Prof. Dr.-Ing. Marc Aubreville

Researcher

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

Room 09.157
Martensstr. 3
91058 Erlangen

Phone number: +49 9131 85-27891
Fax number: +49 9131 85-27270
Email: marc.aubreville@fau.de
Website: https://lme.tf.fau.de/person/aubreville/

Curriculum vitae

Academic career:

Since 10/2020:
Research professor (Image understanding and medical application of AI) at Technische Hochschule Ingolstadt
05/2020-09/2020:
Post-doc at the pattern recognition lab.
08/2016 – 05/2020:
Researcher and PhD student at the pattern recognition lab. Main fields of interest include image processing and recognition of brightfield microscopy and confocal laser endomicroscopy images.
10/2003 – 11/2009:
Student (Electrical Engineering and Information Technology) at Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.
Focus topics: Biomedical engineering and signal processing.

Professional career:

04/2017-09/2020:
System architect, Sivantos GmbH, Erlangen, Germany
Interface design, technical coordination of projects, hearing aid system architecture development, requirements engineering
02/2010 – 03/2017:
R&D engineer in signal processing, Sivantos GmbH, Erlangen, Germany.
Development of hearing instrument signal processing algorithms, from prototyping (MATLAB/Simulink) to product implementation (fixpoint C++), firmware/hardware co-design, coordination of international research projects

Projects

2019

Deep Learning based Noise Reduction for Hearing Aids

(Third Party Funds Single)

Term: February 1, 2019 - January 31, 2023
Funding source: Industrie

Abstract

Reduction of unwanted environmental noises is an important feature of today’s hearing aids, which is why noise reduction is nowadays included in almost every commercially available device. The majority of these algorithms, however, is restricted to the reduction of stationary noises. Due to the large number of different background noises in daily situations, it is hard to heuristically cover the complete solution space of noise reduction schemes. Deep learning-based algorithms pose a possible solution to this dilemma, however, they sometimes lack robustness and applicability in the strict context of hearing aids.
In this project we investigate several deep learning.based methods for noise reduction under the constraints of modern hearing aids. This involves a low latency processing as well as the employing a hearing instrument-grade filter bank. Another important aim is the robustness of the developed methods. Therefore, the methods will be applied to real-world noise signals recorded with hearing instruments.

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2017

Digital Pathology - New Approaches to the Automated Image Analysis of Histologic Slides

(Own Funds)

Term: since January 16, 2017

Abstract

The pathologist is still the gold standard in the diagnosis of diseases in tissue slides. Due to its human nature, the pathologist is on one side able to flexibly adapt to the high morphological and technical variability of histologic slides but of limited objectivity due to cognitive and visual traps.

In diverse project we are applying and validating currently available tools and solutions in digital pathology but are also developing new solution in automated image analysis to complement and improve the pathologist especially in areas of quantitative image analysis.

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2014

Automatic classification and image analysis of confocal laser endomicroscopy images

(Own Funds)

Term: since October 1, 2014

Abstract

The goal of this project is to detect cancerous tissue in confocal lasermicroendoscopy (CLE) images of the oral cavity and the vocal cord. The current treatment of these diseases is a histological analysis of specimen and a surgical resection, which has a rather high long-term survival rate, or radiation therapy with a lower survival rate. An early detection of cancerous tissue could lead to a lowered complication rate for further treatment, as well as a better overall prognosis for patients. Further, an in-vivo diagnosis during operation could narrow down the area for the necessary surgical excision, which is especially beneficial for cancer of the vocal cords.

For this reason, we are applying methods of pattern recognition to facilitate and support diagnosis. We were able to show that these can be applied with high accuracies on CLE images.

