Research Interests
Theoretical
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Methodical
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Main Applications
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Publications
You can find a full and up-to-date list of my scientific publications on my google scholar profile.
Five Key Publications
- F. Lucka, M. Pérez-Liva, B.E. Treeby and B.T. Cox. High resolution 3D ultrasonic breast imaging by time-domain full waveform inversion. Inverse Problems 38(2):025008, 2021.
- F. Lucka, N. Huynh, , M.M. Betcke, E.Zhang, P. Beard, B.T. Cox, and S.R Arridge. Enhancing Compressed Sensing 4D Photoacoustic Tomography by Simultaneous Motion Estimation. SIAM Journal on Imaging Science 11(4):2224-2253, 2018.
- M. Burger and F. Lucka. Maximum a posteriori estimates in linear inverse problems with log-concave priors are proper Bayes estimators. Inverse Problems 30(11):114004, 2014.
- F. Lucka. Fast Markov chain Monte Carlo sampling for sparse Bayesian inference in high-dimensional inverse problems using L1-type priors. Inverse Problems 28(12):125012, 2012.
- F. Lucka, S. Pursiainen, M. Burger, and C.H. Wolters. Hierarchical Bayesian inference for the EEG inverse problem using realistic FE head models: Depth localization and source separation for focal primary currents. NeuroImage 61(4):1364--1382, 2012.
Dissertation
I submitted my PhD thesis with the title Bayesian Inversion in Biomedical Imaging in December, 2014, and defended it on the 23rd of January, 2015. You can find a post-print version with slightly less typos here. Here is a short abstract:
Biomedical imaging techniques became a key technology to assess the structure or function of living organisms in a non-invasive way. Besides innovations in the instrumentation, the development of new and improved methods for processing and analysis of the measured data has become a vital field of research. Building on traditional signal processing, this area nowadays also comprises mathematical modeling, numerical simulation and inverse problems. The latter describes the reconstruction of quantities of interest from measured data and a given generative model. Unfortunately, most inverse problems are ill-posed, which means that a robust and reliable reconstruction is not possible unless additional a-priori information on the quantity of interest is incorporated into the solution method. Bayesian inversion is a mathematical methodology to formulate and employ a-priori information in computational schemes to solve the inverse problem. This thesis develops a recent overview on Bayesian inversion and exemplifies the presented concepts and algorithms in various numerical studies including challenging biomedical imaging applications with experimental data. A particular focus is on using sparsity as a-priori information within the Bayesian framework.
Reviews
Reviewer for the following journals / conferences (check out my publons profile):
- Biomedical Optics Express
- Biomedical Physics & Engineering Express
- Cognitive Neurodynamics
- Computer Methods and Programs in Biomedicine
- Computational Statistics and Data
- IEEE Transactions on Computational Imaging
- IEEE Transactions on Medical Imaging
- IEEE Transactions on Image Processing
- Inverse Problems
- Inverse Problems and Imaging
- Inverse Problems in Science and Engineering
- Journal of Biomedical Optics
- Journal of Computational Methods in Sciences and Engineering
- Journal of Computational Physics
- Journal of Inverse and Ill-posed Problems
- Journal of Mathematical Imaging and Vision
- Journal of Imaging
- Jounal of Optics
- Journal of the Acoustical Society of America
- Journal of the Optical Society of America A
- Mathematical Problems in Engineering
- Medical Image Analysis
- Medical Physics
- NeuroImage
- Neurological Research
- Optics Express
- Physics in Medicine & Biology
- SIAM Journal on Imaging Sciences
- SIAM Journal on Scientific Computing
- Scientific Reports
- SPARS
- Zeitschrift für Medizinische Physik
Referee for:
- Air Force Office of Scientific Research
- Dutch Research Council (NWO)
- German National Academic Foundation (Studienstiftung des deutschen Volkes)
- University of Innsbruck, Austria
- University of Eastern Finland
Organization of Symposia and Workshops
- "Second annual meeting of the Dutch Inverse Problems Community", in Lunteren, November 10-11, 2022.
- "FleX-ray Lab 5 Years Anniversary Symposium", CWI, May 19, 2022.
- "First annual meeting of the Dutch Inverse Problems Community", in Lunteren, November 25-26, 2021.
- "MUMMERING Workshop on Dynamic Imaging", in Leiden, September 06-08, 2019.
- Minisymposium on "Deep Learning and Inverse Problems", at the ICIAM in Valencia, July 15-19, 2019.
- Minisymposium on "Tomographic Imaging: Recent Advances, Exciting Applications and New Horizons", at the Applied Inverse Problems Conference, Grenoble, July 08-12, 2019.
