GlobalBioIm SIGNED
Global integrative framework for Computational Bio-Imaging
Total Cost €
0EC-Contrib. €
0Partnership
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Explore the words cloud of the GlobalBioIm project. It provides you a very rough idea of what is the project "GlobalBioIm" about.
Project "GlobalBioIm" data sheet
The following table provides information about the project.
| Coordinator |
ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE
Organization address contact info |
| 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.
| # | ||||
|---|---|---|---|---|
| 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 |
|---|---|---|---|
| 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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