Jun.-Prof. Dr.-Ing.

Johannes Stegmaier

Juniorprofessor

 105
 +49 241 80 22901
 +49 241 80 22200
 Johannes.Stegmaier@lfb.rwth-aachen.de



Curriculum Vitae

04/2018 – jetzt Juniorprofessor (W1) für biomedizinische Bildverarbeitung, RWTH Aachen
10/2016 – 01/2017 Postdoc am Center for Advanced Methods in Biological Image Analysis, Caltech, CA, USA
02/2015 – 12/2017 Postdoc am Institut für Angewandte Informatik, Karlsruher Institut für Technologie
06/2016 Promotion (Dr.-Ing.) an der Fakultät für Maschinenbau am Karlsruher Institut für Technologie. Dissertation: “New Methods to Improve Large-Scale Microscopy Image Analysis with Prior Knowledge and Uncertainty”
01/2014 – 05/2014 Short Term Scholar am Janelia Research Campus, Ashburn, VA, USA
02/2012 – 01/2015 Wissenschaftlicher Mitarbeiter am Institut für Angewandte Informatik, Karlsruher Institut für Technologie
10/2009 – 12/2011 Master of Science in Bioinformatik und Systembiologie, Albert-Ludwidgs-Universität Freiburg i. Br.
10/2006 – 09/2009 Bachelor of Science in Bioinformatik an der Eberhard-Karls-Universität Tübingen

Publications

Books and Book Chapters

2018
V. Bedell, E. Buglo, D. Marcato, C. Pylatiuk, R. Mikut, J. Stegmaier, W. Scudder, M. Wray, S. Züchner, U. Strähle, R. Peravali, J. E. Dallman
Zebrafish: A Pharmacogenetic Model for Anesthesia
In: Methods in Enzymology

 

2016
J. Stegmaier
New Methods to Improve Large-Scale Microscopy Image Analysis with Prior Knowledge and Uncertainty
In: KIT Scientific Publishing

 

 

Journal Publications

2019

M. Grösche, A. E. Zoheir, J. Stegmaier, R. Mikut, D. Mager, J. G. Korvink, K. S. Rabe and C. M. Niemeyer
Microfluidic Chips for Life Sciences—A Comparison of Low Entry Manufacturing Technologies
In: Small

2019

V. Gerber, L. Yang, M. Takamiya, V. Ribes, V. Gourain, R. Peravali, J. Stegmaier, R. Mikut, M. Reischl, M. Ferg, U. Strähle
The HMG Box Transcription Factors Sox1a and Sox1b Specify a New Class of Glycinergic Interneuron in the Spinal Cord of Zebrafish Embryos
In: Development 146 (4)

2019

A. Bartschat, S. Allgeier, T. Scherr, J. Stegmaier, S. Bohnand an K.-M. Reichert, A. Kuijper, M. Reischl, O. Stachs, B. Köhler, R. Mikut
Fuzzy Tissue Detection for Real-Time Focal Control in Corneal Confocal Microscopy
In: at Automatisierungstechnik

2018

B. Mattes, Y. Dang, G. Greicius, L. T. Kaufmann, S. Özbek, B. Prunsche, J. Rosenbauer, J. Stegmaier, R. Mikut, G. U. Nienhaus, A. Schug, D. M. Virshup, S. Scholpp
Wnt/PCP Controls Spreading of Wnt/b-Catenin Signals by Cytonemes in Vertebrates
In: eLife

2018

H. M. T. Choi, M. Schwarzkopf, M. E. Fornace, A. Acharya, G. Artavanis, J. Stegmaier, A. Cunha, N. A. Pierce
Third-Generation In Situ Hybridization Chain Reaction: Multiplexed, Quantitative, Sensitive, Versatile, Robust
In: Development

2018

B. Schott, M. Traub, C. Schlagenhauf, M. Takamiya, T. Antritter, A. Bartschat, K. Löffler, D. Blessing, J. C. Otte, A. Y. Kobitski, G. U. Nienhaus, U. Strähle, R. Mikut, J. Stegmaier
EmbryoMiner: A New Framework for Interactive Knowledge Discovery in Large-Scale Cell Tracking Data of Developing Embryos
In: PLOS Computational Biology 14 (4)

2017

J. Stegmaier, R. Mikut
Fuzzy-based Propagation of Prior Knowledge to Improve Large-Scale Image Analysis Pipelines
In: PLOS ONE

 

