Mareike Thies

Mareike Thies, M. Sc.

Researcher

Department of Computer Science
Chair of Computer Science 5 (Pattern Recognition)

Room 09.155
Martensstr. 3
91058 Erlangen

Phone number: +49 9131 85-25247
Fax number: +49 9131 85-27270
Email: mareike.thies@fau.de
Website: https://lme.tf.fau.de/person/thies/

Academic CV

11/2020 – 12/2024:
Researcher and Ph.D. candidate at Pattern Recognition Lab, Friedrich-Alexander-Universität Erlangen-Nürnberg
10/2019 – 06/2020:
Master’s thesis at Johns Hopkins University, Baltimore
04/2018 – 10/2020:
Master’s student in Medical Engineering at Friedrich-Alexander-Universität Erlangen-Nürnberg
10/2014 – 10/2017:
Bachelor’s student in Medical Engineering at Universität zu Lübeck

Projects

2019

Advancing osteoporosis medicine by observing bone microstructure and remodelling using a four-dimensional nanoscope

(Third Party Funds Single)

Term: April 1, 2019 - March 31, 2025
Funding source: European Research Council (ERC)
URL: https://cordis.europa.eu/project/id/810316

Abstract

Due to Europe's ageing society, there has been a dramatic increase in the occurrence of osteoporosis (OP) and related diseases. Sufferers have an impaired quality of life, and there is a considerable cost to society associated with the consequent loss of productivity and injuries. The current understanding of this disease needs to be revolutionized, but study has been hampered by a lack of means to properly characterize bone structure, remodeling dynamics and vascular activity. This project, 4D nanoSCOPE, will develop tools and techniques to permit time-resolved imaging and characterization of bone in three spatial dimensions (both in vitro and in vivo), thereby permitting monitoring of bone remodeling and revolutionizing the understanding of bone morphology and its function.

To advance the field, in vivo high-resolution studies of living bone are essential, but existing techniques are not capable of this. By combining state-of-the art image processing software with innovative 'precision learning' software methods to compensate for artefacts (due e.g. to the subject breathing or twitching), and innovative X-ray microscope hardware which together will greatly speed up image acquisition (aim is a factor of 100), the project will enable in vivo X-ray microscopy studies of small animals (mice) for the first time. The time series of three-dimensional X-ray images will be complemented by correlative microscopy and spectroscopy techniques (with new software) to thoroughly characterize (serial) bone sections ex vivo.

The resulting three-dimensional datasets combining structure, chemical composition, transport velocities and local strength will be used by the PIs and international collaborators to study the dynamics of bone microstructure. This will be the first time that this has been possible in living creatures, enabling an assessment of the effects on bone of age, hormones, inflammation and treatment.

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Publications

2025

Unpublished Publications

Sun Y., Huang Y., Schneider LS., Thies M., Gu M., Mei S., Bayer S., Maier A.:
EAGLE: An Edge-Aware Gradient Localization Enhanced Loss for CT Image Reconstruction
(2025)
DOI: 10.48550/arXiv.2403.10695
BibTeX: Download

