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, Suliana Manley, Cédric René Jean Vonesch, 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, John Paul Ward, Hagay Kirshner

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, Arash Amini, Pouya Dehghani Tafti, Hagay Kirshner

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, John Paul Ward, Aurélien Bourquard, Hagay Kirshner

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, John Paul Ward, Aurélien Bourquard, Hagay Kirshner

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