2017
V. Ulman, M. Maska, K. Magnusson, O. Ronneberger, C. Haubold, N. Harder, P. Matula, P. Matula, D. Svoboda, M. Radojevic, I. Smal, K. Rohr, J. Jaldén, H. Blau, O. Dzyubachyk, B. Lelieveldt, P. Xiao, Y. Li, S. Cho, A. Dufour, J. Olivo-Marin, C. Reyes-Aldasoro, J. Solis-Lemus, R. Bensch, T. Brox, J. Stegmaier, R. Mikut, S. Wolf, F. Hamprecht, T. Esteves, P. Quelhas, Ö. Demirel, L. Malmström, F. Jug, P. Tomancak, E. Meijering, A. Munoz-Barrutia, M. Kozubek, C. Ortiz-de-Solorzano
An Objective Comparison of Cell Tracking Algorithms
In: Nature Methods

 

2017
C. Etard, S. Joshi, J. Stegmaier, R. Mikut, U. Strähle
TIDE is a Simple and Effective Method to Assess Efficiency of Guide RNAs in Zebrafish
In: Zebrafish

 

2016
J. Stegmaier, B. Schott, E. Hübner, M. Traub, M. Shahid, M. Takamiya, A. Kobitski, V. Hartmann, R. Stotzka, J. v. Wezel, A. Streit, G. U. Nienhaus, U. Strähle, M. Reischl, R. Mikut
Automation Strategies for Large-Scale 3D Image Analysis
In: at-Automatisierungstechnik

 

2016
M. Shahid, M. Takamiya, J. Stegmaier, V. Middel, N. Klüver, R. Mikut, S. Rastegar, S. Scholz, T. Dickmeis, L. Yang, U. Strähle
Zebrafish Biosensor for Toxicant Induced Muscle Hyperactivity
In: Scientific Reports

 

2016
J. Stegmaier, F. Amat, B. Lemon, K. McDole, Y. Wan, G. Teodoro, R. Mikut, P. J. Keller
Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos
In: Developmental Cell

 

2016
A. Bartschat, E. Hübner, M. Reischl, R. Mikut, J. Stegmaier
XPIWIT – An XML Pipeline Wrapper for the Insight Toolkit
In: Bioinformatics

 

2015
A. Kobitski, J. C. Otte, M. Takamiya, B. Schäfer, J. Mertes, J. Stegmaier, S. Rastegar, F. Rindone, V. Hartmann, R. Stotzka, A. García, J. v. Wezel, R. Mikut, U. Strähle, G. U. Nienhaus
An Ensemble-Averaged Digital Model of Zebrafish Embryo Development based on High-Speed Light-Sheet Microscopy at Single-Cell Resolution
In: Scientific Reports

 

2014
J. Stegmaier, J. C. Otte, A. Kobitski, A. Bartschat, A. Garcia, G. U. Nienhaus, U. Strähle, R. Mikut
Fast Segmentation of Stained Nuclei in Terabyte-Scale, Time Resolved 3D Microscopy Image Stacks
In: PLOS ONE

 

2014
J. Stegmaier, M. Shahid, M. Takamiya, L. Yang, S. Rastegar, M. Reischl, U. Strähle, R. Mikut
Automated Prior Knowledge-Based Quantification of Neuronal Patterns in the Spinal Cord of Zebrafish
In: Bioinformatics

 

2013
J. Stegmaier, D. Skanda, D. Lebiedz
Robust Optimal Design of Experiments for Model Discrimination using an Interactive Software Tool
In: PLOS ONE

 

Conference Publications

2019

Dennis Eschweiler, Tim Klose, Florian Nicolas Müller-Fouarge, Marcin Kopaczka, Johannes Stegmaier
Towards Annotation-Free Segmentation of Fluorescently Labeled Cell Membranes in Confocal Microscopy Images
In: MICCAI Workshop on Simulation and Synthesis in Medical Imaging (SASHIMI)

2019

Dennis Eschweiler, Thiago V. Spina, Rohan C. Choudhury, Elliot Meyerowitz, Alexandre Cunha, Johannes Stegmaier
CNN-based Preprocessing to Optimize Watershed-based Cell Segmentation in 3D Confocal Microscopy Images
In: IEEE International Symposium on Biomedical Imaging (ISBI)

2019

Daniel Bug, Dennis Eschweiler, Qianyu Liu, Justus Schock, Leon Weninger, Friedrich Feuerhake, Julia Schüler, Johannes Stegmaier and Dorit Merhof
Combined Learning for Similar Tasks with Domain-Switching Networks
In: International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI)

