Publications by Hagay Kirshner

Quantitative evaluation of software packages for single-molecule localization microscopy

Michaël Unser, Daniel Sage, Suliana Manley, Hagay Kirshner, Thomas Pengo

The quality of super-resolution images obtained by single-molecule localization microscopy (SMLM) depends largely on the software used to detect and accurately localize point sources. In this work, we focus on the computational aspects of super-resolution ...

Nature Publishing Group2015

FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data

Michaël Unser, Cédric René Jean Vonesch, Suliana Manley, Hagay Kirshner, Seamus John Holden, Lina Carlini

Super resolution microscopy such as STORM and (F) PALM is now a well known method for biological studies at the nanometer scale. However, conventional imaging schemes based on sparse activation of photo-switchable fluorescent probes have inherently slow te ...

Nature Publishing Group2014

On the Unique Identification of Continuous-Time Autoregressive Models From Sampled Data

Michaël Unser, Hagay Kirshner, John Paul Ward

In this work, we investigate the relationship between continuous-time autoregressive (AR) models and their sampled version. We consider uniform sampling and derive criteria for uniquely determining the continuous-time parameters from sampled data; the mode ...

Ieee-Inst Electrical Electronics Engineers Inc2014

A Unified Formulation of Gaussian Versus Sparse Stochastic Processes-Part II: Discrete-Domain Theory

Michaël Unser, Pouya Dehghani Tafti, Hagay Kirshner, Arash Amini

This paper is devoted to the characterization of an extended family of continuous-time autoregressive moving average (CARMA) processes that are solutions of stochastic differential equations driven by white Levy innovations. These are completely specified ...

Ieee-Inst Electrical Electronics Engineers Inc2014

Adaptive Image Resizing Based on Continuous-Domain Stochastic Modeling

Michaël Unser, Aurélien Bourquard, Hagay Kirshner, John Paul Ward

We introduce an adaptive continuous-domain modeling approach to texture and natural images. The continuous-domain image is assumed to be a smooth function, and we embed it in a parameterized Sobolev space. We point out a link between Sobolev spaces and sto ...

Ieee-Inst Electrical Electronics Engineers Inc2014

Benchmarking Image-Processing Algorithms for Biomicroscopy: Reference Datasets and Perspectives

Michaël Unser, Daniel Sage, Cédric René Jean Vonesch, Hagay Kirshner, Stamatios Lefkimmiatis

As the field of bioimage informatics matures, the issue of the validation of image reconstruction algorithms and the definition of proper performance criteria becomes more pressing. In this work, we discuss benchmarking aspects of fluorescence microscopy q ...

EUSIPCO2013

Identification of Rational Transfer Functions from Sampled Data

Michaël Unser, Hagay Kirshner, John Paul Ward

We consider the task of estimating an operator from sampled data. The operator, which is described by a rational transfer function, is applied to continuous-time white noise and the resulting continuous-time process is sampled uniformly. The main question ...

SampTA2013

3-D PSF fitting for fluorescence microscopy: implementation and localization application

Michaël Unser, Daniel Sage, François Aguet, Hagay Kirshner

Localization microscopy relies on computationally efficient Gaussian approximations of the point spread function for the calculation of fluorophore positions. Theoretical predictions show that under specific experimental conditions, localization accuracy i ...

Wiley-Blackwell2013

Linear Interpolation Of Biomedical Images Using A Data-Adaptive Kernel

Michaël Unser, Aurélien Bourquard, Hagay Kirshner, John Paul Ward

In this work, we propose a continuous-domain stochastic model that can be applied to image data. This model is autoregressive, and accounts for Gaussian-type as well as for non-Gaussian-type innovations. In order to estimate the corresponding parameters fr ...

IEEE2013

Can Localization Microscopy Benefit From Approximation Theory?

Michaël Unser, Cédric René Jean Vonesch, Hagay Kirshner

We introduce a general and computationally efficient approach to 3-D localization microscopy. The main idea is to construct a continuous-domain representation of the PSF by expanding it in a polynomial B-spline basis. This allows us to fit the PSF to the d ...

IEEE2013

Continuous Localization Using Sparsity Constraints for High-Density Super-Resolution Microscopy

Michaël Unser, Cédric René Jean Vonesch, Hagay Kirshner

Super-resolution localization microscopy relies on sparse activation of photo-switchable probes. Such activation, however, introduces limited temporal resolution. High-density imaging overcomes this limitation by allowing several neighboring probes to be a ...

IEEE2013

Is Uniqueness Lost for Under-Sampled Continuous-Time Auto-Regressive Processes?

Michaël Unser, Hagay Kirshner, John Paul Ward

We consider the problem of sampling continuous-time auto-regressive processes on a uniform grid. We investigate whether a given sampled process originates from a single continuous-time model, and address this uniqueness problem by introducing an alternativ ...

IEEE Institute of Electrical and Electronics Engineers2012

A Psf-Based Approach To Biplane Calibration In 3D Super-Resolution Microscopy

Michaël Unser, Daniel Sage, Suliana Manley, Hagay Kirshner, Thomas Pengo

Super-resolution localization microscopy methods such as PALM and STORM have been shown to provide imaging with resolutions up to a few tens of nanometers while using relatively simple setups. Biplane PALM has extended the PALM technique to three-dimension ...

Ieee2012

Maximum-Likelihood Identification of Sampled Gaussian Processes

Michaël Unser, Simona Maggio, Hagay Kirshner

This work considers sampled data of continuous-domain Gaussian processes. We derive a maximum-likelihood estimator for identifying autoregressive moving average parameters while incorporating the sampling process into the problem formulation. The proposed ...

SampTA2011

Resolution-Invariant Separable Arma Modeling Of Images

Michaël Unser, Aurélien Bourquard, Hagay Kirshner

We suggest a continuous-domain stochastic modeling of images that is invariant to spatial resolution. Specifically, we are proposing an estimator that is calibrated with respect to the sampling step, and that can potentially handle aliased data. Motivated ...

Ieee Service Center, 445 Hoes Lane, Po Box 1331, Piscataway, Nj 08855-1331 Usa2011

A Sampling Theory Approach for Continuous ARMA Identification

Michaël Unser, Simona Maggio, Hagay Kirshner

The problem of estimating continuous-domain autoregressive moving-average processes from sampled data is considered. The proposed approach incorporates the sampling process into the problem formulation while introducing exponential models for both the cont ...

IEEE2011

Continuous-Time AR Model Identification: Does Sampling Rate Really Matter?

Michaël Unser, Simona Maggio, Hagay Kirshner

We address the problem of identifying continuous-time auto regressive (CAR) models from sampled data. The exponential nature of CAR autocorrelation functions is taken into account by means of exponential B-splines modelling, allowing one to associate the a ...

EURASIP2010

A Stochastic Minimum-Norm Approach to Image and Texture Interpolation

Michaël Unser, Hagay Kirshner

We introduce an exponential-based consistent approach to image scaling. Our model stems from Sobolev reproducing kernels, motivated by their role in continuous-domain stochastic autoregressive processes. The proposed approach imposes consistency and applie ...

EURASIP2010