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Praveen Pankajakshan
Former PhD Student
 Keywords : Variational methods, MCMC, Wavelets, Parameter Estimation, Deconvolution, 3D Reconstruction
 Project : P2R France-Israel
 Demo : see this author's demo
 Contact :
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| Abstract :
I am currently working on the parametric blind deconvolution of Confocal Laser Scanning Microscope (CLSM) images. The CLSM is an optical fluorescence microscope that scans sections of a specimen in 3D and uses a pinhole to reject most out-of-focus light. However, the quality of confocal microscope images suffers from two basic physical limitations.
First, out-of-focus blurs due to the diffraction-limited nature of the optical microscope and secondly, the confocal pinhole drastically reduces the amount of photons detected by the photomultiplier causing poisson noise. The images produces by the CLSM can therefore benefit from post processing by deconvolution methods designed to reduce the blur and noise.
Our current goal is to develop a fast and efficient algorithm for
simultaneous estimation of the point-spread function (PSF) of the microscope and the specimen function. We realize that a good estimation of the PSF is very important for restoration of the original specimen.
However, estimation of the PSF is an undetermined problem with no known unique solution. We overcome this problem by using a physical acquisition model of the microscope and by introducing a priori knowledge about the specimen. This stabilizes the estimation procedure and helps in deciding
between candidate solutions. |
Last publications in Ariana Research Group :
Wavefront sensing for aberration modeling in fluorescence MACROscopy.
P. Pankajakshan and A. Dieterlen and G. Engler and Z. Kam and L. Blanc-Féraud and J. Zerubia and J.C. Olivo-Marin. In Proc. IEEE International Symposium on Biomedical Imaging (ISBI), Chicago, USA, April 2011.
Keywords : fluorescence MACROscopy , phase retrieval, field aberration.
@INPROCEEDINGS{PanjakshanISBI2011,
|
| author |
= |
{Pankajakshan, P. and Dieterlen, A. and Engler, G. and Kam, Z. and Blanc-Féraud, L. and Zerubia, J. and Olivo-Marin, J.C.}, |
| title |
= |
{Wavefront sensing for aberration modeling in fluorescence MACROscopy}, |
| year |
= |
{2011}, |
| month |
= |
{April}, |
| booktitle |
= |
{Proc. IEEE International Symposium on Biomedical Imaging (ISBI)}, |
| address |
= |
{Chicago, USA}, |
| url |
= |
{http://hal.inria.fr/inria-00563988/en/}, |
| keyword |
= |
{fluorescence MACROscopy , phase retrieval, field aberration} |
| } |
Abstract :
In this paper, we present an approach to calculate the wavefront in
the back pupil plane of an objective in a fluorescent MACROscope.
We use the three-dimensional image of a fluorescent bead because it
contains potential pupil information in the ‘far’ out-of-focus planes
for sensing the wavefront at the back focal plane of the objective.
Wavefront sensing by phase retrieval technique is needed for several
reasons. Firstly, the point-spread function of the imaging system
can be calculated from the estimated pupil phase and used for image
restoration. Secondly, the aberrations in the optics of the objective
can be determined by studying this phase. Finally, the estimated
wavefront can be used to correct the aberrated optical path with-
out a wavefront sensor. In this paper, we estimate the wavefront of
a MACROscope optical system by using Bayesian inferencing and
derive the Gerchberg-Saxton algorithm as a special case. |
Point-spread function model for fluorescence MACROscopy imaging.
P. Pankajakshan and Z. Kam and A. Dieterlen and G. Engler and L. Blanc-Féraud and J. Zerubia and J.C. Olivo-Marin. In Asilomar Conference on Signals, Systems and Computers, pages 1364-136, Pacific Grove, CA, USA , November 2010.
Keywords : fluorescence MACROscopy , point-spread function, pupil function, vignetting .
@INPROCEEDINGS{PanjakshanASILOMAR2010,
|
| author |
= |
{Pankajakshan, P. and Kam, Z. and Dieterlen, A. and Engler, G. and Blanc-Féraud, L. and Zerubia, J. and Olivo-Marin, J.C.}, |
| title |
= |
{Point-spread function model for fluorescence MACROscopy imaging}, |
| year |
= |
{2010}, |
| month |
= |
{November}, |
| booktitle |
= |
{Asilomar Conference on Signals, Systems and Computers}, |
| pages |
= |
{1364-136}, |
| address |
= |
{Pacific Grove, CA, USA }, |
| url |
= |
{http://hal.inria.fr/inria-00555940/}, |
| keyword |
= |
{fluorescence MACROscopy , point-spread function, pupil function, vignetting } |
| } |
Abstract :
In this paper, we model the point-spread function (PSF) of a fluorescence MACROscope with a field aberration. The MACROscope is an imaging arrangement that is designed to directly study small and large specimen preparations without physically sectioning them. However, due to the different optical components of the MACROscope, it cannot achieve the condition of lateral spatial invariance for all magnifications. For example, under low zoom settings, this field aberration becomes prominent, the PSF varies in the lateral field, and is proportional to the distance from the center of the field. On the other hand, for larger zooms, these aberrations become gradually absent. A computational approach to correct this aberration often relies on an accurate knowledge of the PSF. The PSF can be defined either theoretically using a scalar diffraction model or empirically by acquiring a three-dimensional image of a fluorescent bead that approximates a point source. The experimental PSF is difficult to obtain and can change with slight deviations from the physical conditions. In this paper, we model the PSF using the scalar diffraction approach, and the pupil function is modeled by chopping it. By comparing our modeled PSF with an experimentally obtained PSF, we validate our hypothesis that the spatial variance is caused by two limiting optical apertures brought together on different conjugate planes. |
Space non-invariant point-spread function and its estimation in fluorescence microscopy.
P. Pankajakshan and L. Blanc-Féraud and Z. Kam and J. Zerubia. Research Report 7157, INRIA, December 2009.
Keywords : Confocal Laser Scanning Microscopy, point spread function, Bayesian estimation, MAP estimation, 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 |
= |
{December}, |
| institution |
= |
{INRIA}, |
| type |
= |
{Research Report}, |
| number |
= |
{7157}, |
| url |
= |
{http://hal.archives-ouvertes.fr/inria-00438719/en/}, |
| keyword |
= |
{Confocal Laser Scanning Microscopy, point spread function, Bayesian estimation, MAP estimation, 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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All publications in Ariana Research Group
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2011 Activity report
