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Global integrative framework for Computational Bio-Imaging

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Publications

Multi-CryoGAN: Reconstruction of Continuous Conformations in Cryo-EM Using Generative Adversarial Networks

Author(s): Harshit Gupta, Thong H. Phan, Jaejun Yoo, Michael Unser
Published in: Computer Vision – ECCV 2020 Workshops - Glasgow, UK, August 23–28, 2020, Proceedings, Part I, Issue 12535, 2020, Page(s) 429-444
DOI: 10.1007/978-3-030-66415-2_28

Adaptive Regularization for Three-Dimensional Optical Diffraction Tomography

Author(s): Thanh-an Pham, Emmanuel Soubies, Ahmed Ayoub, Demetri Psaltis, Michael Unser
Published in: 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI), 2020, Page(s) 182-186
DOI: 10.1109/isbi45749.2020.9098523

Diffraction Tomography from Single-Molecule Localization Microscopy: Numerical Feasibility

Author(s): Thanh-an Pham, Emmanuel Soubies, Ferréol Soulez, M. Unser
Published in: Proceedings of the Eighteenth IEEE International Symposium on Biomedical Imaging (ISBI'21), 2021, Page(s) pp. 854-857

User-Friendly Building of Reconstruction Algorithms with GlobalBioIm

Author(s): Laurène Donati, Emmanuel Soubies, Michael Unser
Published in: Proceedings of the 2020 Quantitative BioImaging Conference (QBI'20), Issue January 6-9, 2020, 2020, Page(s) paper no. 345

Optimal-Transport-Based Metric for SMLM

Author(s): Quentin Denoyelle, Thanh-an Pham, Pol del Aguila Pla, Daniel Sage, Michael Unser
Published in: Proceedings of the Eighteenth IEEE International Symposium on Biomedical Imaging (ISBI'21), 2021, Page(s) pp. 797-801

User-Friendly Building of Reconstruction Algorithms for Solving Inverse Problems

Author(s): Laurène Donati, Emmanuel Soubies, Thanh-An Pham, Michael Unser
Published in: Proceedings of the Seventeenth IEEE International Symposium on Biomedical Imaging (ISBI'20), Issue April 5-7, 2020, 2020, Page(s) pp. 1307

General surface energy for spinal cord and aorta segmentation

Author(s): Harshit Gupta, Daniel Schmitter, Virginie Uhlmann, Michael Unser
Published in: 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017), 2017, Page(s) 319-322
DOI: 10.1109/ISBI.2017.7950528

GlobalBioIm: A Unifying Computational Framework for Solving Inverse Problems

Author(s): Michael Unser, Emmanuel Soubies, Ferrèol Soulez, Michael McCann, Laurène Donati
Published in: Imaging and Applied Optics 2017 (3D, AIO, COSI, IS, MATH, pcAOP), 2017, Page(s) CTu1B.1
DOI: 10.1364/COSI.2017.CTu1B.1

Dictionary Learning Based on Sparse Distribution Tomography

Author(s): P. Pad, F. Salehi, E. Celis, P. Thiran, M. Unser
Published in: Proceedings of the Thirty-Fourth International Conference on Machine Learning (ICML'17), 2017, Page(s) paper no. PMLR 70:2731-2740

Compressed sensing for dose reduction in STEM tomography

Author(s): L. Donati, M. Nilchian, M. Unser, S. Trepout, C. Messaoudi, S. Marcoy
Published in: 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017), 2017, Page(s) 23-27
DOI: 10.1109/ISBI.2017.7950459

Inner-Loop-Free Admm For Cryo-Em

Author(s): Laurene Donati, Emmanuel Soubies, Michael Unser
Published in: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), 2019, Page(s) 307-311
DOI: 10.1109/isbi.2019.8759194

Improving 3D MA-TIRF Reconstruction with Deconvolution and Background Estimation

Author(s): Emmanuel Soubies, Laure Blanc-Feraud, Sebastien Schaub, Ellen Van Obberghen-Schilling
Published in: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), 2019, Page(s) 316-320
DOI: 10.1109/isbi.2019.8759103

Closed-Form Expression Of The Fourier Ring-Correlation For Single-Molecule Localization Microscopy

Author(s): Thanh-an Pham, Emmanuel Soubies, Daniel Sage, Michael Unser
Published in: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), 2019, Page(s) 321-324
DOI: 10.1109/isbi.2019.8759279

Solving Continuous-domain Problems Exactly with Multiresolution B-splines

Author(s): Thomas Debarre, Julien Fageot, Harshit Gupta, Michael Unser
Published in: ICASSP 2019 - 2019 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 2019, Page(s) 5122-5126
DOI: 10.1109/icassp.2019.8683214