2024

Journal Articles

Pfaff L., Darwish O., Wagner F., Thies M., Vysotskaya N., Hoßbach J., Weiland E., Benkert T., Eichner C., Nickel D., Wuerfl T., Maier A.:
Enhancing diffusion-weighted prostate MRI through self-supervised denoising and evaluation
In: Scientific Reports 14 (2024), Article No.: 24292
ISSN: 2045-2322
DOI: 10.1038/s41598-024-75007-x
BibTeX: Download
Maul N., Birkhold A., Wagner F., Thies M., Rohleder M., Berg P., Kowarschik M., Maier A.:
Simulation-informed learning for time-resolved angiographic contrast agent concentration reconstruction
In: Computers in Biology and Medicine 182 (2024), Article No.: 109178
ISSN: 0010-4825
DOI: 10.1016/j.compbiomed.2024.109178
BibTeX: Download
Thies M., Wagner F., Maul N., Yu H., Goldmann M., Schneider LS., Gu M., Mei S., Folle L., Preuhs A., Manhart M., Maier A.:
A gradient-based approach to fast and accurate head motion compensation in cone-beam CT
In: IEEE Transactions on Medical Imaging (2024), p. 1-1
ISSN: 0278-0062
DOI: 10.1109/TMI.2024.3474250
BibTeX: Download
Yu H., Liu C., Thies M., Wagner F., Wang A., Zhang G., Huang Y., Liu F., Maier A.:
Reducing penumbral blur in computed tomography by learning the inverse finite focal spot model
In: Optics Express 32 (2024), p. 23674-23686
ISSN: 1094-4087
DOI: 10.1364/OE.527304
BibTeX: Download
Yu H., Ni S., Thies M., Wagner F., Huang Y., Liu F., Maier A.:
Multiple Source Translation Micro-CT Improves Both Field-of-View and Spatial Resolution
In: IEEE Transactions on Instrumentation and Measurement 73 (2024), p. 1-11
ISSN: 0018-9456
DOI: 10.1109/TIM.2024.3385839
URL: https://ieeexplore.ieee.org/document/10494784
BibTeX: Download
Rohleder M., Thies M., Riedl S., Bullert B., Gierse J., Privalov M., Mandelka E., Vetter S., Maier A., Kreher B.:
An interactive task-based method for the avoidance of metal artifacts in CBCT
In: International Journal of Computer Assisted Radiology and Surgery (2024)
ISSN: 1861-6410
DOI: 10.1007/s11548-024-03103-4
BibTeX: Download

Conference Contributions

Thies M., Maul N., Mei S., Pfaff L., Vysotskaya N., Gu M., Utz J., Possart D., Folle L., Wagner F., Maier A.:
Differentiable Score-Based Likelihoods: Learning CT Motion Compensation from Clean Images
Medical Image Computing and Computer Assisted Intervention – MICCAI 2024
In: Medical Image Computing and Computer Assisted Intervention – MICCAI 2024, Cham: 2024
DOI: 10.1007/978-3-031-72104-5_25
BibTeX: Download
Mei S., Fan F., Wagner F., Thies M., Gu M., Sun Y., Maier A.:
Segmentation-Guided Knee Radiograph Generation using Conditional Diffusion Models
The 8th International Conference on Image Formation in X-Ray Computed Tomography (Bamberg, Germany, August 5, 2024 - August 9, 2024)
DOI: 10.48550/arXiv.2404.03541
URL: https://arxiv.org/pdf/2404.03541
BibTeX: Download
Sun Y., Schneider LS., Fan F., Thies M., Gu M., Mei S., Zhou Y., Bayer S., Maier A.:
Data-Driven Filter Design in FBP: Transforming CT Reconstruction with Trainable Fourier Series
(2024)
DOI: 10.48550/arXiv.2401.16039
BibTeX: Download
Thies M., Wagner F., Gu M., Mei S., Huang Y., Pechmann S., Aust O., Weidner D., Neag G., Uderhardt S., Schett G., Christiansen S., Maier A.:
Exploring Epipolar Consistency Conditions for Rigid Motion Compensation in In-vivo X-ray Microscopy
German Conference on Medical Image Computing, BVM 2024 (Erlangen, March 10, 2024 - March 12, 2024)
In: Andreas Maier, Thomas M. Deserno, Heinz Handels, Klaus Maier-Hein, Christoph Palm, Thomas Tolxdorff (ed.): Bildverarbeitung für die Medizin 2024. BVM 2024, Wiesbaden: 2024
DOI: 10.1007/978-3-658-44037-4_60
URL: https://arxiv.org/abs/2303.00449
BibTeX: Download
Augustin L., Wagner F., Thies M., Maier A.:
Neural Network-based Sinogram Upsampling in Real-measured CT Reconstruction
German Conference on Medical Image Computing, BVM 2024 (Erlangen, March 10, 2024 - March 12, 2024)
In: Andreas Maier, Thomas M. Deserno, Heinz Handels, Klaus Maier-Hein, Christoph Palm, Thomas Tolxdorff (ed.): Bildverarbeitung für die Medizin 2024. BVM 2024, Wiesbaden: 2024
DOI: 10.1007/978-3-658-44037-4_80
BibTeX: Download
Thies M., Wagner F., Maul N., Mei S., Gu M., Pfaff L., Vysotskaya N., Yu H., Maier A.:
On the influence of smoothness constraints in computed tomography motion compensation
8th International Conference on Image Formation in X-Ray Computed Tomography (CT Meeting) (Bamberg, August 5, 2024 - August 9, 2024)
URL: https://www.ct-meeting.org/?p=program
BibTeX: Download