2018

T. Scherr, A. Bartschat, M. Reischl, J. Stegmaier, R. Mikut
Best Practices in Deep Learning-Based Segmentation of Microscopy Images
In: Proceedings 28. Workshop Computational Intelligence

2018

T. V. Spina, J. Stegmaier, A. Falcao, E. Meyerowitz, A. Cunha
SEGMENT3D: A Web-based Application for Collaborative Segmentation of 3D Images used in the Shoot Apical Meristem
In: IEEE International Symposium on Biomedical Imaging (ISBI), Washington D.C., USA

2018

J. Stegmaier, T. V. Spina, A. Falcao, A. Bartschat, R. Mikut, E. Meyerowitz, A. Cunha
Cell Segmentation in 3D Microscopy Images using Supervoxel Merge-Forests with CNN-based Hypothesis Selection
In: IEEE International Symposium on Biomedical Imaging (ISBI), Washington D.C., USA

2018

A. Bartschat, T. Unger, T. Scherr, J. Stegmaier, M. Reischl, R. Mikut
Robustness of Deep Learning Architectures with Respect to Training Data Variation
In: Proceedings 28. Workshop Computational Intelligence

2017
A. Bartschat, J. Stegmaier, S. Allgeier, K. M. Reichert, S. Bohn, O. Stachs, B. Köhler, R. Mikut
Augmentations of the Bag of Visual Words Approach for Real-Time Fuzzy and Partial Image Classification
In: Proc., 27. Workshop Computational Intelligence, Dortmund, Germany

 

2016
A. Bartschat, L. Toso, J. Stegmaier, A. Kuijper, R. Mikut, B. Köhler, S. Allgeier
Automatic Corneal Tissue Classification Using Bag-of-Visual-Words Approaches
In: Forum Bildverarbeitung, Karlsruhe, Germany

 

2016
J. Stegmaier, N. Peter, J. Portl, I. Mang, H. Leitte, R. Mikut, M. Reischl
A Framework for Feedback-based Segmentation of 3D Image Stacks
In: Current Directions in Biomedical Engineering

 

2016
J. Stegmaier, J. Arz, B. Schott, J. C. Otte, A. Kobitski, G. U. Nienhaus, U. Strähle, P. Sanders, R. Mikut
Generating Semi-Synthetic Validation Benchmarks for Embryomics
In: IEEE International Symposium on Biomedical Imaging (ISBI)

 

2016
B. Schott, J. Stegmaier, A. Arbaud, M. Reischl, R. Mikut, F. Lévi
Robust Individual Circadian Parameter Estimation for Biosignal-based Personalization of Cancer Chronotherapy
In: Proc., Workshop Biosignal Processing, Berlin

 

2015
B. Schott, J. Stegmaier, M. Takamiya, R. Mikut
Challenges of Integrating A Priori Information Efficiently in the Discovery of Spatio-Temporal Objects in Large Databases
In: Proc., 25. Workshop Computational Intelligence, Dortmund

 

2015
J. Portl, J. Stegmaier, I. V. Mang, M. Reischl, R. Schröder, H. Leitte
Visualization for Error-controlled Surface Reconstruction from Large Electron Microscopy Image Stacks
In: IEEE Vis, Chicago

 

2012
J. Stegmaier, A. Khan, M. Reischl, R. Mikut
Challenges of Uncertainty Propagation in Image Analysis
In: Proc., 22. Workshop Computational Intelligence, Dortmund

 

2012
J. Stegmaier, R. Alshut, M. Reischl, R. Mikut
Information Fusion of Image Analysis, Video Object Tracking, and Data Mining of Biological Images using the Open Source MATLAB Toolbox Gait-CAD
In: Biomedizinische Technik

 

Conference Abstracts

09/2018
T. Scherr, B. Schott, M. Traub, M. Takamiya, A. Bartschat, A. Kobitski, G. U. Nienhaus, U. Strähle, R. Mikut, J. Stegmaier
Deep Learning Approaches to Improve Cell Segmentation and Tracking Accuracy for Interactive Knowledge Discovery in Zebrafish Embryos
In: Zebrafish Models for Human Eye Diseases, Freiburg, Germany

 

