apart from the specimen, it is sufficient to estimated only one free parameter.
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2 Conference articles |
1 - Blind deconvolution for diffraction-limited fluorescence microscopy.
P. Pankajakshan and B. Zhang and L. Blanc-Féraud and Z. Kam and J.C. Olivo-Marin and J. Zerubia. In Proc. IEEE International Symposium on Biomedical Imaging (ISBI), pages 740-743, Paris, France, May 2008.
Keywords : Confocal microscopy, Blind Deconvolution, point spread function, Richardson-Lucy algorithm, total variation regularization.
Copyright : This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible.
@INPROCEEDINGS{ppankajakshan08a,
|
| author |
= |
{Pankajakshan, P. and Zhang, B. and Blanc-Féraud, L. and Kam, Z. and Olivo-Marin, J.C. and Zerubia, J.}, |
| title |
= |
{Blind deconvolution for diffraction-limited fluorescence microscopy}, |
| year |
= |
{2008}, |
| month |
= |
{May}, |
| booktitle |
= |
{Proc. IEEE International Symposium on Biomedical Imaging (ISBI)}, |
| pages |
= |
{740-743}, |
| address |
= |
{Paris, France}, |
| pdf |
= |
{ftp://ftp-sop.inria.fr/ariana/Articles/2008_ppankajakshan08a.pdf}, |
| keyword |
= |
{Confocal microscopy, Blind Deconvolution, point spread function, Richardson-Lucy algorithm, total variation regularization} |
| } |
Abstract :
Optical Sections of biological samples obtained from a fluorescence Confocal Laser Scanning Microscopes (CLSM) are often degraded by out-of-focus blur and photon counting noise. Such physical constraints on the observation are a result of the diffraction-limited nature of the optical system, and the reduced amount of light detected by the photomultiplier respectively. Hence, the image stacks can benefit from postprocessing restoration methods based on deconvolution. The parameters of the acquisition system’s Point Spread Function (PSF) may vary during the course of experimentation, and so they have to be estimated directly from the observation data. We describe here an alternate minimization algorithm for the simultaneous blind estimation of the specimen 3D distribution of fluorescent sources and the PSF. Experimental results on real data show that the algorithm provides very good deconvolution results in comparison to theoretical microscope PSF models. |
|
2 - Parametric blind deconvolution for confocal laser scanning microscopy.
P. Pankajakshan and B. Zhang and L. Blanc-Féraud and Z. Kam and J.C. Olivo-Marin and J. Zerubia. In Proc. 29th International Conference of IEEE EMBS (EMBC-07), pages 6531-6534, August 2007.
Keywords : Confocal microscopy, Blind Deconvolution, Poisson noise, Total variation, EM algorithm, Bayesian estimation.
Copyright : ©2007 IEEE. 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.
@INPROCEEDINGS{Pankajakshan07a,
|
| author |
= |
{Pankajakshan, P. and Zhang, B. and Blanc-Féraud, L. and Kam, Z. and Olivo-Marin, J.C. and Zerubia, J.}, |
| title |
= |
{Parametric blind deconvolution for confocal laser scanning microscopy}, |
| year |
= |
{2007}, |
| month |
= |
{August}, |
| booktitle |
= |
{Proc. 29th International Conference of IEEE EMBS (EMBC-07)}, |
| pages |
= |
{6531-6534}, |
| pdf |
= |
{http://ieeexplore.ieee.org/iel5/4352184/4352185/04353856.pdf?tp=&isnumber=&arnumber=4353856}, |
| keyword |
= |
{Confocal microscopy, Blind Deconvolution, Poisson noise, Total variation, EM algorithm, Bayesian estimation} |
| } |
Abstract :
In this paper, we propose a method for the
iterative restoration of fluorescence Confocal Laser Scanning
Microscopic (CLSM) images and parametric estimation of the
acquisition system’s Point Spread Function (PSF). The CLSM is
an optical fluorescence microscope that scans a specimen in 3D
and uses a pinhole to reject most of the out-of-focus light. However,
the quality of the images suffers from two basic physical
limitations. The diffraction-limited nature of the optical system,
and the reduced amount of light detected by the photomultiplier
cause blur and photon counting noise respectively. These images
can hence benefit from post-processing restoration methods
based on deconvolution. An efficient method for parametric
blind image deconvolution involves the simultaneous estimation
of the specimen 3D distribution of fluorescent sources and
the microscope PSF. By using a model for the microscope
image acquisition physical process, we reduce the number of
free parameters describing the PSF and introduce constraints.
