Emmanuel Soubies

Thanh-An Pham, Emmanuel Soubies, Ferréol Soulez, Michael Unser. Optical diffraction tomography from single-molecule localization microscopy. Optics Communications, Elsevier, 2021, 499, pp.127290. ⟨10.1016/j.optcom.2021.127290⟩. ⟨hal-03290069⟩

Cassio Dantas, Emmanuel Soubies, Cédric Févotte. Expanding boundaries of Gap Safe screening. Journal of Machine Learning Research, Microtome Publishing, 2021, 22 (236), pp.1-57. ⟨hal-03147502v2⟩

Emmanuel Soubies, Adilson Chinatto, Pascal Larzabal, João Romano, Laure Blanc-Féraud. Direction-of-Arrival Estimation through Exact Continuous l20-Norm Relaxation. IEEE Signal Processing Letters, Institute of Electrical and Electronics Engineers, 2021, 28, pp.16-20. ⟨10.1109/LSP.2020.3042771⟩. ⟨hal-03047201⟩

Thanh-An Pham, Emmanuel Soubies, Ahmed Ayoub, Joowon Lim, Demetri Psaltis, et al.. Three-Dimensional Optical Diffraction Tomography with Lippmann-Schwinger Model. IEEE Transactions on Computational Imaging, IEEE, 2020, 6 (1), pp.727-738. ⟨10.1109/TCI.2020.2969070⟩. ⟨hal-02457399⟩

Mona Zehni, Laurène Donati, Emmanuel Soubies, Zhizhen J. Zhao, Michael Unser. Joint Angular Refinement and Reconstruction for Single-Particle Cryo-EM. IEEE Transactions on Image Processing, Institute of Electrical and Electronics Engineers, 2020, ⟨10.1109/TIP.2020.2984313⟩. ⟨hal-02516898⟩

Sixin Zhang, Emmanuel Soubies, Cédric Févotte. On the Identifiability of Transform Learning for Non-negative Matrix Factorization. IEEE Signal Processing Letters, Institute of Electrical and Electronics Engineers, 2020, 27, pp.1555 - 1559. ⟨10.1109/LSP.2020.3020431⟩. ⟨hal-02542653v3⟩

Emmanuel Soubies, Laure Blanc-Féraud, Gilles Aubert. New Insights on the Optimality Conditions of the l2-l0 Minimization Problem. Journal of Mathematical Imaging and Vision, Springer Verlag, 2020, Special Issue on Memory of Mila Nikolova, 62, pp.808-824. ⟨10.1007/s10851-019-00917-9⟩. ⟨hal-02144528v2⟩

Emmanuel Soubies, Michael Unser. Computational Super-Sectioning for Single-Slice Structured-Illumination Microscopy. IEEE Transactions on Computational Imaging, IEEE, 2019, 5 (2), pp.240-250. ⟨10.1109/TCI.2018.2887136⟩. ⟨hal-02428166⟩

Emmanuel Soubies, Ferréol Soulez, Michael T. Mccann, Thanh-An Pham, Laurène Donati, et al.. Pocket Guide to Solve Inverse Problems with GlobalBioIm. Inverse Problems, IOP Publishing, 2019, 35 (10), pp.104006. ⟨10.1088/1361-6420/ab2ae9⟩. ⟨hal-02162546⟩

Quentin Denoyelle, Vincent Duval, Gabriel Peyré, Emmanuel Soubies. The Sliding Frank-Wolfe Algorithm and its Application to Super-Resolution Microscopy. Inverse Problems, IOP Publishing, In press, ⟨10.1088/1361-6420/ab2a29⟩. ⟨hal-01921604⟩

Emmanuel Soubies, Agata Radwanska, Dominique Grall, Laure Blanc-Féraud, Ellen van Obberghen-Schilling, et al.. Nanometric axial resolution of fibronectin assembly units achieved with an efficient reconstruction approach for multi-angle-TIRF microscopy. Scientific Reports, Nature Publishing Group, 2019, 9 (1), ⟨10.1038/s41598-018-36119-3⟩. ⟨hal-02017844⟩

Thanh-An Pham, Emmanuel Soubies, Alexandre Goy, Joowon Lim, Ferréol Soulez, et al.. Versatile reconstruction framework for diffraction tomography with intensity measurements and multiple scattering. Optics Express, Optical Society of America - OSA Publishing, 2018, 26 (3), pp.2749-2763. ⟨insu-01690828⟩

Emmanuel Soubies, Thanh-An Pham, Michael Unser. Efficient inversion of multiple-scattering model for optical diffraction tomography. Optics Express, Optical Society of America - OSA Publishing, 2017, 25 (18), pp.21786. ⟨10.1364/OE.25.021786⟩. ⟨hal-02428165⟩

Emmanuel Soubies, Laure Blanc-Féraud, Gilles Aubert. A Unified View of Exact Continuous Penalties for l2-l0 Minimization. SIAM Journal on Optimization, Society for Industrial and Applied Mathematics, 2017, 27 (3), ⟨10.1137/16M1059333⟩. ⟨hal-01267701v2⟩