08/2018
T. Scherr, B. Schott, M. Traub, M. Takamiya, A. Bartschat, A. Kobitski, G. U. Nienhaus, U. Strähle, J. Stegmaier, R. Mikut
Interactive Cell Tracking Analysis of Light-Sheet Microscopy Data in Zebrafish Embryos using EmbryoMiner
In: 10th Anniversary Light-Sheet Fluorescence Microscopy Conference, Dresden, Germany

03/2018
R. Peravali, D. Marcato, J. Stegmaier, C. Pylatiuk, J. Dallman, R. Mikut, U. Strähle
Automated and High-Throughput Screening Platforms for Assessing Early Zebrafish Behavior
In: 5th European Zebrafish Principal Investigator Meeting, Trento, Italy

 

10/2017
B. Schott, M. Traub, T. Antritter, C. Schlagenhauf, A. Barschat, M. Takamiya, J. C. Otte,
A. Kobitski, G. U. Nienhaus, P. Sanders, U. Strähle, R. Mikut, J. Stegmaier
Interactive Knowledge Discovery in Large-Scale 3D+T Cell Tracking Data
In: EMBL Symposium ‚Seeing is Believing – Imaging the Processes of Life‘, Heidelberg, Germany

 

07/2017
B. Schott, M. Traub, T. Antritter, C. Schlagenhauf, A. Barschat, M. Takamiya, J. C. Otte, A. Kobitski, G. U. Nienhaus, P. Sanders, U. Strähle, R. Mikut, J. Stegmaier
A New Framework for Interactive Knowledge-Discovery in Large-Scale Trajectory Data of Zebrafish Embryos
In: 10th European Zebrafish Meeting, Budapest, Hungary

 

07/2017
R. Peravali, D. Marcato, J. Stegmaier, R. Geisler, C. Pylatiuk, M. Reischl, J. v. Wezel, R. Mikut, J. Dallman, U. Strähle
High-Throughput Screening and Analysis of Startle Response Behavior in Zebrafish
In: 10th European Zebrafish Meeting, Budapest, Hungary

 

04/2017
S. Rubin, T. Stern, J. Stegmaier, E. Zelzer
A Novel Method For Studying 3D Cellular Architecture in the Growth Plate
In: Cartilage Biology & Pathology, Lucca, Italy

 

07/2016
R. Peravali, A. Popova, D. Marcato, E. Gursky, J. Stegmaier, R. Alshut, H. Breitwieser, R. Geisler, C. Pylatiuk, J. v. Wezel, P. Levkin, R. Mikut, U. Strähle
Automated Approaches to Sample Handling and High-Throughput Behavioral Screening of Zebrafish
In: Zebrafish Genetics, Orlando, USA

 

05/2016
D. Marcato, E. Gursky, J. Stegmaier, R. Alshut, M. Shahid, H. Breitwieser, R. Geisler, C. Pylatiuk, J. v. Wezel, R. Mikut, U. Strähle, R. Peravali
Automated and High-Throughput Zebrafish Embryonic Behavioral Screening Platforms
In: Measuring Behavior, Dublin, Ireland

 

10/2015
J. Stegmaier, R. Mikut
Exploiting Biological Prior Knowledge and Uncertainty for Large-Scale Image Analysis
In: EMBL Symposium ‚Seeing is Believing – Imaging the Processes of Life‘, Heidelberg, Germany

 

04/2015
J. Stegmaier, R. Mikut
Enhancing Image Analysis Pipelines with Uncertainty Treatment
In: IEEE International Symposium on Biomedical Imaging, New York City, USA

 

10/2014
J. Stegmaier, F. Amat, M. Takamiya, A. Bartschat, J. C. Otte, A. Kobitski, W. C. Lemon, K. McDole, Y. Wan, G. U. Nienhaus, U. Strähle, P. J. Keller, R. Mikut
Efficient Extraction of Cell Shapes and Nuclei from 3D Light-sheet Microscopy Images
In: BioImage Informatics, Leuven, Belgium

 

10/2013
J. Stegmaier, J. C. Otte, A. Kobitski, G. U. Nienhaus, U. Strähle, R. Mikut
Embedding Biological Prior Knowledge into Efficient Processing Operators for Terabyte-Scale Image Analysis
In: EMBL Symposium ‚Seeing is Believing – Imaging the Processes of Life‘, Heidelberg, Germany

 

04/2013
J. Stegmaier, R. Alshut, M. Reischl, R. Mikut
Methods for Automated Analysis of Zebrafish-related Experiments to Keep Pace with Modern High-Throughput Acquisition Technology
In: COST Workshop – Automation Methods for Zebrafish Research, Leiden, Netherlands