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Publications

2021

Journal Articles

Marzahl C., Aubreville M., Bertram CA., Maier J., Bergler C., Kröger C., Voigt J., Breininger K., Klopfleisch R., Maier A.:
EXACT: a collaboration toolset for algorithm-aided annotation of images with annotation version control
In: Scientific Reports 11 (2021), Article No.: 4343
ISSN: 2045-2322
DOI: 10.1038/s41598-021-83827-4
BibTeX: Download
Sievert M., Oetter N., Aubreville M., Stelzle F., Maier A., Eckstein M., Mantsopoulos K., Gostian AO., Mueller SK., Koch M., Agaimy A., Iro H., Goncalves M.:
Feasibility of intraoperative assessment of safe surgical margins during laryngectomy with confocal laser endomicroscopy: A pilot study
In: Auris Nasus Larynx (2021)
ISSN: 0385-8146
DOI: 10.1016/j.anl.2021.01.005
BibTeX: Download

Conference Contributions

Marzahl C., Bertram CA., Aubreville M., Petrick A., Weiler K., Gläsel AC., Fragoso M., Merz S., Bartenschlager F., Hoppe J., Langenhagen A., Jasensky AK., Voigt J., Klopfleisch R., Maier A.:
Abstract: Are Fast Labeling Methods Reliable?: A Case Study of Computer-aided Expert Annotations on Microscopy Slides
German Workshop on Medical Image Computing, 2021 (Regensburg, March 7, 2021 - March 9, 2021)
In: Christoph Palm, Heinz Handels, Klaus Maier-Hein, Thomas M. Deserno, Andreas Maier, Thomas Tolxdorff (ed.): Informatik aktuell 2021
DOI: 10.1007/978-3-658-33198-6_71
BibTeX: Download
Marzahl C., Aubreville M., Bertram CA., Stayt J., Jasensky AK., Bartenschlager F., Fragoso M., Barton AK., Elsemann S., Jabari S., Krauth J., Madhu P., Voigt J., Hill J., Klopfleisch R., Maier A.:
Abstract: Deep Learning-based Quantification of Pulmonary Hemosiderophages in Cytology Slides
German Workshop on Medical Image Computing, 2021 (Regensburg, March 7, 2021 - March 9, 2021)
In: Christoph Palm, Heinz Handels, Klaus Maier-Hein, Thomas M. Deserno, Andreas Maier, Thomas Tolxdorff (ed.): Informatik aktuell 2021
DOI: 10.1007/978-3-658-33198-6_13
BibTeX: Download
Bertram CA., Donovan TA., Tecilla M., Bartenschlager F., Fragoso M., Wilm F., Marzahl C., Breininger K., Maier A., Klopfleisch R., Aubreville M.:
Dataset on Bi- and Multi-nucleated Tumor Cells in Canine Cutaneous Mast Cell Tumors
German Workshop on Medical Image Computing, 2021 (Regensburg, March 7, 2021 - March 9, 2021)
In: Christoph Palm, Heinz Handels, Klaus Maier-Hein, Thomas M. Deserno, Andreas Maier, Thomas Tolxdorff (ed.): Informatik aktuell 2021
DOI: 10.1007/978-3-658-33198-6_33
BibTeX: Download
Wilm F., Bertram CA., Marzahl C., Bartel A., Donovan TA., Assenmacher CA., Becker K., Bennett M., Corner S., Cossic B., Denk D., Dettwiler M., Gonzalez BG., Gurtner C., Heier A., Lehmbecker A., Merz S., Plog S., Schmidt A., Sebastian F., Smedley RC., Tecilla M., Thaiwong T., Breininger K., Kiupel M., Maier A., Klopfleisch R., Aubreville M.:
Influence of Inter-Annotator Variability on Automatic Mitotic Figure Assessment
German Workshop on Medical Image Computing, 2021 (Regensburg, March 7, 2021 - March 9, 2021)
In: Christoph Palm, Heinz Handels, Klaus Maier-Hein, Thomas M. Deserno, Andreas Maier, Thomas Tolxdorff (ed.): Informatik aktuell 2021
DOI: 10.1007/978-3-658-33198-6_56
BibTeX: Download