Emmanuel Soubies, Laure Blanc-Féraud, Gilles Aubert. ERRATUM: A Continuous Exact l0 penalty (CEL0) for least squares regularized problem. SIAM Journal on Imaging Sciences, Society for Industrial and Applied Mathematics, 2016, 9 (1), pp.490-494. ⟨10.1137/15M1038384⟩. ⟨hal-01267679⟩

Emmanuel Soubies, Laure Blanc-Féraud, Gilles Aubert. A Continuous Exact l0 penalty (CEL0) for least squares regularized problem. SIAM Journal on Imaging Sciences, Society for Industrial and Applied Mathematics, 2015, 8 (3), pp. 1607-1639 (33 p.). ⟨10.1137/151003714⟩. ⟨hal-01102492v2⟩

Cassio Dantas, Emmanuel Soubies, Cédric Févotte. Safe screening for sparse regression with the Kullback-Leibler divergence. IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Jun 2021, Toronto (virtual), Canada. ⟨hal-03147345v2⟩

Thanh-An Pham, Emmanuel Soubies, Ferréol Soulez, Michael Unser. DIFFRACTION TOMOGRAPHY FROM SINGLE-MOLECULE LOCALIZATION MICROSCOPY: NUMERICAL FEASIBILITY. IEEE 18th International Symposium on Biomedical Imaging (ISBI), Apr 2021, Nice (Virtual), France. ⟨hal-03184774⟩

Shayan Aziznejad, Emmanuel Soubies, Michael Unser. Dictionary Learning with Statistical Sparsity in the Presence of Noise. 28th European Signal Processing Conference - EUSIPCO 2020, Jan 2021, Amsterdam, Netherlands. pp.2026-2029. ⟨hal-02966135⟩

Thanh-An Pham, Emmanuel Soubies, Ahmed Ayoub, Demetri Psaltis, Michael Unser. Adaptive Regularization for Three-dimensional Optical Diffraction Tomography. , 2020 IEEE 16th International Symposium on Biomedical Imaging (ISBI), Apr 2020, Iowa City, United States. ⟨10.1109/ISBI45749.2020.9098523⟩. ⟨hal-02444659⟩

Laurène Donati, Emmanuel Soubies, Michael Unser. User-friendly Building of Reconstruction Algorithms with GlobalBioIm. Quantitative BioImaging Conference 2020, Jan 2020, Oxford, United Kingdom. ⟨hal-02433452⟩

Quentin Denoyelle, Vincent Duval, Gabriel Peyré, Emmanuel Soubies. The Sliding Frank-Wolfe Algorithm for the BLASSO. Workshop on Signal Processing with Adaptative Sparse Structured Representations - SPARS 2019, Sep 2019, Toulouse, France. ⟨hal-03012568⟩

Thanh-An Pham, Emmanuel Soubies, Daniel Sage, Michael Unser. Closed-Form Expression of the Fourier Ring-Correlation for Single-Molecule Localization Microscopy. ISBI 2019 - IEEE International Symposium on Biomedical Imaging, Apr 2019, Venise, Italy. ⟨hal-02048083⟩

Lauréne Donati, Emmanuel Soubies, Michael Unser. Inner-Loop Free ADMM for Cryo-EM. ISBI 2019 - IEEE International Symposium on Biomedical Imaging, Apr 2019, Venise, Italy. ⟨hal-02048101⟩

Mona Zehni, Lauréne Donati, Emmanuel Soubies, Zhizhen Zhao, Minh Do, et al.. Joint density map and continuous angular refinement in cryo-electron microscopy. IS&T International Symposium on Electronic Imaging, Jan 2019, Burlingame, United States. pp.133-1-133-5, ⟨10.2352/ISSN.2470-1173.2019.13.COIMG-133⟩. ⟨hal-02428184⟩

Emmanuel Soubies, Laure Blanc-Féraud, Gilles Aubert. On the Local Minimizers of the CEL0 Relaxation. SPARS 2019 - Signal Processing with Adaptive Sparse Structured Representations - Workshop, Jul 2019, Toulouse, France. ⟨hal-02263782⟩

Emmanuel Soubies, Laure Blanc-Féraud, Sébastien Schaub, Ellen van Obberghen-Schilling. Improving 3D MA-TIRF Reconstruction with Deconvolution and Background Estimation. IEEE International Symposium on Biomedical Imaging, Apr 2019, Venise, Italy. ⟨10.1109/ISBI.2019.8759103⟩. ⟨hal-02017862⟩

Thanh-An Pham, Emmanuel Soubies, Joowon Lim, Alexandre Goy, Ferréol Soulez, et al.. PHASELESS DIFFRACTION TOMOGRAPHY WITH REGULARIZED BEAM PROPAGATION. IEEE International Symposium on Biomedical Imaging (ISBI), 2018, Washington, United States. ⟨hal-01978525⟩