- Minisymposium on "Imaging with Light and Sound", at the SIAM conference on Imaging Science in Bologna, June 05-08, 2018.
- Minisymposium on "New tricks for old problems: Novel computational methods for inverse problems", at the Applied Inverse Problems conference in Hangzhou, May 29 - Jun 02, 2017.
- Minisymposium on "Imaging in the fast lane: in pursuit of dynamical information", at the SIAM conference on Imaging Science in Albuquerque, May 23-26, 2016.
- Minisymposium on "Bayesian Computation" , at the Applied Inverse Problems conference in Helsinki, May 25-29, 2015.
Talks and Posters
(for very similar talks/posters, I only uploaded the latest version to this website to save space; just email me if you're interested in something not available here)
- "Photoacoustic and Ultrasonic Tomography for Breast Imaging", Medical Physics Seminar, MLU Halle-Wittenberg, November 16, 2023.
- "Photoacoustic and Ultrasonic Tomography for Breast Imaging", Applied Inverse Problems Conference, Göttingen, September 7, 2023.
- "Photoacoustic and Ultrasonic Tomography for Breast Imaging", Tomographic Inverse Problems: Mathematical Challenges and Novel Applications , Oberwolfach Workshop 2318, May 4, 2023.
- "Photoacoustic and Ultrasonic Tomography for Breast Imaging", Rich and non-linear tomography in medical imaging, materials and non destructive testing (RNTW02) workshop, Isaac Newton Institute, Cambridge UK, March 30, 2023.
- "Ultrasonic Breast Tomography via 3D Full Waveform Inversion", Department of Imaging Physics, TU Delft, June 16, 2022.
- "Deep Learning in Computational Imaging", AI & Mathematics Workshop, CWI, June 5, 2022.
- "The FleX-ray Lab – Past, Present and Future", "FleX-ray Lab 5 Years Anniversary Symposium", CWI, May 19, 2022.
- "Photoacoustic & Ultrasonic Tomography for Breast Cancer Imaging", 3rd IMA Conference on Inverse Problems from Theory to Application, ICMS, Edinburgh, May 5, 2022.
- "X-Ray Computed Tomography", lecture given in the Mastermath course "Inverse Problems in Imaging", online, March 21, 2022.
- "Photoacoustic and Ultrasonic Tomography for Breast Imaging", SIAM Imaging Science, online, March 21, 2022.
- "Image Reconstruction - A Playground for Applied Mathematicians", Applied Analysis Seminar, Radboud University, Feb 24, 2022.
- "Computational and Experimental Challenges of 3D Ultrasound Tomography", Conference on Mathematics of Wave Phenomena”, KIT, online, Feb 14, 2022.
- "Deep Learning in Computational Imaging", MaLGA Seminar Series”, online, Nov 08, 2021.
- "Computational Challenges in Photoacoustic and Ultrasonic Breast Imaging", Excalibur SLE Workshop on “Inverse Problems and Optimisation”, online, May 07, 2021.
- "X-Ray Computed Tomography", lecture given in the Mastermath course "Inverse Problems in Imaging", online, Mar 22, 2021.
- "Simultaneous Tomographic Image Reconstruction and Motion Estimation", UGCT Seminar, online, Feb 23, 2021.
- "Joint Tomographic Image Reconstruction and Motion Estimation", SIAM Imaging Science, online, Jul 17, 2020.
- "Imaging the Acoustic and Optical Properties of the Breast with USCT and PAT", SIAM Imaging Science, online, Jul 08, 2020.
- "X-Ray Computed Tomography", lecture given in the Mastermath course "Inverse Problems in Imaging", CWI, Mar 09, 2020.
- "Image Reconstruction: A Playground for Applied Mathematicians", Partial differential equations and applications, TU Delft, Feb 20, 2020.
- "Image Reconstruction: A Playground for Curious Applied Mathematicians", CWI Scientific Meetings , Amsterdam, Feb 14, 2020.
- "Time-Domain Full Waveform Inversion for High Resolution 3D Ultrasound Computed Tomography of the Breast", International Workshop on Medical Ultrasound Tomography (MUST 2019) , Detroit, Oct 15, 2019.
- "Dynamic Image Reconstruction & Motion Estimation", MUMMERING Workshop on Dynamic Imaging, Leiden, Sep 10, 2019.
- "4D Computed Tomography with Sequential Scanning Systems", IMA, London, Sep 6, 2019.
- "New Applications and Challenges in X-Ray Tomography", ICIAM, Valencia, Jul 17, 2019.
