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Variational Framework for Continuous Angular Refinement and Reconstruction in Cryo-EM14 Aug 2018

Mona Zehni
EPFL STI LIB

14:00

In the field of single particle reconstruction (SPR) in Cryo-electron microscopy (Cryo-EM), the target is to recover a high resolution density map of the molecule from a set of particle images. In this imaging modality, each particle image corresponds to the X-ray transform of the molecule from an unknown 3D pose corrupted by contrast transfer function (CTF) of the microscope and noise. In this presentation, we describe a variational framework that performs a joint optimization of the density map and the underlying angular variables. We solve this joint optimization problem by taking alternating ADMM and gradient descent steps to update the density map and 3D pose variables iteratively. Note that, our method serves as a 3D refinement step in the whole Cryo-EM pipeline. Thus, we start from an initial map and some rough estimations of the 3D poses and then refine both gradually. In our framework, unlike the current state of the art reconstruction techniques, we resolve the 3D pose variables on the continuum. Meaning that rather than descretizing the space of 3D poses, we represent these variables in their continuous form. This enables us to perform gradient steps on the angular variables in order to minimize the cost function. Thus, rather than comparing each particle image with a set of template projections of the density map taken from discretized points on the sphere, which is the essence of projection matching methods, we perform gradient steps in order to update these variables. Our preliminary results indicate that starting from a coarse estimation of the map and the angles, refinement of both is achievable.

Looking beyond Pixels: Theory, Algorithms and Applications of Continuous Sparse Recovery07 Aug 2018

Hanjie Pan
Audiovisual Communications Laboratory (LCAV, EPFL

A L1 representer theorem of vector-valued learning17 Jul 2018

Shayan Aziznejad
EPFL STI LIB

Local Rotation Invariance and Directional Sensitivity of 3D Texture Operators: Comparing Classical Radiomics, CNNs and Spherical Harmonics26 Jun 2018

Adrien Depeursinge
EPFL STI LIB

Computational Super-Sectioning for Single-Slice Structured-Illumination Microscopy 19 Jun 2018

Emmanuel Soubies
EPFL STI LIB

Theoretical and Numerical Analysis of Super-Resolution without Grid19 Jun 2018

Quentin Denoyelle
Université Paris Dauphine

Subdivision-Based Active Contours --- Statistical optimality of Hermite splines for the reconstruction of self-similar signals --- The Role of Discretisation in X-Ray CT Reconstruction29 May 2018

Anaïs Badoual, Virginie Uhlmann, Michael McCann
EPFL STI LIB

Influence of spatial context over color perception: unifying chromatic assimilation and simultaneous contrast into a neural field model22 May 2018

Anna Song
EPFL STI LIB

Fast rotational dictionary learning using steerability 08 May 2018

Mike McCann
EPFL STI LIB

Hybrid spline dictionaries for continuous-domain inverse problems24 Apr 2018

Thomas Debarre
EPFL STI LIB

Fast Multiresolution Reconstruction for Cryo-EM17 Apr 2018

Laurène Donati
EPFL STI LIB

Direct Reconstruction of Clipped Peaks in Bandlimited OFDM Signals13 Mar 2018

Kyong Hwan Jin
EPFL STI LIB

Sparsity-based techniques for diffraction tomography27 Feb 2018

Thanh-an Pham
EPFL STI LIB

Structured Illumination and the Analysis of Single Molecules in Cells09 Feb 2018

Rainer Heintzmann
Institute of Photonic Technology,Jena, Germany

Periodic Splines and Gaussian Processes for the Resolution of Linear Inverse Problems30 Jan 2018

Anaïs Badoual
EPFL STI LIB

Fast Piecewise-Affine Motion Estimation Without Segmentation19 Dec 2017

Denis Fortun
EPFL STI LIB

Continuous Representations in Bioimage Analysis: a Bridge from Pixels to the Real World12 Dec 2017

Virginie Uhlmann
EPFL STI LIB

Steer&Detect on Images 14 Nov 2017

Julien Fageot
EPFL STI LIB

Fundamental computational barriers in inverse problems and the mathematics of information27 Oct 2017

Alexander Bastounis
Cambridge University

Variational use of B-splines and Kernel Based Functions27 Oct 2017

Christophe Rabut
INSA Toulouse

Deep learning based data manifold projection - a new regularization for inverse problems17 Oct 2017

Harshit Gupta
EPFL STI LIB

GlobalBioIm Lib - v2: new tools, more flexibility, and improved composition rules.03 Oct 2017

Emmanuel Soubies
EPFL STI LIB

Exact Discretization of Continuous-Domain Linear Inverse Problems with Generalized TV Regularization Using B-Splines​24 Aug 2017

Thomas Debarre
EPFL STI LIB

Fractional Integral transforms and Time-Frequency Representations02 Jun 2017

Prof. Ahmed I. Zayed
Department of Mathematical Sciences DePaul University

First steps toward fast PET reconstruction30 May 2017

Mike McCann
EPFL STI LIB

Lipid membranes and surface reconstruction - a biologically inspired method for 3D segmentation16 May 2017

Nicolas Chiaruttini
University of Geneva

Optical Diffraction Tomography: Principles and Algorithms09 May 2017

Thanh-an Pham
EPFL STI LIB

Compressed Sensing for Dose Reduction in STEM Tomography11 Apr 2017

Laurène Donati
EPFL STI LIB

Chasing Mycobacteria10 Apr 2017

Virginie Uhlmann
EPFL STI LIB

Multifractal analysis for signal and image classification23 Mar 2017

Stéphane Jaffard
UPEC

3D SIM and measurements time-reallocation for scanning based systems: Introduction and preliminary results on these two problems14 Mar 2017

Emmanuel Soubies
EPFL STI LIB

Inverse problems and multimodality for biological imaging28 Feb 2017

Denis Fortun
EPFL STI LIB