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Publications about Confocal microscopy
Result of the query in the list of publications :
2 Articles |
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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2 - Richardson-Lucy Algorithm with Total Variation Regularization for 3D Confocal Microscope Deconvolution.
N. Dey and L. Blanc-Féraud and C. Zimmer and Z. Kam and P. Roux and J.C. Olivo-Marin and J. Zerubia. Microscopy Research Technique, 69: pages 260-266, April 2006.
Keywords : Confocal microscopy, Variational methods, Total variation, 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 |
= |
{April}, |
| journal |
= |
{Microscopy Research Technique}, |
| volume |
= |
{69}, |
| pages |
= |
{260-266}, |
| url |
= |
{http://dx.doi.org/10.1002/jemt.20294}, |
| keyword |
= |
{Confocal microscopy, Variational methods, Total variation, 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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3 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. |
|
3 - Wavelet-based restoration methods: application to 3D confocal microscopy images.
C. Chaux and L. Blanc-Féraud and J. Zerubia. In Proc. SPIE Conference on Wavelets, 2007.
Keywords : Restoration, Deconvolution, 3D images, Confocal microscopy, Poisson noise, Wavelets.
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 |
= |
{Restoration, Deconvolution, 3D images, Confocal microscopy, Poisson noise, Wavelets} |
| } |
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2 Technical and Research Reports |
1 - Restauration d'Images Biologiques 3D en Microscopie Confocale par Transformée en Ondelettes Complexes.
G. Pons Bernad and L. Blanc-Féraud and J. Zerubia. Research Report 5507, INRIA, France, February 2005.
Keywords : Confocal microscopy, Complex 3D Wavelet Transform, Restoration, Denoising, Deconvolution.
@TECHREPORT{5507,
|
| author |
= |
{Pons Bernad, G. and Blanc-Féraud, L. and Zerubia, J.}, |
| title |
= |
{Restauration d'Images Biologiques 3D en Microscopie Confocale par Transformée en Ondelettes Complexes}, |
| year |
= |
{2005}, |
| month |
= |
{February}, |
| institution |
= |
{INRIA}, |
| type |
= |
{Research Report}, |
| number |
= |
{5507}, |
| address |
= |
{France}, |
| url |
= |
{https://hal.inria.fr/inria-00070500}, |
| pdf |
= |
{https://hal.inria.fr/file/index/docid/70500/filename/RR-5507.pdf}, |
| ps |
= |
{https://hal.inria.fr/docs/00/07/05/00/PS/RR-5507.ps}, |
| keyword |
= |
{Confocal microscopy, Complex 3D Wavelet Transform, Restoration, Denoising, Deconvolution} |
| } |
Résumé :
La microscopie confocale est une méthode puissante pour l'imagerie 3D de spécimens biologiques. Néanmoins, les images acquises sont dégradées non seulement par du flou dû à la lumière provenant de zones non focalisées du spécimen, mais aussi par un bruit de Poisson dû à la détection. Plusieurs algorithmes de déconvolution ont été proposés pour réduire ces dégradations. Un des plus utilisés est l'algorithme itératif de Richardson-Lucy, qui calcule un maximum de vraisemblance adapté à une statistique poissonienne. Mais cet algorithme tend à amplifier le bruit. Une solution consiste alors à introduire une contrainte de régularisation (par exemple, fondée sur la Variation Totale). Ici, nous nous concentrons sur des méthodes fondées sur l'analyse par ondelettes, en particulier sur des méthodes de débruitage via la transformée en ondelettes, qui semblent être plus appropriées à la microscopie en fluorescence 3D. Nous développons dans ce rapport un algorithme de Transformation en Ondelettes Complexes 3D introduit par N. Kingsbury. Celui-ci permet une décomposition invariante par translation et rotation et une sélectivité directionnelle des coefficients en ondelettes. Nous montrons sur des images synthétiques et sur des images réelles les résultats de cet algorithme de débruitage. Ce dernier est ensuite inséré dans le processus de déconvolution. |
Abstract :
Confocal laser scanning microscopy is a powerful technique for 3D imaging of biological specimens. However the acquired images are degraded by blur from out-of-focus light and Poisson noise. Several deconvolution algorithms have been proposed to reduce these degradations, including the Richardson-Lucy iterative algorithm, which computes a maximum likelihood estimation adapted to Poisson statistics. Nevertheless, this algorithm tends to amplify noise. Other solutions exist which combine Richardson-Lucy algorithm and regularization (for example with a Total Variation constraint). In this report, we will concentrate on methods based on wavelet analysis, in particular on wavelet denoising methods, which turn out to be very effective in application to 3D confocal images. To obtain a translation and rotation invariant decomposition algorithm, we have developped the 3D Complex Wavelet Transform introduced by Nick Kingsbury. These wavelets allow moreover a directional selectivity of the wavelet coefficients. We show on simulated and real images the denoising results. This algorithm is then used for the deconvolution purpose. |
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2 - 3D Microscopy Deconvolution using Richardson-Lucy Algorithm with Total Variation Regularization.