- "Hierarchical Bayesian Uncertainty Quantication for EEG/MEG Source Reconstruction", ICIAM, Valencia, Jul 17, 2019.
- "Computational and Practical Challenges of 4D Tomography Applications", Applied Inverse Problems Conference, Grenoble, Jul 12, 2019.
- "Deep Learning for Computed Tomography Applications", Applied Inverse Problems Conference, Grenoble, Jul 11, 2019.
- "Challenges of Mathematical Image Reconstruction", DIAMANT symposium, Eindhoven, Apr 4, 2019.
- "On Challenges in Quantitative Photoacoustic Tomography and Ultrasound Computed Tomography", Mathematical and Numerical Approaches for Multi-Wave Inverse Problems, Marseille, Apr 2, 2019.
- "X-Ray Computed Tomography", lecture given in the Mastermath course "Inverse Problems in Imaging", CWI, Mar 26, 2019.
- "Challenges of Mathematical Image Reconstruction", Colloquium Mathematics, Groningen, Nov 27 , 2018.
- "Hierarchical Bayesian Uncertainty Quantification for EEG/MEG Source Reconstruction", SIAM Conference on Imaging Science, Bologna, June 5 - 8, 2018.
- "Variational Models for Dynamic Tomography", Inverse Problems: Modeling and Simulation, Malta, May 21 - 25, 2018.
- "Sparse Bayesian Inference & Uncertainty Quantication for Inverse Imaging Problems", Statistics for Structures Seminar, University of Leiden, Oct 20, 2017.
- "Enhancing Dynamic, Sub-Sampled 3D Photoacoustic Tomography by Simultaneous Motion Estimation", IMA Conference on Inverse Problems from Theory to Application, Cambridge, Sep 19 - 21, 2017.
- "Challenges of Sparse Bayesian Inversion and Uncertainty Quantication" Bayesian and Nonlinear Inverse Problems, Lorenz Center, Leiden, Aug 28 - Sep 1, 2017.
- "An Experimental Study of Blood Oxygen Saturation Imaging via Quantitative Photoacoustic Tomography", Applied Inverse Problems (AIP), Hangzhou, May 29 - Jun 2, 2017.
- "Enhancing Dynamic, Sub-Sampled 3D Photoacoustic Tomography by Simultaneous Motion Estimation", Applied Inverse Problems (AIP), Hangzhou, May 29 - Jun 2, 2017.
- "Total Variation Regularization and Related Topics", three lectures given in the course "GV08 Optimization and Inverse Problems in Imaging" by Simon Arridge, Mar. 2017.
- "Enhancing Compressed Sensing Photoacoustic Tomography by Simultaneous Motion Estimation.", Workshop: Shape, Images and Optimization , Münster, Mar 2, 2017.
- "The Ill-Posedness Always Rings Twice - Risk Estimators for Choosing Regularization Parameters in Inverse Problems", Interdisciplinary data science workshop , Cambridge, Feb 9, 2017.
- "Compressed Sensing for High Resolution 3D Photoacoustic Tomography", INdAM Workshop on Biomedical Imaging , Rome, Feb 9, 2017.
- "Sparse Dynamic High Resolution Photoacoustic Tomography", Centre for Inverse Problems Seminar, UCL, London, Jan 27, 2017.
- "Sub-Sampled Dynamic Photoacoustic Tomography with Sparsity Constraints", IFIP WG 7.4 Workshop on Inverse Problems and Imaging, Mülheim a.d. Ruhr, Dec 19, 2016.
- "An Experiment in Quantitative Photoacoustic Tomography", QPAT Workshop @ UCL, London, Nov 10, 2016.
- "Variational Image Reconstruction for Dynamic High Resolution Photoacoustic Tomography", Developments in Healthcare Imaging - Connecting with Industry, Cambridge, Oct 19, 2016.
- "Accelerated High-Resolution Photoacoustic Tomography via Compressed Sensing", SIAM Imaging Science conference, Albuquerque, May 24, 2016.
- "Can Compressed Sensing Accelerate High-Resolution Photoacoustic Tomography?", Numerical Analysis and Scientific Computing" seminar at Emory, Atlanta, May 19, 2016.
- "Can Compressed Sensing Accelerate High-Resolution Photoacoustic Tomography?", "Applied Math Colloquium", WWU, Apr. 20, 2016.
- "High-Dimensional Bayesian Inversion with Priors Far from Gaussians.", SIAM Uncertainty Quantification conference, Lausanne, Apr. 6, 2016.
- "Recent Advances in Bayesian Inference for Biomedical Imaging.", "Workshop on Inverse Problems", Edinburgh: Mar. 17, 2016.