Phaseless diffraction tomography with regularized beam propagation

Author(s): Thanh-an Pham, Emmanuel Soubies, Joowon Lim, Alexandre Goy, Ferreol Soulez, Demetri Psaltis, Michael Unser
Published in: 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018), 2018, Page(s) 1268-1271
DOI: 10.1109/isbi.2018.8363802

The Sliding Frank-Wolfe Algorithm for the BLASSO

Author(s): Quentin Denoyelle, V. Duval, Gabriel Peyré, Emmanuel Soubies
Published in: Proceedings of the Workshop on Signal Processing with Adaptive Sparse Structured Representations (SPARS'19), Issue July 1-4, 2019, 2019, Page(s) paper no. 172

Three-Dimensional Optical Diffraction Tomography With Lippmann-Schwinger Model

Author(s): Thanh-an Pham, Emmanuel Soubies, Ahmed Ayoub, Joowon Lim, Demetri Psaltis, Michael Unser
Published in: IEEE Transactions on Computational Imaging, Issue 6, 2020, Page(s) 727-738, ISSN 2333-9403
DOI: 10.1109/tci.2020.2969070

Gaussian and Sparse Processes Are Limits of Generalized Poisson Processes

Author(s): Julien Fageot, Virginie Uhlmann, Michael Unser
Published in: Applied and Computational Harmonic Analysis, Issue vol. 48, no. 3, 2020, Page(s) pp. 1045-1065, ISSN 1063-5203
DOI: 10.1016/j.acha.2018.10.004

Deep Neural Networks With Trainable Activations and Controlled Lipschitz Constant

Author(s): Shayan Aziznejad, Harshit Gupta, Joaquim Campos, Michael Unser
Published in: IEEE Transactions on Signal Processing, Issue 68, 2020, Page(s) 4688-4699, ISSN 1053-587X
DOI: 10.1109/tsp.2020.3014611

Learning Activation Functions in Deep (Spline) Neural Networks

Author(s): Pakshal Bohra, Joaquim Campos, Harshit Gupta, Shayan Aziznejad, Michael Unser
Published in: IEEE Open Journal of Signal Processing, Issue 1, 2020, Page(s) 295-309, ISSN 2644-1322
DOI: 10.1109/ojsp.2020.3039379

Wavelet Analysis of the Besov Regularity of Lévy White Noise

Author(s): Shayan Aziznejad, Julien Fageot
Published in: Electronic Journal of Probability, 2020, Page(s) pp. 1-38, ISSN 1083-6489
DOI: 10.1214/20-ejp554

The sliding Frank–Wolfe algorithm and its application to super-resolution microscopy

Author(s): Quentin Denoyelle, Vincent Duval, Gabriel Peyré, Emmanuel Soubies
Published in: Inverse Problems, Issue 36/1, 2020, Page(s) 014001, ISSN 0266-5611
DOI: 10.1088/1361-6420/ab2a29

Joint Angular Refinement and Reconstruction for Single-Particle Cryo-EM

Author(s): Mona Zehni, Laurène Donati, Emmanuel Soubies, Z. Zhao, Michael Unser
Published in: IEEE Transactions on Image Processing, Issue vol. 29, 2020, 2020, Page(s) pp. 6151-6163, ISSN 1057-7149
DOI: 10.1109/tip.2020.2984313

Deep-Learning Projector for Optical Diffraction Tomography

Author(s): Fangshu Yang, Thanh-an Pham, Harshit Gupta, Michael Unser, J. Ma
Published in: Optics Express, Issue vol. 28, no. 3, 2020, Page(s) pp. 3905-3921, ISSN 1094-4087
DOI: 10.1364/oe.381413

Deep Convolutional Neural Network for Inverse Problems in Imaging

Author(s): Kyong Hwan Jin, Michael T. McCann, Emmanuel Froustey, Michael Unser
Published in: IEEE Transactions on Image Processing, Issue 26/9, 2017, Page(s) 4509-4522, ISSN 1057-7149
DOI: 10.1109/TIP.2017.2713099

High-Quality Parallel-Ray X-Ray CT Back Projection Using Optimized Interpolation

Author(s): Michael T. McCann, Michael Unser
Published in: IEEE Transactions on Image Processing, Issue 26/10, 2017, Page(s) 4639-4647, ISSN 1057-7149
DOI: 10.1109/TIP.2017.2706521