2023

Journal Articles

Thies M., Wagner F., Maul N., Folle L., Meier M., Rohleder M., Schneider LS., Pfaff L., Gu M., Utz J., Denzinger F., Manhart M., Maier A.:
Gradient-based geometry learning for fan-beam CT reconstruction
In: Physics in Medicine and Biology 68 (2023), Article No.: 205004
ISSN: 0031-9155
DOI: 10.1088/1361-6560/acf90e
URL: https://iopscience.iop.org/article/10.1088/1361-6560/acf90e
BibTeX: Download
Folle L., Fenzl P., Fagni F., Thies M., Christlein V., Meder C., Simon D., Minopoulou I., Sticherling M., Schett G., Maier A., Kleyer A.:
Author Correction: DeepNAPSI multi-reader nail psoriasis prediction using deep learning.
In: Scientific Reports 13 (2023)
ISSN: 2045-2322
DOI: 10.1038/s41598-023-37790-x
BibTeX: Download

Book Contributions

Folle L., Fenzl P., Fagni F., Thies M., Christlein V., Meder C., Simon D., Minnopoulou I., Sticherling M., Schett G., Maier A., Kleyer A.:
DeepNAPSI multi-reader nail psoriasis prediction using deep learning
In: Nature Scientific Reports, 2023, p. 5329
DOI: 10.1038/s41598-023-32440-8
BibTeX: Download