- "4D PAT based on Sparse Variational Methods.", "New trends in Hybrid Ultrasonic Imaging" conference, Orléans, Mar. 9, 2016.
- "Sparse Bayesian Inversion in Biomedical Imaging.", "Signal Image Processing" seminar, Telecom ParisTech Paris, Mar. 3, 2016.
- "Variational Image Reconstruction for Dynamic High Resolution Photoacoustic Tomography" , SPIE Photonics West, San Francisco, Feb. 13-18, 2016.
- "Variational Image Reconstruction in 4D Photoacoustic Tomography" , Compressive Sensing and Sparsity: Theory and Applications in Tomography, Manchester, Nov. 12-13, 2015.
- "Variational Methods for Dynamic High-Resolution Photoacoustic Tomography", Variational Methods for Dynamic Inverse Problems and Imaging, Münster, Sep. 28-30, 2015.
- "Hierarchical Bayesian Inference for Combined EEG/MEG Source Analysis" , BaCI, Utrecht, Sep. 1-5, 2015.
- "Towards Dynamic High Resolution Photoacoustic Tomography", ICIAM, Beijing, Aug. 10-14, 2015.
- "Sample-based Sparse Bayesian Inversion in Biomedical Imaging" , ICIAM, Beijing, Aug. 10-14, 2015.
- "Towards 4D Photoacoustic Tomography" , SPARS, Cambridge, Jul. 6-9, 2015.
- "Challenges of 4D Photoacoustic Tomography" , Challenges in Dynamic Imaging Data Workshop, Cambridge, Jun. 9-11, 2015.
- "Recent Advances in Bayesian Inference for Inverse Problems" , Applied Inverse Problems, Helsinki, May 25-29, 2015.
- "Towards Dynamic High Resolution Photoacoustic Tomography" , A talk given in the seminar of our Center for Medical Image Computing, Apr. 15, 2015.
- "Total Variation Regularization and Related Topics", three lectures given in the course "GV08 Optimization and Inverse Problems in Imaging" by Simon Arridge, Mar. 2015.
- "Sample-based Bayesian Inference in Inverse Problems" , Applied Maths Seminar, Warwick, Feb. 13, 2015.
- "Challenges of Dynamic High Resolution Photoacoustic Tomography" , Institute for Applied Mathematics, Münster, Feb. 2, 2015.
- "Sample-based Bayesian Inversion" , Inverse Days, Tampere, Dec. 9-11, 2014.
- "Sparse Recovery Conditions and Realistic Forward Modeling in EEG/MEG Source Reconstruction" , UCL-Duke Workshop on Sensing and Analysis of High-Dimensional Data - SAHD, London, Sep. 4-5, 2014.
- "Sparse Recovery Conditions and Realistic Forward Modeling in EEG/MEG Source Reconstruction" , Conference ""Inverse Problems - from Theory to Applications" - IPTA, Bristol, Aug. 26-28, 2014.
- "Sparse Recovery Conditions and Realistic Forward Modeling in EEG/MEG Source Reconstruction" , Workshop "Innovative Verarbeitung bioelektrischer und biomagnetischer Signale" - bbs2014 , Berlin, Apr. 10-11, 2014.
- "Sparse Recovery Conditions and Realistic Forward Modeling in EEG/MEG Source Reconstruction" , Matheon Workshop on Compressed Sensing and its Applications , Berlin, Dec. 09-13, 2013.
- "Hierarchical Fully-Bayesian Inference for Combined EEG/MEG Source Analysis of Evoked Responses: From Simulations to Real Data" , Neurovisionen 9, Cologne, Nov. 29, 2013.
- "Computational and Theoretical Aspects of L1-type Priors in Bayesian Inverse Problems" , International Workshop on Inverse Problems and Regularization Theory, Fudan University, Shanghai, Sep. 26-29, 2013.
- "Recent Results on L1-type Priors in Bayesian Inverse Problems", Shanghai International Workshop on Recent Advances in Inverse Problems and Imaging Science, Shanghai Jiao Tong University, Sep. 21-22, 2013.
- "Hierarchical Fully-Bayesian Inference for Combined EEG/MEG Source Analysis of Evoked Responses: From Simulations to Real Data" , International Conference on Basic and Clinical Multimodal Imaging (BaCI) , Geneva, Sep. 05-08, 2013.
- "Computational and Theoretical Aspects of Sparsity-Constraints in Bayesian Inversion" , Applied Inverse Problems Conference , Daejeon, Jul. 01-05, 2013.