Learning Convex Regularizers for Optimal Bayesian Denoising

Author(s): Ha Q. Nguyen, Emrah Bostan, Michael Unser
Published in: IEEE Transactions on Signal Processing, Issue 66/4, 2018, Page(s) 1093-1105, ISSN 1053-587X
DOI: 10.1109/TSP.2017.2777407

Efficient inversion of multiple-scattering model for optical diffraction tomography

Author(s): Emmanuel Soubies, Thanh-An Pham, Michael Unser
Published in: Optics Express, Issue 25/18, 2017, Page(s) 21786, ISSN 1094-4087
DOI: 10.1364/OE.25.021786

Compact lensless phase imager

Author(s): Manon Rostykus, Ferréol Soulez, Michael Unser, Christophe Moser
Published in: Optics Express, Issue 25/4, 2017, Page(s) 4438, ISSN 1094-4087
DOI: 10.1364/OE.25.004438

DeconvolutionLab2: An open-source software for deconvolution microscopy

Author(s): Daniel Sage, Lauréne Donati, Ferréol Soulez, Denis Fortun, Guillaume Schmit, Arne Seitz, Romain Guiet, Cédric Vonesch, Michael Unser
Published in: Methods, Issue 115, 2017, Page(s) 28-41, ISSN 1046-2023
DOI: 10.1016/j.ymeth.2016.12.015

Splines Are Universal Solutions of Linear Inverse Problems with Generalized TV Regularization

Author(s): Michael Unser, Julien Fageot, John Paul Ward
Published in: SIAM Review, Issue 59/4, 2017, Page(s) 769-793, ISSN 0036-1445
DOI: 10.1137/16M1061199

Versatile reconstruction framework for diffraction tomography with intensity measurements and multiple scattering

Author(s): Thanh-An Pham, Emmanuel Soubies, Alexandre Goy, Joowon Lim, Ferréol Soulez, Demetri Psaltis, Michael Unser
Published in: Optics Express, Issue 26/3, 2018, Page(s) 2749, ISSN 1094-4087
DOI: 10.1364/OE.26.002749

Compressed sensing for STEM tomography

Author(s): Laurène Donati, Masih Nilchian, Sylvain Trépout, Cédric Messaoudi, Sergio Marco, Michael Unser
Published in: Ultramicroscopy, Issue 179, 2017, Page(s) 47-56, ISSN 0304-3991
DOI: 10.1016/j.ultramic.2017.04.003

Fast Segmentation From Blurred Data in 3D Fluorescence Microscopy

Author(s): Martin Storath, Dennis Rickert, Michael Unser, Andreas Weinmann
Published in: IEEE Transactions on Image Processing, Issue 26/10, 2017, Page(s) 4856-4870, ISSN 1057-7149
DOI: 10.1109/TIP.2017.2716843

CNN-Based Projected Gradient Descent for Consistent CT Image Reconstruction

Author(s): Harshit Gupta, Kyong Hwan Jin, Ha Q. Nguyen, Michael T. McCann, Michael Unser
Published in: IEEE Transactions on Medical Imaging, Issue 37/6, 2018, Page(s) 1440-1453, ISSN 0278-0062
DOI: 10.1109/TMI.2018.2832656

Periodic Splines and Gaussian Processes for the Resolution of Linear Inverse Problems

Author(s): Anais Badoual, Julien Fageot, Michael Unser
Published in: IEEE Transactions on Signal Processing, Issue 66/22, 2018, Page(s) 6047-6061, ISSN 1053-587X
DOI: 10.1109/TSP.2018.2873514

Continuous-Domain Solutions of Linear Inverse Problems With Tikhonov Versus Generalized TV Regularization

Author(s): Harshit Gupta, Julien Fageot, Michael Unser
Published in: IEEE Transactions on Signal Processing, Issue 66/17, 2018, Page(s) 4670-4684, ISSN 1053-587X
DOI: 10.1109/TSP.2018.2860549

Computational Super-Sectioning for Single-Slice Structured-Illumination Microscopy

Author(s): Emmanuel Soubies, Michael Unser
Published in: IEEE Transactions on Computational Imaging, Issue 5/2, 2019, Page(s) 240-250, ISSN 2333-9403
DOI: 10.1109/tci.2018.2887136

Nanometric axial resolution of fibronectin assembly units achieved with an efficient reconstruction approach for multi-angle-TIRF microscopy

Author(s): Emmanuel Soubies, Agata Radwanska, Dominique Grall, Laure Blanc-Féraud, Ellen Van Obberghen-Schilling, Sébastien Schaub
Published in: Scientific Reports, Issue 9/1, 2019, ISSN 2045-2322
DOI: 10.1038/s41598-018-36119-3

