Publications de Masih Nilchian

Overload blunts baroreflex only in overreached athletes

Jean-Marc Vesin, Grégoire Millet, Masih Nilchian, Sasan Yazdani

Heart rate variability (HRV) is commonly used to diagnose overreaching and monitor athletes’ responses to training. Baroreflex sensitivity (BRS) is modified by changes in training load and might be another means to detect overreaching. The goal of this stu ...

2018

Fast multiscale reconstruction for Cryo-EM

Michaël Unser, Masih Nilchian, Laurène Donati

We present a multiscale reconstruction framework for single-particle analysis (SPA). The representation of three-dimensional (3D) objects with scaled basis functions permits the reconstruction of volumes at any desired scale in the real-space. This multisc ...

Elsevier2018

Compressed Sensing for Dose Reduction in STEM Tomography

Michaël Unser, Masih Nilchian, Laurène Donati

We designed a complete acquisition-reconstruction framework to reduce the radiation dosage in 3D scanning transmission electron microscopy (STEM). Projection measurements are acquired by randomly scanning a subset of pixels at every tilt-view (i.e., random ...

IEEE2017

System and Method for Defining Watertight and Locally Refinable Surfaces with Interpolatory Control Points

Michaël Unser, Daniel Andreas Schmitter, Masih Nilchian

A method for creating a watertight boundary between two graphical elements including the steps of displaying a first surface having a first shape and a second surface having a second shape on the display, an open space existing between the first surface an ...

2017

Compressed sensing for STEM tomography

Michaël Unser, Masih Nilchian, Laurène Donati

A central challenge in scanning transmission electron microscopy (STEM) is to reduce the electron radiation dosage required for accurate imaging of 3D biological nano-structures. Methods that permit tomographic reconstruction from a reduced number of STEM ...

2017

Variational Phase Imaging Using the Transport-of-Intensity Equation

Michaël Unser, Daniel Sage, Emrah Bostan, Masih Nilchian, Emmanuel Augustin Julien Froustey

We introduce a variational phase retrieval algorithm for the imaging of transparent objects. Our formalism is based on the transport-of-intensity equation (TIE), which relates the phase of an optical field to the variation of its intensity along the direct ...

IEEE2016

A Forward Regridding Method with Minimal Oversampling for Accurate and Efficient Iterative Tomographic Algorithms

Masih Nilchian, Marco Stampanoni

Reconstruction of underconstrained tomographic data sets remains a major challenge. Standard analytical techniques frequently lead to unsatisfactory results due to insufficient information. Several iterative algorithms, which can easily integrate a priori ...

IEEE2016

Slice-by-Slice versus Fully 3D Reconstruction for Parallel-Beam x-Ray Microtomography

Michaël Unser, Masih Nilchian, Michael Thompson McCann

We present a 3D iterative reconstruction method for microtomography, where iterative methods have previously been limited by their high computational cost. Our preliminary results show that it improves reconstruction quality over the traditional slice-by-s ...

OSA2016

Joint absorption and phase retrieval in grating-based x-ray radiography

Michaël Unser, Emrah Bostan, Masih Nilchian, Mohammad Reza Nilchiyan, Marco Stampanoni

Given the raw absorption and differential phase-contrast images obtained from a grating-based x-ray radiography, we formulate the joint denoising of the absorption image and retrieval of the non-differential phase image as a regularized inverse problem. Th ...

Optical Society of America2016

Fast 3D reconstruction method for differential phase contrast X-ray CT

Michaël Unser, Masih Nilchian, Marco Stampanoni, Michael Thompson McCann

We present a fast algorithm for fully 3D regularized X-ray tomography reconstruction for both traditional and differential phase contrast measurements. In many applications, it is critical to reduce the X-ray dose while producing high-quality reconstructio ...

2016

High Performance Reconstruction Framework for Straight Ray Tomography : from Micro to Nano Resolution Imaging

Masih Nilchian

We develop a high-performance scheme to reconstruct straight-ray tomographic scans. We preserve the quality of the state-of-the-art schemes typically found in traditional computed tomography but reduce the computational cost substantially. Our approach is ...

EPFL2015

Spline based iterative phase retrieval algorithm for X-ray differential phase contrast radiography

Michaël Unser, Masih Nilchian, Marco Stampanoni

Differential phase contrast imaging using grating interferometer is a promising alternative to conventional X-ray radiographic methods. It provides the absorption, differential phase and scattering information of the underlying sample simultaneously. Phase ...

Optical Soc Amer2015

Optimized Kaiser-Bessel Window Functions for Computed Tomography

Michaël Unser, Cédric René Jean Vonesch, Masih Nilchian, John Paul Ward

Kaiser-Bessel window functions are frequently used to discretize tomographic problems because they have two desirable properties: 1) their short support leads to a low computational cost and 2) their rotational symmetry makes their imaging transform indepe ...

Ieee-Inst Electrical Electronics Engineers Inc2015

Fast iterative reconstruction of differential phase contrast X-ray tomograms

Michaël Unser, Cédric René Jean Vonesch, Masih Nilchian, Peter Modregger, Marco Stampanoni

Differential phase-contrast is a recent technique in the context of X-ray imaging. In order to reduce the specimen's exposure time, we propose a new iterative algorithm that can achieve the same quality as FBP-type methods, while using substantially fewer ...

Optical Society of America2013

Constrained regularized reconstruction of X-ray-DPCI tomograms with weighted-norm

Michaël Unser, Cédric René Jean Vonesch, Masih Nilchian, Stamatios Lefkimmiatis, Peter Modregger, Marco Stampanoni

In this paper we introduce a new reconstruction algorithm for X-ray differential phase-contrast Imaging (DPCI). Our approach is based on 1) a variational formulation with a weighted data term and 2) a variable-splitting scheme that allows for fast converge ...

Optical Society of America2013

Sparse Stochastic Processes and Discretization of Linear Inverse Problems

Michaël Unser, Ulugbek Kamilov, Emrah Bostan, Masih Nilchian

We present a novel statistically-based discretization paradigm and derive a class of maximum a posteriori (MAP) estimators for solving ill-conditioned linear inverse problems. We are guided by the theory of sparse stochastic processes, which specifies cont ...

Ieee-Inst Electrical Electronics Engineers Inc2013

Iterative FBP For Improved Reconstruction Of X-Ray Differential Phase-Contrast Tomograms

Michaël Unser, Cédric René Jean Vonesch, Masih Nilchian, Peter Modregger, Marco Stampanoni

X-ray differential phase-contrast tomography is a recently-developed modality for the imaging of low-contrast biological samples. Its mathematical model is based on the first derivative of the Radon transform and the images, in practice, are reconstructed ...

IEEE2013

A Box Spline Calculus for the Discretization of Computed Tomography Reconstruction Problems

Michaël Unser, Masih Nilchian

B-splines are attractive basis functions for the continuous-domain representation of biomedical images and volumes. In this paper, we prove that the extended family of box splines are closed under the Radon transform and derive explicit formulae for their ...

Institute of Electrical and Electronics Engineers2012

Differential Phase-Contrast X-Ray Computed Tomography: From Model Discretization To Image Reconstruction

Michaël Unser, Masih Nilchian

Our contribution in this paper is two fold. First, we propose a novel discretization of the forward model for differential phase-contrast imaging that uses B-spline basis functions. The approach yields a fast and accurate algorithm for implementing the for ...

Ieee2012