Conference Contributions

Wagner F., Thies M., Maul N., Pfaff L., Aust O., Pechmann S., Syben C., Maier A.:
Geometric Constraints Enable Self-Supervised Sinogram Inpainting in Sparse-View Tomography
17th International Meeting on Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine (Fully3D) (Stony Brook University, NY, USA, July 16, 2023 - July 21, 2023)
DOI: 10.48550/arXiv.2302.06436
URL: https://arxiv.org/pdf/2302.06436.pdf
BibTeX: Download
Raghunath A., Wagner F., Thies M., Gu M., Pechmann S., Aust O., Weidner D., Neag G., Schett G., Christiansen SH., Uderhardt S., Maier A.:
Unsupervised Super Resolution in X-ray Microscopy using a Cycle-consistent Generative Model
BVM Workshop Bildverarbeitung für die Medizin 2023 (Braunschweig, July 2, 2023 - July 4, 2023)
In: Bildverarbeitung für die Medizin 2023 2023
DOI: 10.1007/978-3-658-41657-7_19
BibTeX: Download
Schneider LS., Thies M., Schielein R., Syben C., Unberath M., Maier A.:
Learning-based Trajectory Optimization for a Twin Robotic CT System
12th Conference on Industrial Computed Tomography (iCT) 2023 (Fürth, February 27, 2023 - March 2, 2023)
In: NDT.net Issue: 2023-03 2023
DOI: 10.58286/27748
BibTeX: Download
Gu M., Thies M., Wagner F., Pechmann S., Aust O., Weidner D., Neag G., Pan Z., Utz J., Schett G., Christiansen S., Uderhardt S., Maier A.:
Cavity Segmentation in X-ray Microscopy Scans of Mouse Tibiae
Bildverarbeitung für die Medizin Workshop, BVM 2023 (Braunschweig, DEU, July 2, 2023 - July 4, 2023)
In: Thomas M. Deserno, Heinz Handels, Andreas Maier, Klaus Maier-Hein, Christoph Palm, Thomas Tolxdorff (ed.): Informatik aktuell 2023
DOI: 10.1007/978-3-658-41657-7_56
BibTeX: Download
Folle L., Fenzl P., Fagni F., Thies M., Christlein V., Meder C., Sticherling M., Simon D., Schett G., Maier A., Kleyer A.:
Deepnapsi: Deep Learning for Nail Psoriasis Prediction
20th IEEE International Symposium on Biomedical Imaging, ISBI 2023 (Cartagena, April 18, 2023 - April 21, 2023)
In: Proceedings - International Symposium on Biomedical Imaging 2023
DOI: 10.1109/ISBI53787.2023.10230472
BibTeX: Download
Rohleder M., Pradel C., Wagner F., Thies M., Maul N., Denzinger F., Maier A., Kreher B.:
Enabling Geometry Aware Learning Through Differentiable Epipolar View Translation
26th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2023 (Vancouver, BC, CAN, October 8, 2023 - October 12, 2023)
In: Hayit Greenspan, Hayit Greenspan, Anant Madabhushi, Parvin Mousavi, Septimiu Salcudean, James Duncan, Tanveer Syeda-Mahmood, Russell Taylor (ed.): Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2023
DOI: 10.1007/978-3-031-43898-1_6
BibTeX: Download
Utz J., Schlereth M., Qiu J., Thies M., Wagner F., Brahim OB., Gu M., Uderhardt S., Breininger K.:
McLabel: A Local Thresholding Tool for Efficient Semi-automatic Labelling of Cells in Fluorescence Microscopy
Bildverarbeitung für die Medizin Workshop, BVM 2023 (Braunschweig, DEU, July 2, 2023 - July 4, 2023)
In: Thomas M. Deserno, Heinz Handels, Andreas Maier, Klaus Maier-Hein, Christoph Palm, Thomas Tolxdorff (ed.): Informatik aktuell 2023
DOI: 10.1007/978-3-658-41657-7_20
BibTeX: Download
Wagner F., Thies M., Pfaff L., Maul N., Pechmann S., Gu M., Utz J., Aust O., Weidner D., Neag G., Uderhardt S., Choi JH., Maier A.:
Noise2Contrast: Multi-contrast Fusion Enables Self-supervised Tomographic Image Denoising
28th International Conference on Information Processing in Medical Imaging, IPMI 2023 (San Carlos de Bariloche, ARG, June 18, 2023 - June 23, 2023)
In: Alejandro Frangi, Marleen de Bruijne, Demian Wassermann, Nassir Navab (ed.): Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2023
DOI: 10.1007/978-3-031-34048-2_59
BibTeX: Download
Wagner F., Thies M., Pfaff L., Aust O., Pechmann S., Weidner D., Maul N., Rohleder M., Gu M., Utz J., Denzinger F., Maier A.:
On the Benefit of Dual-Domain Denoising in a Self-Supervised Low-Dose CT Setting
20th IEEE International Symposium on Biomedical Imaging, ISBI 2023 (Cartagena, April 18, 2023 - April 21, 2023)
In: Proceedings - International Symposium on Biomedical Imaging 2023
DOI: 10.1109/ISBI53787.2023.10230511
BibTeX: Download
Thies M., Wagner F., Maul N., Pfaff L., Schneider LS., Syben C., Maier A.:
Optimizing CT Scan Geometries With and Without Gradients
17th International Meeting on Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine (Fully3D) (Stony Brook University, New York, July 16, 2023 - July 21, 2023)
Open Access: https://arxiv.org/abs/2302.06251
BibTeX: Download
Pfaff L., Wagner F., Hoßbach J., Preuhs E., Maul N., Thies M., Denzinger F., Nickel MD., Wuerfl T., Maier A.:
Robust multi-contrast MRI denoising using trainable bilateral filters without noise-free targets
International Symposium on Biomedical Imaging (ISBI)
BibTeX: Download
Schneider LS., Thies M., Syben C., Schielein R., Unberath M., Maier A.:
Task-based Generation of Optimized Projection Sets using Differentiable Ranking
Fully3D 2023 (Stony Brook State University of New York, July 16, 2023 - July 21, 2023)
In: Fully3D 2023 Proceedings 2023
DOI: 10.48550/arXiv.2303.11724
URL: https://arxiv.org/abs/2303.11724
BibTeX: Download
Maul N., Zinn K., Wagner F., Thies M., Rohleder M., Pfaff L., Kowarschik M., Birkhold A., Maier A.:
Transient Hemodynamics Prediction Using an Efficient Octree-Based Deep Learning Model
28th International Conference on Information Processing in Medical Imaging, IPMI 2023 (San Carlos de Bariloche, June 18, 2023 - June 23, 2023)
In: Alejandro Frangi, Marleen de Bruijne, Demian Wassermann, Nassir Navab (ed.): Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2023
DOI: 10.1007/978-3-031-34048-2_15
BibTeX: Download