- "Hierarchical Bayesian Modeling for EEG/MEG: From Simulated to Experimental Data" , Applied Inverse Problems Conference , Daejeon, Jul. 01-05, 2013.
- "Hierarchical Bayesian Modeling and Another Type of Sparsity" , Applied Math Colloquium, UCLA, May 29, 2013.
- "The Bayesian Approach to Inverse Problems and Imaging" , two introductory talks given at Stanley Osher's level set collective seminar, UCLA: Talk I (April 30, 2013) , Talk II (May 5, 2013) .
- "Sparsity Constraints in Bayesian Inversion" , 18-th "Inverse Days" Conference , Jyväskylä, Dec. 17-19, 2012.
- "The Bayesian Approach to Inverse Problems" , three introductory talks given at the DAMTP, Centre for Mathematical Sciences, University of Cambridge, Nov. 13.-15., 2012. Overview , Talk I , Talk II , Talk III .
- "Hierarchical Fully-Bayesian Inference for EEG/MEG combination: Examination of Depth Localization and Source Separation using Realistic FE Head Models" , Neurovisionen 8, Aachen, Oct. 26, 2012.
- "Hierarchical Fully-Bayesian Inference for EEG and MEG" , a talk given at during the visit of Matti Hämäläinen, WWU Münster, Oct. 12, 2012.
- "Hierarchical Fully-Bayesian Inference for EEG/MEG combination: Examination of Depth Localization and Source Separation using Realistic FE Head Models" , 18-th International Conference on Biomagnetism (Biomag 2012), Paris, Aug. 26-30, 2012.
- "MCMC Sampling for Bayesian Inference using L1-type Priors" , a talk given at a seminar of our workgroup, WWU Münster, June 25, 2012.
- "A lecture on the inverse problem of EEG/MEG" , WWU Münster, May 14, 2012.
- "Hierarchical Bayesian Models for Focal EEG/MEG Inversion" , Workshop "Innovative Verarbeitung bioelektrischer und biomagnetischer Signale" - bbs2012, Berlin, Apr. 19, 2012.
- "Bioelectromagnetism in Neuroscience" , a talk given togehter with Johannes Vorwerk at the Skiseminar of the Institute for Computational and Applied Mathematics 2012 , Feb. 29, 2012.
- "Hierarchical Bayesian Estimation for the EEG Inverse Problem using Realistic FE Head Models: Depth Localization and Source Separation for Focal Primary Currents" , Autumn School "The Multimodal Brain", Tübingen, Oct. 5-6, 2011.
- "Hierarchical Bayesian Models for EEG Inversion: Depth Localization and Source Separation for Focal Sources in Realistic FE Head Models" , Annual meeting of the DGBMT, Freiburg, Sep. 28, 2011.
- "Hierarchical Bayesian Approaches to the Inverse Problem of EEG/MEG Current Density Reconstruction" , Annual meeting of the DMV, Köln, Sep. 20, 2011.
Diploma Thesis (Master's Thesis)
I submitted my diploma thesis with the title Hierarchical Bayesian Approaches to the Inverse Problem of EEG/MEG Current Density Reconstruction in March, 2011. You can find it here. This is the abstract:
This thesis deals with the inverse problem of EEG/MEG source reconstruction: The estimation of the activity-related ion currents by measuring the induced electromagnetic fields outside the skull is a challenging mathematical inverse problem, as the number of free parameters within the corresponding forward model is much larger than the number of measurements. Additionally, the problem is ill-conditioned due to the smoothing propagation characteristics of the fields through the human tissue. The thesis is devoted to the introduction of a special class of statistical models, called hierarchical Bayesian models to overcome both obstacles. For this sake, it consists of four main parts: The mathematical modeling and challenges of bioelectromagnetism, a theoretical introduction of the model, the algorithmical aspects of the implementation and their practical use and properties within simulation studies. Technically, a focus of interest is on a certain class of inference algorithms that are based on alternated conditional walks through the parameter space. The forward computation will be done with a realistic high resolution finite element (FE) model of a human head.
If you're interested in these topics, it might also be worthwhile to check out PhD thesis (see above).Software
- WalnutReconstructionCodes: A collection of Pyhton and MATLAB scripts for loading, pre-processing and reconstructing the X-ray CT data collection we published in this paper on [arXiv](https://arxiv.org/abs/1905.04787).
- FelixMatlabTools: A collection of MATLAB functions that are used by several of my projects.
- L1GibbsSampler.zip : Code and examples for the L1 single component Gibbs Sampler descripted in "Fast Markov chain Monte Carlo sampling for sparse Bayesian inference in high-dimensional inverse problems using L1-type priors", Inverse Problems, 2012.