Fabian Wagner

Dr.-Ing. Fabian Wagner

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: fabian.wagner@fau.de
Website: https://lme.tf.fau.de/person/wagner/

You are working with noisy image data? Try out our open-source, fully Trainable Bilateral Filter Layer (PyTorch) to get rid of noise. It only adds FOUR trainable parameters to your network and you can integrate it in your model the same way as any convolutional layer.

Academic CV

10/2020 – 12/2023:
Ph.D. Student at Pattern Recognition Lab, FAU Erlangen-Nürnberg
01/2019 – 01/2020:
Master’s thesis at Northwestern University, Illinois and University of Wisconsin-Madison
10/2014 – 09/2020:
B. Sc. and M. Sc. Physics, FAU Erlangen-Nürnberg

Projects

Robust and interpretable low-dose CT denoising in context of the 4D+nanoSCOPE:

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

Journal Articles

Lee W., Wagner F., Galdran A., Shi Y., Xia W., Wang G., Mou X., Ahamed MA., Imran AAZ., Oh JE., Kim K., Baek JT., Lee D., Hong B., Tempelman P., Lyu D., Kuiper A., van Blokland L., Calisto MB., Hsieh S., Han M., Baek J., Maier A., Wang A., Gold GE., Choi JH.:
Low-dose computed tomography perceptual image quality assessment
In: Medical Image Analysis 99 (2025), Article No.: 103343
ISSN: 1361-8415
DOI: 10.1016/j.media.2024.103343
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

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
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

Pfaff L., Hoßbach J., Preuhs E., Wagner F., Arroyo Camejo S., Kannengiesser S., Nickel D., Wuerfl T., Maier A.:
Self-supervised MRI denoising: leveraging Stein’s unbiased risk estimator and spatially resolved noise maps
In: Scientific Reports 13 (2023), Article No.: 22629
ISSN: 2045-2322
DOI: 10.1038/s41598-023-49023-2
BibTeX: Download
Fan F., Ritschl L., Beister M., Biniazan R., Wagner F., Kreher BW., Gottschalk T., Kappler S., Maier A.:
Simulation-driven training of vision transformers enables metal artifact reduction of highly truncated CBCT scans
In: Medical Physics (2023)
ISSN: 0094-2405
DOI: 10.1002/mp.16919
BibTeX: Download
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

Conference Contributions

Denzinger F., Wels M., Taubmann O., Kordon F., Wagner F., Mehltretter S., Gülsün MA., Schöbinger M., André F., Buß SJ., Görich J., Sühling M., Maier A., Breininger K.:
Handling Label Uncertainty on the Example of Automatic Detection of Shepherd’s Crook RCA in Coronary CT Angiography
2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI) (Cartagena, April 18, 2023 - April 21, 2023)
In: Proceedings - International Symposium on Biomedical Imaging 2023
DOI: 10.1109/ISBI53787.2023.10230565
BibTeX: Download
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
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
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., Nickel MD., Wuerfl T., Maier A.:
Quantitative evaluation of denoising algorithms without noise-free ground-truth data
ISMRM
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
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
Pfaff L., Wagner F., Hoßbach J., Preuhs E., Gadjimuradov F., Benkert T., Nickel MD., Wuerfl T., Maier A.:
Unsupervised denoising of prostate DWI
ISMRM
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

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

Wagner F., Schiffers F., Willomitzer F., Cossairt O., Velten A.:
Intensity interferometry-based 3D imaging
In: Optics Express 29 (2021), p. 4733-4745
ISSN: 1094-4087
DOI: 10.1364/OE.412688
BibTeX: Download

Conference Contributions

Huang Y., Mill L., Stoll R., Kling L., Aust O., Wagner F., Grüneboom A., Schett G., Christiansen SH., Maier A.:
Semi-Permeable Filters for Interior Region of Interest Dose Reduction in X-Ray Microscopy
BVM 2021 (Regensburg, March 7, 2021 - March 9, 2021)
In: Bildverarbeitung für die Medizin 2021
DOI: 10.1007/978-3-658-33198-6_16
URL: https://link.springer.com/chapter/10.1007/978-3-658-33198-6_16
BibTeX: Download

2020

Journal Articles

Boolakee T., Heide C., Wagner F., Ott C., Schlecht MT., Ristein J., Weber HB., Hommelhoff P.:
Length-dependence of light-induced currents in graphene
In: Journal of Physics B-Atomic Molecular and Optical Physics (2020)
ISSN: 0953-4075
DOI: 10.1088/1361-6455/ab9075
URL: https://iopscience.iop.org/article/10.1088/1361-6455/ab9075
BibTeX: Download

Conference Contributions

Wagner F., Schiffers F., Willomitzer F., Cossairt O., Velten A.:
Intensity interferometry-based depth ranging
Computational Optical Sensing and Imaging 2020
DOI: 10.1364/COSI.2020.CTh3C.5
BibTeX: Download

Lectures

Projekt Flat-Panel CT Reconstruction (ProjFCR): Do 10:00 – 12:00, 2 SWS (5 ECTS)

Student theses

Type	Title	Status
BA thesis	Statistical Assessment of Deep Neural Networks in Industrial Applications	finished
MA thesis	Diffusion-based Super Resolution for X-ray Microscopy	finished
MA thesis	Classification of Detector Artifacts in Angiographic Imaging using Neural Networks	finished
Project	Super-short Scans in Bone XRM Acquisitions	finished
Project	Sparse-angle CT Super Resolution using Known Operators	finished
Project	Deep Learning-based XRM Projection Super Resolution	finished
Project	Unsupervised Super Resolution in X-ray Microscopy Using a Cycle-Consistent Generative Model	finished
MA thesis	Learning-based reduction of non-significant changes in subtraction volumes	finished
MA thesis	Micro CT Denoising Using Low Parameter Models	finished

Dr.-Ing. Fabian Wagner

Academic CV Academic CV

Projects Projects

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

Publications Publications

2025

Journal Articles

2024

Journal Articles

Conference Contributions

2023

Journal Articles

Conference Contributions

2022

Journal Articles

Conference Contributions

2021

Journal Articles

Conference Contributions

2020

Journal Articles

Conference Contributions

Lectures Lectures

Student theses Student theses

Academic CV

Projects

Publications

Lectures

Student theses