Michael Unser, Emmanuel Soubies, Ferréol Soulez, Michael Mccann, Laurène Donati. GlobalBioIm: A Unifying Computational Framework for Solving Inverse Problems. OSA Imaging and Applied Optics Congress on Computational Optical Sensing and Imaging (COSI'17), 2017, San Francisco, United States. ⟨insu-01632807⟩

Simon Gazagnes, Emmanuel Soubies, Laure Blanc-Féraud. High density molecule localization for super-resolution microscopy using CEL0 based sparse approximation. ISBI 2017 - IEEE International Symposium on Biomedical Imaging, Apr 2017, Melbourne, Australia. pp.4, ⟨10.1109/ISBI.2017.7950460⟩. ⟨hal-01443565⟩

Emmanuel Soubies, Laure Blanc-Féraud, Gilles Aubert. Quelles relaxations continues pour le critère $l2-l0$ ?. Colloque Gretsi, Sep 2017, Juan-Les-Pins, France. pp.4. ⟨hal-01560319⟩

Laure Blanc-Féraud, Emmanuel Soubies, Gilles Aubert. Some results on sparse L2-L0 reconstruction: Continuous Exact L0 penalties. NCMIP 2016 - New Computational Methods for Inverse Problem , ENS Cachan, Apr 2016, Cachan, France. ⟨hal-01349670⟩

Laure Blanc-Féraud, Emmanuel Soubies, Gilles Aubert. Some results on sparse L2-L0 reconstruction: Continuous Exact L0 penalties. Workshop ATLAS on mathematical and algorithmimcal approaches for high dimensional problems in data sciences. , GdR MaDICS, May 2016, Grenoble, France. ⟨hal-01358112⟩

Emmanuel Soubies, Sébastien Schaub, Agata Radwanska, Ellen van Obberghen-Schilling, Laure Blanc-Féraud, et al.. A Framework for Multi-angle Tirf Microscope Calibration. ISBI - International Symposium on Biomedical Imaging, Apr 2016, Prague, Czech Republic. pp.4, ⟨10.1109/ISBI.2016.7493355⟩. ⟨hal-01257736⟩

Adilson Chinatto, Emmanuel Soubies, Cynthia Junqueira, Joâo M. T. Romano, Pascal Larzabal, et al.. L0-Optimization for Channel and DOA Sparse Estimation. International Workshop on Computational Advances in Multi-Sensor Adaptive Processing (CAMSAP), Dec 2015, Cancun, Mexico. pp.305-308, ⟨10.1109/CAMSAP.2015.7383797⟩. ⟨hal-01212042⟩

Emmanuel Soubies, Laure Blanc-Féraud, Gilles Aubert. CEL0: a continuous alternative to l0 penalty. Signal Processing with Adaptive Sparse Structured Representations (SPARS), Jul 2015, Cambridge, United Kingdom. ⟨hal-01167192⟩

Emmanuelle Poulain, Sylvain Prigent, Emmanuel Soubies, Xavier Descombes. Cells Detection Using Segmentation Competition. ISBI - International Symposium on Biomedical Imaging, Apr 2015, Brooklyn, United States. ⟨10.1109/ISBI.2015.7164090⟩. ⟨hal-01113167⟩

Emmanuel Soubies, Laure Blanc-Féraud, Gilles Aubert. Seuillage CEL0 pour la minimisation l2- l0 : comparaisons avec IHT. Colloque Gretsi, Sep 2015, Lyon, France. pp.4. ⟨hal-01169557⟩

Emmanuel Soubies, Laure Blanc-Féraud, Sébastien Schaub, Gilles Aubert. A 3D model with shape prior information for biological structures reconstruction using Multiple-Angle Total Internal Reflection Fluorescence Microscopy. ISBI - International Symposium on Biomedical Imaging, Apr 2014, Beijing, China. pp.608 - 611, ⟨10.1109/ISBI.2014.6867944⟩. ⟨hal-00914998⟩

Emmanuel Soubies, Laure Blanc-Féraud, Sébastien Schaub, Gilles Aubert. Sparse reconstruction from Multiple-Angle Total Internal Reflection Fluorescence Microscopy. ICIP - International Conference on Image Processing, Oct 2014, Paris, France. pp.2844 - 2848, ⟨10.1109/ICIP.2014.7025575⟩. ⟨hal-01037895⟩

Emmanuel Soubiès, Pierre Weiss, Xavier Descombes. A 3D segmentation algorithm for ellipsoidal shapes. Application to nuclei extraction.. ICPRAM - International Conference on Pattern Recognition Applications and Methods, Feb 2013, Barcelona, Spain. pp.97-105. ⟨hal-00733187⟩

Emmanuel Soubies, Pierre Weiss, Xavier Descombes. Graph Cut Based Segmentation of Predefined Shapes: Applications to Biological Imaging. Pattern Recognition Applications and Methods., 318, Springer-Verlag, pp.153-170, 2015, Advances in Intelligent Systems and Computing, 978-3-319-12610-4. ⟨10.1007/978-3-319-12610-4_10⟩. ⟨hal-01088384⟩