2020

Journal Articles

Bertram CA., Aubreville M., Gurtner C., Bartel A., Corner SM., Dettwiler M., Kershaw O., Noland EL., Schmidt A., Sledge DD., Smedley RC., Thaiwong T., Kiupel M., Maier A., Klopfleisch R.:
Computerized Calculation of Mitotic Count Distribution in Canine Cutaneous Mast Cell Tumor Sections: Mitotic Count Is Area Dependent
In: Veterinary Pathology 57 (2020), p. 214-226
ISSN: 0300-9858
DOI: 10.1177/0300985819890686
URL: https://journals.sagepub.com/doi/10.1177/0300985819890686
BibTeX: Download
Aubreville M., Bertram CA., Donovan TA., Marzahl C., Maier A., Klopfleisch R.:
A completely annotated whole slide image dataset of canine breast cancer to aid human breast cancer research
In: Scientific Data 7 (2020), Article No.: 417
ISSN: 2052-4463
DOI: 10.1038/s41597-020-00756-z
BibTeX: Download
Aubreville M., Bertram CA., Marzahl C., Gurtner C., Dettwiler M., Schmidt A., Bartenschlager F., Merz S., Fragoso M., Kershaw O., Klopfleisch R., Maier A.:
Deep learning algorithms out-perform veterinary pathologists in detecting the mitotically most active tumor region
In: Scientific Reports 10 (2020), Article No.: 16447
ISSN: 2045-2322
DOI: 10.1038/s41598-020-73246-2
BibTeX: Download
Marzahl C., Aubreville M., Bertram CA., Stayt J., Jasensky AK., Bartenschlager F., Fragoso-Garcia M., Barton AK., Elsemann S., Jabari S., Krauth J., Madhu P., Voigt J., Hill J., Klopfleisch R., Maier A.:
Deep Learning-Based Quantification of Pulmonary Hemosiderophages in Cytology Slides
In: Scientific Reports 10 (2020), Article No.: 9795
ISSN: 2045-2322
DOI: 10.1038/s41598-020-65958-2
BibTeX: Download

Book Contributions

Aubreville M., Bertram CA., Jabari S., Marzahl C., Klopfleisch R., Maier A.:
Inter-Species, Inter-Tissue Domain Adaptation for Mitotic Figure Assessment - Learning New Tricks from Old Dogs
In: Tolxdorff T., Deserno T., Handels H., Maier A., Maier-Hein K., Palm C. (ed.): Bildverarbeitung für die Medizin 2020, Wiesbaden: Springer Vieweg, 2020, p. 1-7
ISBN: 9783658292669
DOI: 10.1007/978-3-658-29267-6_1
URL: https://arxiv.org/pdf/1911.10873.pdf
BibTeX: Download