N. Dey and L. Blanc-Féraud and C. Zimmer and P. Roux and Z. Kam and J.C. Olivo-Marin and J. Zerubia. Research Report 5272, INRIA, France, July 2004.
Keywords : Confocal microscopy, Deconvolution, Impulse answer, Total variation.
@TECHREPORT{5272,
|
| author |
= |
{Dey, N. and Blanc-Féraud, L. and Zimmer, C. and Roux, P. and Kam, Z. and Olivo-Marin, J.C. and Zerubia, J.}, |
| title |
= |
{3D Microscopy Deconvolution using Richardson-Lucy Algorithm with Total Variation Regularization}, |
| year |
= |
{2004}, |
| month |
= |
{July}, |
| institution |
= |
{INRIA}, |
| type |
= |
{Research Report}, |
| number |
= |
{5272}, |
| address |
= |
{France}, |
| url |
= |
{http://hal.inria.fr/inria-00070726/fr/}, |
| pdf |
= |
{https://hal.inria.fr/file/index/docid/70726/filename/RR-5272.pdf}, |
| ps |
= |
{http://hal.inria.fr/docs/00/07/07/26/PS/RR-5272.ps}, |
| keyword |
= |
{Confocal microscopy, Deconvolution, Impulse answer, Total variation} |
| } |
Résumé :
La microscopie confocale (Confocal laser scanning microscopy ou microscopie confocale à balayage laser) est une méthode puissante de plus en plus populaire pour l'imagerie 3D de spécimens biologiques. Malheureusement, les images acquises sont dégradées non seulement par du flou dû à la lumière provenant de zones du spécimen non focalisées, mais aussi par un bruit de Poisson dû à la détection, qui se fait à faible flux de photons. Plusieurs méthodes de déconvolution ont été proposées pour réduire ces dégradations, avec en particulier l'algorithme itératif de Richardson-Lucy, qui calcule un maximum de vraisemblance adapté à une statistique poissonienne. Mais cet algorithme utilisé comme tel ne converge pas nécessairement vers une solution adaptée, car il tend à amplifier le bruit. Si par contre on l'utilise avec une contrainte de régularisation (connaissance a priori sur l'objet que l'on cherche à restaurer, par exemple), Richardson-Lucy régularisé converge toujours vers une solution adaptée, sans amplification du bruit. Nous proposons ici de combiner l'algorithme de Richardson-Lucy avec une contrainte de régularisation basée sur la Variation Totale, dont l'effet d'adoucissement permet d'éviter les oscillations d'intensité tout en préservant les bords des objets. Nous montrons sur des images synthétiques et sur des images réelles que cette contrainte de régularisation améliore les résultats de la déconvolution à la fois qualitativement et quantitativement. Nous comparons plusieurs méthodes de déconvolution bien connues à la méthode que nous proposons, comme Richardson-Lucy standard (pas de régularisation), Richardson-Lucy régularisé avec Tikhonov-Miller, et un algorithme basé sur la descente de gradients (sous l'hypothèse d'un bruit additif gaussien). |
Abstract :
Confocal laser scanning microscopy is a powerful and increasingly popular technique for 3D imaging of biological specimens. However the acquired images are degraded by blur from out-of-focus light and 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. However this algorithm does not necessarily converge to a suitable solution, as it tends to amplify noise. If it is used with a regularizing constraint (some prior knowledge on the data), Richardson-Lucy regularized with a well-chosen constraint, always converges to a suitable solution. Here, we propose to combine the Richardson-Lucy algorithm with a regularizing constraint based on Total Variation, whose smoothing avoids oscillations while preserving object edges. We show on simulated and real images that this constraint improves the deconvolution results both visually and using quantitative measures. We compare several well-known deconvolution methods to the proposed method, such as standard Richardson-Lucy (no regularization), Richardson-Lucy with Tikhonov-Miller regularization, and an additive gradient-based algorithm. |
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