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GlobalBioIm SIGNED

Global integrative framework for Computational Bio-Imaging

Total Cost €

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EC-Contrib. €

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Partnership

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 GlobalBioIm project word cloud

Explore the words cloud of the GlobalBioIm project. It provides you a very rough idea of what is the project "GlobalBioIm" about.

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Project "GlobalBioIm" data sheet

The following table provides information about the project.

Coordinator
ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE 

Organization address
address: BATIMENT CE 3316 STATION 1
city: LAUSANNE
postcode: 1015
website: www.epfl.ch

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Switzerland [CH]
 Project website http://bigwww.epfl.ch/globalbioim/
 Total cost 2˙499˙515 €
 EC max contribution 2˙499˙515 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2015-AdG
 Funding Scheme ERC-ADG
 Starting year 2016
 Duration (year-month-day) from 2016-10-01   to  2021-09-30

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE CH (LAUSANNE) coordinator 2˙499˙515.00

Map

 Project objective

A powerful strategy for increasing the quality and resolution of medical and biological images is to acquire larger quantities of data (Fourier samples for MRI, projections for X-ray imaging) and to jointly reconstruct the complete signal by correctly reallocating the measurements in 3D space/time and integrating all the information available. The underlying image sequence is reconstructed globally as the result of a very large-scale optimization that exploits the redundancy of the signal (spatio-temporal correlation, sparsity) to improve the solution. Due to recent advances in the field, we are arguing that such a “bigger data” integration is now within reach and that our team is ideally qualified to lead the way. A successful outcome will profoundly impact the design of future bioimaging systems. We are proposing a unifying framework for the development of such next-generation reconstruction algorithms with a clear separation between the physical (forward model) and signal-related (regularization, incorporation of prior constraints) aspects of the problem. The pillars of our formulation are: an operator algebra with a corresponding set of fast linear solvers; an advanced statistical framework for the principled derivation of reconstruction methods; and learning schemes for parameter optimization and self-tuning. These core technologies will be incorporated into a modular software library featuring the key components for the implementation and testing of iterative reconstruction algorithms. We shall apply our framework to improve upon the state of the art in the following modalities: 1) phase-contrast X-ray tomography in full 3D; 2) structured illumination microscopy; 3) single-particle analysis in cryo-electron tomography; 4) a novel multipose fluorescence microscopy; 5) real-time MRI, and 6) a new multimodal digital microscope. In all instances, we shall work in close collaboration with the imaging scientists who are in charge of the instrumentation.