2022

Journal Articles

Dutta B., Root K., Ullmann I., Wagner F., Mayr M., Seuret M., Thies M., Stromer D., Christlein V., Schür J., Maier A., Huang Y.:
Deep learning for terahertz image denoising in nondestructive historical document analysis
In: Scientific Reports 12 (2022), p. 1-11
ISSN: 2045-2322
DOI: 10.1038/s41598-022-26957-7
URL: https://www.nature.com/articles/s41598-022-26957-7
BibTeX: Download
Wagner F., Thies M., Denzinger F., Gu M., Patwari M., Ploner S., Maul N., Pfaff L., Huang Y., Maier A.:
Trainable joint bilateral filters for enhanced prediction stability in low-dose CT
In: Scientific Reports 12 (2022), Article No.: 17540
ISSN: 2045-2322
DOI: 10.1038/s41598-022-22530-4
BibTeX: Download
Thies M., Wagner F., Huang Y., Gu M., Kling L., Pechmann S., Aust O., Grüneboom A., Schett G., Christiansen SH., Maier A.:
Calibration by differentiation – Self-supervised calibration for X-ray microscopy using a differentiable cone-beam reconstruction operator
In: Journal of Microscopy (2022)
ISSN: 0022-2720
DOI: 10.1111/jmi.13125
BibTeX: Download
Wagner F., Thies M., Gu M., Huang Y., Pechmann S., Patwari M., Ploner S., Aust O., Uderhardt S., Schett G., Christiansen SH., Maier A.:
Ultra low‐parameter denoising: Trainable bilateral filter layers in computed tomography
In: Medical Physics 49 (2022), p. 5107-5120
ISSN: 0094-2405
DOI: 10.1002/mp.15718
BibTeX: Download