The parameters of the PSF may vary during the course of
experimentation, and so they have to be estimated directly from
the observed data. A priori model of the specimen is further
applied to stabilize the alternate minimization algorithm and to
converge to the solutions. |
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Technical and Research Report |
1 - Parametric blind deconvolution for confocal laser scanning microscopy-proof of concept.
P. Pankajakshan and L. Blanc-Féraud and B. Zhang and Z. Kam and J.C. Olivo-Marin and J. Zerubia. Research Report 6493, INRIA, April 2008.
Keywords : Confocal Laser Scanning Microscopy, Bayesian restoration, Blind Deconvolution, point spread function, Richardson-Lucy algorithm, Total variation.
Copyright : ARIANA/INRIA
@TECHREPORT{ppankajakshan08b,
|
| author |
= |
{Pankajakshan, P. and Blanc-Féraud, L. and Zhang, B. and Kam, Z. and Olivo-Marin, J.C. and Zerubia, J.}, |
| title |
= |
{Parametric blind deconvolution for confocal laser scanning microscopy-proof of concept}, |
| year |
= |
{2008}, |
| month |
= |
{April}, |
| institution |
= |
{INRIA}, |
| type |
= |
{Research Report}, |
| number |
= |
{6493}, |
| url |
= |
{https://hal.inria.fr/inria-00269265}, |
| pdf |
= |
{http://hal.inria.fr/docs/00/27/02/92/PDF/report.pdf}, |
| keyword |
= |
{Confocal Laser Scanning Microscopy, Bayesian restoration, Blind Deconvolution, point spread function, Richardson-Lucy algorithm, Total variation} |
| } |
Résumé :
Nous proposons une méthode de restauration itérative d’images de fluorescence
CLSM et d’estimation paramétrique de la fonction de flou (PSF) du système d’acquisition.
Le CLSM est un microscope qui balaye un échantillon en 3D et utilise une sténopée pour
rejeter la lumière en dehors du point de focalisation. Néanmoins, la qualité des images
souffre de deux limitations physiques. La première est due à la diffraction due au système
optique et la seconde est due à la quantité réduite de lumière détectée par le tube
photo-multiplicateur (PMT). Ces limitations induisent respectivement un flou et du bruit
de comptage de photons. Les images peuvent alors bénéficier d’un post-traitement de
restauration fondé sur la déconvolution. Le problème à traiter est l’estimation simultanée
de la distribution 3D de l’échantillon des sources fluorescentes et de la PSF du microscope
(i.e. de déconvolution aveugle). En utilisant un modèle de processus physique
d’acquisition d’images microscopiques (CLSM), on réduit le nombre de paramètres libres
décrivant la PSF et on introduit des contraintes. On introduit aussi des connaissances a
priori sur l’échantillon ce qui permet de stabiliser le processus d’estimation et de favoriser
la convergence. Des expériences sur des données synthétiques montrent que la PSF peut
être estimée avec précision. Des expériences sur des données réelles montrent de bons
resultats de déconvolution en comparaison avec le modèle théorique de la PSF du microscope. |
Abstract :
We propose a method for the iterative restoration of fluorescence Confocal Laser Scanning Microscope (CLSM) images with parametric estimation of the acquisition system’s Point Spread Function (PSF). The CLSM is an optical fluorescence microscope that scans a specimen in 3D and uses a pinhole to reject most of the out-of-focus light. However, the quality of the image suffers from two primary physical limitations. The first is due to the diffraction-limited nature of the optical system and the second is due to the reduced amount of light detected by the photomultiplier tube (PMT). These limitations cause blur and photon counting noise respectively. The images can hence benefit from post-processing restoration methods based on deconvolution. An efficient method for parametric blind image deconvolution involves the simultaneous estimation of the specimen 3D distribution of fluorescent sources and the microscope PSF. By using a model for the microscope image acquisition physical process, we reduce the number of free parameters describing the PSF and introduce constraints. The parameters of the PSF may vary during the course of experimentation, and so they have to be estimated directly from the observation data. We also introduce a priori knowledge of the specimen that permits stabilization of the estimation process and favorizes the convergence. Experiments on simulated data show that the PSF could be estimatedwith a higher degree of accuracy and those done on real data show very good deconvolution results in comparison to the theoretical microscope PSF model. |
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