Conference Contributions

Schröter H., Rosenkranz T., Escalante Banuelos A., Aubreville M., Maier A.:
CLCNet: Deep learning-based noise reduction for hearing aids using complex linear coding
IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) (Barcelona, May 4, 2020 - May 8, 2020)
In: ICASSP 2020-2020 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) 2020
DOI: 10.1109/icassp40776.2020.9053563
URL: https://rikorose.github.io/CLCNet-audio-samples.github.io/
BibTeX: Download
Bertram CA., Aubreville M., Marzahl C., Maier A., Klopfleisch R.:
How Big is Big Enough?: A Large-Scale Histological Dataset of Mitotic Figures
Bildverarbeitung für die Medizin 2020 (Berlin, March 17, 2020 - March 19, 2020)
In: Tolxdorff T., Deserno T., Handels H., Maier A., Maier-Hein K., Palm C. (ed.): Bildverarbeitung für die Medizin 2020, Wiesbaden: 2020
DOI: 10.1007/978-3-658-29267-6_65
URL: https://link.springer.com/content/pdf/10.1007/978-3-658-29267-6_65.pdf
BibTeX: Download
Marzahl C., Bertram CA., Aubreville M., Petrick A., Weiler K., Gläsel AC., Fragoso M., Merz S., Bartenschlager F., Hoppe J., Langenhagen A., Jasensky AK., Voigt J., Klopfleisch R., Maier A.:
Are fast labeling methods reliable? a case study of computer-aided expert annotations on microscopy slides
23rd International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2020 (Lima, October 4, 2020 - October 8, 2020)
In: Anne L. Martel, Purang Abolmaesumi, Danail Stoyanov, Diana Mateus, Maria A. Zuluaga, S. Kevin Zhou, Daniel Racoceanu, Leo Joskowicz (ed.): Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2020
DOI: 10.1007/978-3-030-59710-8_3
BibTeX: Download
Bertram CA., Veta M., Marzahl C., Stathonikos N., Maier A., Klopfleisch R., Aubreville M.:
Are Pathologist-Defined Labels Reproducible? Comparison of the TUPAC16 Mitotic Figure Dataset with an Alternative Set of Labels
IMIMIC 2020, MIL3ID 2020, LABELS 2020 (Lima, October 4, 2020 - October 8, 2020)
In: Jaime Cardoso, Wilson Silva, Ricardo Cruz, Hien Van Nguyen, Badri Roysam, Nicholas Heller, Pedro Henriques Abreu, Jose Pereira Amorim, Ivana Isgum, Vishal Patel, Kevin Zhou, Steve Jiang, Ngan Le, Khoa Luu, Raphael Sznitman, Veronika Cheplygina, Samaneh Abbasi, Diana Mateus, Emanuele Trucco (ed.): Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2020
DOI: 10.1007/978-3-030-61166-8_22
BibTeX: Download
Marzahl C., Aubreville M., Bertram CA., Gerlach S., Maier J., Voigt J., Hill J., Klopfleisch R., Maier A.:
Is crowd-algorithm collaboration an advanced alternative to crowd-sourcing on cytology slides?
International workshop on Algorithmen - Systeme - Anwendungen, 2020 (Berlin, March 15, 2020 - March 17, 2020)
In: Thomas Tolxdorff, Thomas M. Deserno, Heinz Handels, Andreas Maier, Klaus H. Maier-Hein, Christoph Palm (ed.): Informatik aktuell 2020
DOI: 10.1007/978-3-658-29267-6_5
BibTeX: Download

Thesis

Aubreville M.:
Computer-Aided Tumor Diagnosis of Microscopy Images (Dissertation, 2020)
URL: https://opus4.kobv.de/opus4-fau/frontdoor/index/index/docId/13755
BibTeX: Download

2019

Journal Articles

Bertram CA., Aubreville M., Marzahl C., Maier A., Klopfleisch R.:
A large-scale dataset for mitotic figure assessment on whole slide images of canine cutaneous mast cell tumor
In: Scientific Data 6 (2019), p. 1-9
ISSN: 2052-4463
DOI: 10.1038/s41597-019-0290-4
URL: https://www.nature.com/articles/s41597-019-0290-4.pdf
BibTeX: Download
Goncalves M., Aubreville M., Mueller SK., Sievert M., Maier A., Iro H., Bohr C.:
Probe-based confocal laser endomicroscopy in detecting malignant lesions of vocal folds.
In: Acta Otorhinolaryngologica Italica (2019)
ISSN: 0392-100X
DOI: 10.14639/0392-100X-2121
BibTeX: Download
Aubreville M., Stöve M., Oetter N., Goncalves M., Knipfer C., Neumann H., Bohr C., Stelzle F., Maier A.:
Deep learning-based detection of motion artifacts in probe-based confocal laser endomicroscopy images.
In: International Journal of Computer Assisted Radiology and Surgery 14 (2019), p. 31-42
ISSN: 1861-6410
DOI: 10.1007/s11548-018-1836-1
BibTeX: Download

Book Contributions

Marzahl C., Aubreville M., Voigt J., Maier A.:
Classification of leukemic B-Lymphoblast cells from blood smear microscopic images with an attention-based deep learning method and advanced augmentation techniques
In: Anubha Gupta, Ritu Gupta (ed.): ISBI 2019 C-NMC Challenge: Classification in Cancer Cell Imaging, Springer, 2019, p. 13-22 (Lecture Notes in Bioengineering)
DOI: 10.1007/978-981-15-0798-4_2
BibTeX: Download