 Publications

year authors and title journal last update
List of publications.
2019 Thomas Debarre, Julien Fageot, Harshit Gupta, Michael Unser
B-Spline-Based Exact Discretization of Continuous-Domain Inverse Problems With Generalized TV Regularization
published pages: 4457-4470, ISSN: 0018-9448, DOI: 10.1109/tit.2019.2902926
IEEE Transactions on Information Theory 65/7 2019-12-16
2019 Thomas Debarre, Shayan Aziznejad, Michael Unser
Hybrid-Spline Dictionaries for Continuous-Domain Inverse Problems
published pages: 5824-5836, ISSN: 1053-587X, DOI: 10.1109/tsp.2019.2944754
IEEE Transactions on Signal Processing 67/22 2019-12-16
2019 Davide Gambarotto, Fabian U. Zwettler, Maeva Le Guennec, Marketa Schmidt-Cernohorska, Denis Fortun, Susanne Borgers, Jörn Heine, Jan-Gero Schloetel, Matthias Reuss, Michael Unser, Edward S. Boyden, Markus Sauer, Virginie Hamel, Paul Guichard
Imaging cellular ultrastructures using expansion microscopy (U-ExM)
published pages: 71-74, ISSN: 1548-7091, DOI: 10.1038/s41592-018-0238-1
Nature Methods 16/1 2019-08-05
2019 Emmanuel Soubies, Agata Radwanska, Dominique Grall, Laure Blanc-Féraud, Ellen Van Obberghen-Schilling, Sébastien Schaub
Nanometric axial resolution of fibronectin assembly units achieved with an efficient reconstruction approach for multi-angle-TIRF microscopy
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-018-36119-3
Scientific Reports 9/1 2019-08-05
2019 Soubies , Emmanuel; Blanc-Féraud , Laure; Schaub , Sébastien; Van Obberghen-Schilling , Ellen
Improving 3D MA-TIRF Reconstruction with Deconvolution and Background Estimation
published pages: , ISSN: , DOI:
https://hal.inria.fr/hal-02017862 11 2019-08-05
2019 Donati , Lauréne; Soubies , Emmanuel; Unser , Michael
Inner-Loop Free ADMM for Cryo-EM
published pages: 307-311, ISSN: , DOI:
ISBI 2019 - IEEE International Symposium on Biomedical Imaging 3 2019-08-05
2019 Daniel Sage, Thanh-An Pham, Hazen Babcock, Tomas Lukes, Thomas Pengo, Jerry Chao, Ramraj Velmurugan, Alex Herbert, Anurag Agrawal, Silvia Colabrese, Ann Wheeler, Anna Archetti, Bernd Rieger, Raimund Ober, Guy M. Hagen, Jean-Baptiste Sibarita, Jonas Ries, Ricardo Henriques, Michael Unser, Seamus Holden
Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software
published pages: 387-395, ISSN: 1548-7091, DOI: 10.1038/s41592-019-0364-4
Nature Methods 16/5 2019-08-05
2018 Anais Badoual, Julien Fageot, Michael Unser
Periodic Splines and Gaussian Processes for the Resolution of Linear Inverse Problems
published pages: 6047-6061, ISSN: 1053-587X, DOI: 10.1109/TSP.2018.2873514
IEEE Transactions on Signal Processing 66/22 2019-08-05
2018 Laurène Donati, Masih Nilchian, Carlos Oscar S. Sorzano, Michael Unser
Fast multiscale reconstruction for Cryo-EM
published pages: 543-554, ISSN: 1047-8477, DOI: 10.1016/j.jsb.2018.09.008
Journal of Structural Biology 204/3 2019-08-05
2018 Harshit Gupta, Kyong Hwan Jin, Ha Q. Nguyen, Michael T. McCann, Michael Unser
CNN-Based Projected Gradient Descent for Consistent CT Image Reconstruction
published pages: 1440-1453, ISSN: 0278-0062, DOI: 10.1109/TMI.2018.2832656
IEEE Transactions on Medical Imaging 37/6 2019-08-05
2018 Harshit Gupta, Julien Fageot, Michael Unser
Continuous-Domain Solutions of Linear Inverse Problems With Tikhonov Versus Generalized TV Regularization
published pages: 4670-4684, ISSN: 1053-587X, DOI: 10.1109/TSP.2018.2860549
IEEE Transactions on Signal Processing 66/17 2019-08-05
2019 Emmanuel Soubies, Michael Unser
Computational Super-Sectioning for Single-Slice Structured-Illumination Microscopy
published pages: 240-250, ISSN: 2333-9403, DOI: 10.1109/tci.2018.2887136
IEEE Transactions on Computational Imaging 5/2 2019-08-05
2018 Denis Fortun, Martin Storath, Dennis Rickert, Andreas Weinmann, Michael Unser
