Christian Marzahl

Christian Marzahl, M. Sc.

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: christian.marzahl@fau.de
Website: https://lme.tf.fau.de/person/marzahl/

Office hours

Daily Mo, Tu, We, Th, Fr, Room 9.157,

Academic CV

Since 04/2019:
Department of Computer Science

Projects

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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Publications

2023

Journal Articles

Aubreville M., Stathonikos N., Bertram CA., Klopfleisch R., ter Hoeve N., Ciompi F., Wilm F., Marzahl C., Donovan TA., Maier A., Breen J., Ravikumar N., Chung Y., Park J., Nateghi R., Pourakpour F., Fick RH., Ben Hadj S., Jahanifar M., Shephard A., Dexl J., Wittenberg T., Kondo S., Lafarge MW., Koelzer VH., Liang J., Wang Y., Long X., Liu J., Razavi S., Khademi A., Yang S., Wang X., Erber R., Klang A., Lipnik K., Bolfa P., Dark MJ., Wasinger G., Veta M., Breininger K.:
Mitosis domain generalization in histopathology images — The MIDOG challenge
In: Medical Image Analysis 84 (2023), Article No.: 102699
ISSN: 1361-8415
DOI: 10.1016/j.media.2022.102699
BibTeX: Download

2022

Journal Articles

Wilm F., Fragoso M., Marzahl C., Qiu J., Puget C., Diehl L., Bertram CA., Klopfleisch R., Maier A., Breininger K., Aubreville M.:
Pan-tumor CAnine cuTaneous Cancer Histology (CATCH) dataset
In: Scientific Data 9 (2022), Article No.: 588
ISSN: 2052-4463
DOI: 10.1038/s41597-022-01692-w
BibTeX: Download
Marzahl C., Hill J., Stayt J., Bienzle D., Welker L., Wilm F., Voigt J., Aubreville M., Maier A., Klopfleisch R., Breininger K., Bertram CA.:
Inter-species cell detection - datasets on pulmonary hemosiderophages in equine, human and feline specimens
In: Scientific Data 9 (2022)
ISSN: 2052-4463
DOI: 10.1038/s41597-022-01389-0
BibTeX: Download
Bertram CA., Aubreville M., Donovan TA., Bartel A., Wilm F., Marzahl C., Assenmacher CA., Becker K., Bennett M., Corner S., Cossic B., Denk D., Dettwiler M., Gonzalez BG., Gurtner C., Haverkamp AK., Heier A., Lehmbecker A., Merz S., Noland EL., Plog S., Schmidt A., Sebastian F., Sledge DG., Smedley RC., Tecilla M., Thaiwong T., Fuchs-Baumgartinger A., Meuten DJ., Breininger K., Kiupel M., Maier A., Klopfleisch R.:
Computer-assisted mitotic count using a deep learning–based algorithm improves interobserver reproducibility and accuracy
In: Veterinary Pathology 59 (2022), p. 211-226
ISSN: 0300-9858
DOI: 10.1177/03009858211067478
BibTeX: Download
Bertram CA., Aubreville M., Donovan TA., Bartel A., Wilm F., Marzahl C., Assenmacher CA., Becker K., Bennett M., Corner S., Cossic B., Denk D., Dettwiler M., Gonzalez BG., Gurtner C., Haverkamp AK., Heier A., Lehmbecker A., Merz S., Noland EL., Plog S., Schmidt A., Sebastian F., Sledge DG., Smedley RC., Tecilla M., Thaiwong T., Fuchs-Baumgartinger A., Meuten DJ., Breininger K., Kiupel M., Maier A., Klopfleisch R.:
Computer Assistance: A New Gold Standard for the Mitotic Count?
In: Journal of Comparative Pathology 191 (2022)
ISSN: 0021-9975
BibTeX: Download
Bertram CA., Marzahl C., Bartel A., Stayt J., Bonsembiante F., Beeler-Marfisi J., Barton AK., Brocca G., Gelain ME., Glasel A., Du Preez K., Weiler K., Weissenbacher-Lang C., Breininger K., Aubreville M., Maier A., Klopfleisch R., Hill J.:
Cytologic scoring of equine exercise-induced pulmonary hemorrhage: Performance of human experts and a deep learning-based algorithm
In: Veterinary Pathology (2022)
ISSN: 0300-9858
DOI: 10.1177/03009858221137582
BibTeX: Download

Conference Contributions

Kunzmann S., Marzahl C., Denzinger F., Bertram C., Klopfleisch R., Breininger K., Christlein V., Maier A.:
First Steps on Gamification of Lung Fluid Cells Annotations in the Flower Domain
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_48
BibTeX: Download
Öttl M., Mönius J., Marzahl C., Rübner M., Geppert CI., Hartmann A., Beckmann M., Fasching P., Maier A., Erber R., Breininger K.:
Superpixel Pre-segmentation of HER2 Slides for Efficient Annotation
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_54
BibTeX: Download
Wilm F., Marzahl C., Breininger K., Aubreville M.:
Domain Adversarial RetinaNet as a Reference Algorithm for the MItosis DOmain Generalization Challenge
24th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2021 (Strasbourg, FRA, September 27, 2021 - October 1, 2021)
In: Marc Aubreville, David Zimmerer, Mattias Heinrich (ed.): Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2022
DOI: 10.1007/978-3-030-97281-3_1
BibTeX: Download

Thesis

Marzahl C.:
Deep Learning-based Cell Detection in Microscopy Images (Dissertation, 2022)
URL: https://opus4.kobv.de/opus4-fau/frontdoor/index/index/docId/18234
BibTeX: Download

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

Conference Contributions

Marzahl C., Wilm F., Dressler FF., Tharun L., Perner S., Bertram CA., Kröger C., Voigt J., Klopfleisch R., Maier A., Aubreville M., Breininger K.:
Robust Quad-Tree based Registration on Whole Slide Images
MICCAI Computational Pathlogy (COMPAY) Workshop
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.:
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
Aubreville M., Bertram CA., Marzahl C., Gurtner C., Dettwiler M., Schmidt A., Bartenschlager F., Merz S., Fragoso M., Kershaw O., Klopeisch R., Maier A.:
Abstract: Deep Learning Algorithms Out-perform Veterinary Pathologists in Detecting the Mitotically Most Active Tumor Region
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_60
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
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
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_48
BibTeX: Download
Marzahl C., Bertram CA., Wilm F., Voigt J., Barton AK., Klopfleisch R., Breininger K., Maier A., Aubreville M.:
Cell Detection for Asthma on Partially Annotated Whole Slide Images: Learning to be EXACT
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_36
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
Theelke L., Wilm F., Marzahl C., Bertram CA., Klopfleisch R., Maier A., Aubreville M., Breininger K.:
Iterative Cross-Scanner Registration for Whole Slide Images
IEEE/CVF International Conference on Computer Vision (ICCVW)
In: 2021 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW 2021), LOS ALAMITOS: 2021
DOI: 10.1109/ICCVW54120.2021.00071
BibTeX: Download

2020

Journal Articles

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

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
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
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

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

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

Lectures

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Christian Marzahl

Christian Marzahl, M. Sc.

Office hours

Academic CV Academic CV

Projects Projects

2017

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

Publications Publications

2023

Journal Articles

2022

Journal Articles

Conference Contributions

Thesis

2021

Journal Articles

Conference Contributions

2020

Journal Articles

Book Contributions

Conference Contributions

2019

Journal Articles

Book Contributions

Lectures Lectures

Academic CV

Projects

Publications

Lectures