Conference Contributions

Folle L., Meinderink T., Simon D., Liphardt AM., Thies M., Krönke G., Schett G., Kleyer A., Maier A.:
Automated Bone Density Measurements using Deep Learning
QMSKI (Nordwijk, June 12, 2022 - June 17, 2022)
In: Bert van Rietbergen, Harry van Lenthe, Quentin Grimal (ed.): 23 2022
BibTeX: Download
Thies M., Wagner F., Gu M., Folle L., Felsner L., Maier A.:
Learned Cone-Beam CT Reconstruction Using Neural Ordinary Differential Equations
7th International Conference on Image Formation in X-Ray Computed Tomography (Baltimore, June 12, 2022 - June 16, 2022)
In: Proceedings Volume 12304, 7th International Conference on Image Formation in X-Ray Computed Tomography; 1230409 (2022) 2022
DOI: 10.1117/12.2646442
BibTeX: Download
Wagner F., Thies M., Karolczak M., Pechmann S., Huang Y., Gu M., Kling L., Weidner D., Aust O., Schett G., Christiansen S., Maier A.:
Monte Carlo Dose Simulation for In-Vivo X-Ray Nanoscopy
German Workshop on Medical Image Computing, 2022 (Heidelberg, DEU, June 26, 2022 - June 28, 2022)
In: Klaus Maier-Hein, Thomas M. Deserno, Heinz Handels, Andreas Maier, Christoph Palm, Thomas Tolxdorff (ed.): Informatik aktuell 2022
DOI: 10.1007/978-3-658-36932-3_22
BibTeX: Download
Aust O., Thies M., Weidner D., Wagner F., Pechmann S., Mill L., Andreev D., Miyagawa I., Krönke G., Christiansen S., Uderhardt S., Maier A., Grüneboom A.:
Tibia Cortical Bone Segmentation in Micro-CT and X-ray Microscopy Data Using a Single Neural Network
German Workshop on Medical Image Computing, 2022 (Heidelberg, June 26, 2022 - June 28, 2022)
In: Klaus Maier-Hein, Thomas M. Deserno, Heinz Handels, Andreas Maier, Christoph Palm, Thomas Tolxdorff (ed.): Informatik aktuell 2022
DOI: 10.1007/978-3-658-36932-3_68
BibTeX: Download

2021

Journal Articles

Herl G., Hiller J., Thies M., Zaech JN., Unberath M., Maier A.:
Task-Specific Trajectory Optimisation for Twin-Robotic X-Ray Tomography
In: IEEE Transactions on Computational Imaging 7 (2021), p. 894-907
ISSN: 2333-9403
DOI: 10.1109/TCI.2021.3102824
BibTeX: Download

2020

Journal Articles

Gao C., Farvardin A., Grupp R., Bakhtiarinejad M., Ma L., Thies M., Unberath M., Taylor R., Armand M.:
Fiducial-Free 2D/3D Registration for Robot-Assisted Femoroplasty
In: IEEE Transactions on Medical Robotics and Bionics 2 (2020), p. 437-446
ISSN: 2576-3202
DOI: 10.1109/TMRB.2020.3012460
BibTeX: Download
Thies M., Zäch JN., Gao C., Taylor R., Navab N., Maier A., Unberath M.:
A learning-based method for online adjustment of C-arm Cone-beam CT source trajectories for artifact avoidance
In: International Journal of Computer Assisted Radiology and Surgery 15 (2020), p. 1787-1796
ISSN: 1861-6410
DOI: 10.1007/s11548-020-02249-1
BibTeX: Download

2019

Journal Articles

Thies M., Maier J., Eskofier B., Maier A., Levenston M., Gold G., Fahrig R.:
Automatic orientation estimation of inertial sensors in C-Arm CT Projections
In: Current Directions in Biomedical Engineering 5 (2019), p. 195-198
ISSN: 2364-5504
DOI: 10.1515/cdbme-2019-0050
BibTeX: Download

Student thesis

Type	Title	Status
MA thesis	Gradient-Based Automated Computed Tomography Geometry Correction	finished
MA thesis	Automated lung cancer lesions segmentation in 18F-FDG PET/CT	finished
MA thesis	Motion Compensation Using Epipolar Consistency Condition in Computed Tomography	finished

Mareike Thies, M. Sc.

Academic CV Academic CV

Projects Projects

2019

Advancing osteoporosis medicine by observing bone microstructure and remodelling using a four-dimensional nanoscope

Publications Publications

2025

Unpublished Publications

2024

Journal Articles

Conference Contributions

2023

Journal Articles

Book Contributions

Conference Contributions

2022

Journal Articles

Conference Contributions

2021

Journal Articles

2020

Journal Articles

2019

Journal Articles

Student thesis Student thesis

Academic CV

Projects

Publications

Student thesis