Fast Piecewise-Affine Motion Estimation Without Segmentation
published pages: 5612-5624, ISSN: 1057-7149, DOI: 10.1109/tip.2018.2856399
IEEE Transactions on Image Processing 27/11 2019-09-04
2019 Pham , Thanh-An; Soubies , Emmanuel; Sage , Daniel; Unser , Michael
Closed-Form Expression of the Fourier Ring-Correlation for Single-Molecule Localization Microscopy
published pages: 321-324, ISSN: , DOI:
https://hal.archives-ouvertes.fr/hal-02048083 3 2019-08-05
2018 Manon Rostykus, Ferréol Soulez, Michael Unser, Christophe Moser
Compact in-line lensfree digital holographic microscope
published pages: 17-23, ISSN: 1046-2023, DOI: 10.1016/j.ymeth.2017.11.008
Methods 136 2019-08-05
2019 Soubies, Emmanuel; Soulez, Ferréol; McCann, Michael T.; Pham, Thanh-an; Donati, Laurène; Debarre, Thomas; Sage, Daniel; Unser, Michael
Pocket Guide to Solve Inverse Problems with GlobalBioIm
published pages: , ISSN: 0266-5611, DOI:
Inverse Problems 2 2019-09-04
2017 Martin Storath, Dennis Rickert, Michael Unser, Andreas Weinmann
Fast Segmentation From Blurred Data in 3D Fluorescence Microscopy
published pages: 4856-4870, ISSN: 1057-7149, DOI: 10.1109/TIP.2017.2716843
IEEE Transactions on Image Processing 26/10 2019-06-14
2017 P. Pad, F. Salehi, E. Celis, P. Thiran, M. Unser
Dictionary Learning Based on Sparse Distribution Tomography
published pages: paper no. PMLR 7, ISSN: , DOI:
Proceedings of the Thirty-Fourth International Conference on Machine Learning (ICML\'17) 2019-06-14
2017 Kyong Hwan Jin, Michael T. McCann, Emmanuel Froustey, Michael Unser
Deep Convolutional Neural Network for Inverse Problems in Imaging
published pages: 4509-4522, ISSN: 1057-7149, DOI: 10.1109/TIP.2017.2713099
IEEE Transactions on Image Processing 26/9 2019-06-14
2018 Thanh-An Pham, Emmanuel Soubies, Alexandre Goy, Joowon Lim, Ferréol Soulez, Demetri Psaltis, Michael Unser
Versatile reconstruction framework for diffraction tomography with intensity measurements and multiple scattering
published pages: 2749, ISSN: 1094-4087, DOI: 10.1364/OE.26.002749
Optics Express 26/3 2019-06-14
2017 Laurène Donati, Masih Nilchian, Sylvain Trépout, Cédric Messaoudi, Sergio Marco, Michael Unser
Compressed sensing for STEM tomography
published pages: 47-56, ISSN: 0304-3991, DOI: 10.1016/j.ultramic.2017.04.003
Ultramicroscopy 179 2019-06-14
2017 Michael T. McCann, Michael Unser
High-Quality Parallel-Ray X-Ray CT Back Projection Using Optimized Interpolation
published pages: 4639-4647, ISSN: 1057-7149, DOI: 10.1109/TIP.2017.2706521
IEEE Transactions on Image Processing 26/10 2019-06-14
2018 Ha Q. Nguyen, Emrah Bostan, Michael Unser
Learning Convex Regularizers for Optimal Bayesian Denoising
published pages: 1093-1105, ISSN: 1053-587X, DOI: 10.1109/TSP.2017.2777407
IEEE Transactions on Signal Processing 66/4 2019-06-14
2017 Emmanuel Soubies, Thanh-An Pham, Michael Unser
Efficient inversion of multiple-scattering model for optical diffraction tomography
published pages: 21786, ISSN: 1094-4087, DOI: 10.1364/OE.25.021786
Optics Express 25/18 2019-06-14
2017 Michael Unser, Julien Fageot, John Paul Ward
Splines Are Universal Solutions of Linear Inverse Problems with Generalized TV Regularization
published pages: 769-793, ISSN: 0036-1445, DOI: 10.1137/16M1061199
SIAM Review 59/4 2019-06-14
2017 Manon Rostykus, Ferréol Soulez, Michael Unser, Christophe Moser
Compact lensless phase imager
published pages: 4438, ISSN: 1094-4087, DOI: 10.1364/OE.25.004438
Optics Express 25/4 2019-06-14
2017 Daniel Sage, Lauréne Donati, Ferréol Soulez, Denis Fortun, Guillaume Schmit, Arne Seitz, Romain Guiet, Cédric Vonesch, Michael Unser
DeconvolutionLab2: An open-source software for deconvolution microscopy
published pages: 28-41, ISSN: 1046-2023, DOI: 10.1016/j.ymeth.2016.12.015
Methods 115 2019-06-14

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