Conference Contributions

Aubreville M., Bertram CA., Klopfleisch R., Maier A.:
Field of Interest Proposal for Augmented Mitotic Cell Count: Comparison of Two Convolutional Networks
BIOSTEC/BIOIMAGING 2019 (Prague, February 22, 2019 - February 24, 2019)
In: SciTePress (ed.): Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 2: BIOIMAGING 2019
DOI: 10.5220/0007365700300037
URL: http://www.scitepress.org/PublicationsDetail.aspx?ID=t/vdV3xX7x0=&t=1
BibTeX: Download
Aubreville M., Bertram CA., Klopfleisch R., Maier A.:
Augmented Mitotic Cell Count Using Field of Interest Proposal
Workshop on Bildverarbeitung fur die Medizin, 2019 (Lübeck, March 17, 2019 - March 19, 2019)
In: Thomas M. Deserno, Andreas Maier, Christoph Palm, Heinz Handels, Klaus H. Maier-Hein, Thomas Tolxdorff (ed.): Informatik aktuell 2019
DOI: 10.1007/978-3-658-25326-4_71
BibTeX: Download
Aubreville M., Goncalves M., Knipfer C., Oetter N., Würfl T., Neumann H., Stelzle F., Bohr C., Maier A.:
Transferability of Deep Learning Algorithms for Malignancy Detection in Confocal Laser Endomicroscopy Images from Different Anatomical Locations of the Upper Gastrointestinal Tract
11th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2018 (Funchal, January 19, 2018 - January 21, 2018)
In: Sergi Bermúdez i Badia, Alberto Cliquet, Sheldon Wiebe, Reyer Zwiggelaar, Paul Anderson, Ana Fred, Hugo Gamboa, Giovanni Saggio (ed.): Communications in Computer and Information Science 2019
DOI: 10.1007/978-3-030-29196-9_4
BibTeX: Download

2018

Book Contributions

Mualla F., Aubreville M., Maier A.:
Microscopy
In: Medical Imaging Systems: An Introductory Guide, Cham: Springer, 2018, p. 69-90 (Lecture Notes in Computer Science book series (LNCS), Vol.11111)
ISBN: 978-3-319-96520-8
DOI: 10.1007/978-3-319-96520-8_5
BibTeX: Download