Compact in-line lensfree digital holographic microscope

Author(s): Manon Rostykus, Ferréol Soulez, Michael Unser, Christophe Moser
Published in: Methods, Issue 136, 2018, Page(s) 17-23, ISSN 1046-2023
DOI: 10.1016/j.ymeth.2017.11.008

Fast multiscale reconstruction for Cryo-EM

Author(s): Laurène Donati, Masih Nilchian, Carlos Oscar S. Sorzano, Michael Unser
Published in: Journal of Structural Biology, Issue 204/3, 2018, Page(s) 543-554, ISSN 1047-8477
DOI: 10.1016/j.jsb.2018.09.008

Imaging cellular ultrastructures using expansion microscopy (U-ExM)

Author(s): 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
Published in: Nature Methods, Issue 16/1, 2019, Page(s) 71-74, ISSN 1548-7091
DOI: 10.1038/s41592-018-0238-1

Fast Piecewise-Affine Motion Estimation Without Segmentation

Author(s): Denis Fortun, Martin Storath, Dennis Rickert, Andreas Weinmann, Michael Unser
Published in: IEEE Transactions on Image Processing, Issue 27/11, 2018, Page(s) 5612-5624, ISSN 1057-7149
DOI: 10.1109/tip.2018.2856399

Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software

Author(s): 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
Published in: Nature Methods, Issue 16/5, 2019, Page(s) 387-395, ISSN 1548-7091
DOI: 10.1038/s41592-019-0364-4

Pocket guide to solve inverse problems with GlobalBioIm

Author(s): Emmanuel Soubies, Ferréol Soulez, Michael T McCann, Thanh-an Pham, Laurène Donati, Thomas Debarre, Daniel Sage, Michael Unser
Published in: Inverse Problems, Issue 35/10, 2019, Page(s) 104006, ISSN 0266-5611
DOI: 10.1088/1361-6420/ab2ae9

Hybrid-Spline Dictionaries for Continuous-Domain Inverse Problems

Author(s): Thomas Debarre, Shayan Aziznejad, Michael Unser
Published in: IEEE Transactions on Signal Processing, Issue 67/22, 2019, Page(s) 5824-5836, ISSN 1053-587X
DOI: 10.1109/tsp.2019.2944754

B-Spline-Based Exact Discretization of Continuous-Domain Inverse Problems With Generalized TV Regularization

Author(s): Thomas Debarre, Julien Fageot, Harshit Gupta, Michael Unser
Published in: IEEE Transactions on Information Theory, Issue 65/7, 2019, Page(s) 4457-4470, ISSN 0018-9448
DOI: 10.1109/tit.2019.2902926

Support and Approximation Properties of Hermite Splines

Author(s): Julien Fageot, Shayan Aziznejad, Michael Unser, Virginie Uhlmann
Published in: Journal of Computational and Applied Mathematics, Issue vol. 368, paper no. 112503, 2020, Page(s) pp. 1-15, ISSN 0377-0427
DOI: 10.1016/j.cam.2019.112503

Biomedical Image Reconstruction: From the Foundations to Deep Neural Networks

Author(s): Michael T. McCann, Michael Unser
Published in: Foundations and Trends® in Signal Processing, Issue December 3, 2019, 2019, Page(s) pp. 280-359, ISSN 1932-8346
DOI: 10.1561/2000000101

The $$n$$n-term Approximation of Periodic Generalized Lévy Processes

Author(s): Julien Fageot, Michael Unser, John Paul Ward
Published in: Journal of Theoretical Probability, Issue 33/1, 2020, Page(s) 180-200, ISSN 0894-9840
DOI: 10.1007/s10959-018-00877-7

Scaling Limits of Solutions of Linear Stochastic Differential Equations Driven by Lévy White Noises

Author(s): Julien Fageot, Michael Unser
Published in: Journal of Theoretical Probability, Issue 32/3, 2019, Page(s) 1166-1189, ISSN 0894-9840
DOI: 10.1007/s10959-018-0809-1

Sparsest Continuous Piecewise-Linear Representation of Data

Author(s): Thomas Debarre, Quentin Denoyelle, Michael Unser, Julien Fageot
Published in: arXiv, 2020

Time-Dependent Deep Image Prior for Dynamic MRI

Author(s): Jaejun Yoo, Kyong Hwan Jin, Harshit Gupta, Jerome Yerly, Matthias Stuber, Michael Unser
Published in: arXiv, 2019

Shortest Multi-Spline Bases for Generalized Sampling

Author(s): Alexis Goujon, Shayan Aziznejad
Published in: arXiv, 2020