Conference Contributions

Aubreville M., Goncalves M., Knipfer C., Oetter N., Würfl T., Neumann H., Stelzle F., Bohr C., Maier A.:
Patch-based Carcinoma Detection on Confocal Laser Endomicroscopy Images - A Cross-Site Robustness Assessment
BIOIMAGING 2018 (Funchal, January 19, 2018 - January 21, 2018)
In: Sheldon Wiebe, Hugo Gamboa,Ana Fred, Sergi Bermúdez i Badia (ed.): Proceedings of the 11th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2018) 2018
DOI: 10.5220/0006534700270034
URL: http://www.scitepress.org/DigitalLibrary/Link.aspx?doi=10.5220/0006534700270034
BibTeX: Download
Krappmann M., Aubreville M., Bertram CA., Klopfleisch R., Maier A.:
Classification of Mitotic Cells - Potentials Beyond the Limits of Small Data Sets
Bildverarbeitung für die Medizin 2018 (Erlangen, Germany, March 11, 2018 - March 13, 2018)
In: Bildverarbeitung für die Medizin 2018. Informatik aktuell, Berlin, Heidelberg: 2018
DOI: 10.1007/978-3-662-56537-7_66
URL: https://www5.informatik.uni-erlangen.de/Forschung/Publikationen/2018/Krappmann18-COM.pdf
BibTeX: Download
Steffes LM., Aubreville M., Sesselmann S., Krenn V., Maier A.:
Classification of Polyethylene Particles and the Local CD3+ Lymphocytosis in Histological Slice Images
Bildverarbeitung für die Medizin 2018 (Erlangen)
In: Bildverarbeitung für die Medizin 2018. Algorithmen - Systeme - Anwendungen. Proceedings des Workshops vom 11. bis 13. März 2018 in Erlangen, Springer: 2018
DOI: 10.1007/978-3-662-56537-7_63
URL: https://www5.informatik.uni-erlangen.de/Forschung/Publikationen/2018/Steffes18-COP.pdf
BibTeX: Download
Aubreville M., Ehrensperger K., Rosenkranz T., Graf B., Puder H., Maier A.:
Deep Denoising for Hearing Aid Applications
16th International Workshop on Acoustic Signal Enhancement (IWAENC) (Tokyo, JAPAN, September 17, 2018 - September 20, 2018)
In: 2018 16TH INTERNATIONAL WORKSHOP ON ACOUSTIC SIGNAL ENHANCEMENT (IWAENC), NEW YORK: 2018
DOI: 10.1109/iwaenc.2018.8521369
BibTeX: Download
Stöve M., Aubreville M., Oetter N., Knipfer C., Neumann H., Stelzle F., Maier A.:
Motion Artifact Detection in Confocal Laser Endomicroscopy Images
Bildverarbeitung für die Medizin 2018 (Erlangen, Germany, March 11, 2018 - March 13, 2018)
In: Bildverarbeitung für die Medizin 2018. Informatik aktuell., Berlin, Heidelberg: 2018
DOI: 10.1007/978-3-662-56537-7_85
URL: https://www5.informatik.uni-erlangen.de/Forschung/Publikationen/2018/Stoeve18-MAD.pdf
BibTeX: Download
Aubreville M., Bertram CA., Klopfleisch R., Maier A.:
SlideRunner - A Tool for Massive Cell Annotations in Whole Slide Images
Bildverarbeitung für die Medizin 2018 (Erlangen, March 11, 2018 - March 13, 2018)
In: Bildverarbeitung für die Medizin 2018 - Algorithmen - Systeme - Anwendungen. Proceedings des Workshops vom 11. bis 13. März 2018 in Erlangen 2018
DOI: 10.1007/978-3-662-56537-7_81
URL: https://www5.informatik.uni-erlangen.de/Forschung/Publikationen/2018/Aubreville18-S-A.pdf
BibTeX: Download

2017

Journal Articles

Aubreville M., Knipfer C., Oetter N., Jaremenko C., Rodner E., Denzler J., Bohr C., Neumann H., Stelzle F., Maier A.:
Automatic Classification of Cancerous Tissue in Laserendomicroscopy Images of the Oral Cavity using Deep Learning
In: Scientific Reports 7 (2017), p. s41598-017
ISSN: 2045-2322
DOI: 10.1038/s41598-017-12320-8
URL: https://www.nature.com/articles/s41598-017-12320-8.pdf
BibTeX: Download

Conference Contributions

Aubreville M., Krappmann M., Bertram C., Klopfleisch R., Maier A.:
A Guided Spatial Transformer Network for Histology Cell Differentiation
Eurographics Workshop on Visual Computing for Biology and Medicine (Bremen, September 7, 2017 - September 8, 2017)
In: Stefan Bruckner, Anja Hennemuth, Bernhard Kainz, Ingrid Hotz, Dorit Merhof and Christian Rieder (ed.): Eurographics Workshop on Visual Computing for Biology and Medicine 2017
DOI: 10.2312/vcbm.20171233
URL: https://arxiv.org/pdf/1707.08525.pdf
BibTeX: Download

Lectures

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Prof. Dr.-Ing. Marc Aubreville

Prof. Dr.-Ing. Marc Aubreville

Curriculum vitae Curriculum vitae

Projects Projects

2019

Deep Learning based Noise Reduction for Hearing Aids

2017

Digital Pathology - New Approaches to the Automated Image Analysis of Histologic Slides

2014

Automatic classification and image analysis of confocal laser endomicroscopy images

Publications Publications

2021

Journal Articles

Conference Contributions

2020

Journal Articles

Book Contributions

Conference Contributions

Thesis

2019

Journal Articles

Book Contributions

Conference Contributions

2018

Book Contributions

Conference Contributions

2017

Journal Articles

Conference Contributions

Lectures Lectures

Curriculum vitae

Projects

Publications

Lectures