Lehrstuhl
Johannes Stegmaier
Jun.-Prof. Dr.-Ing.
Johannes Stegmaier
Juniorprofessor
- Raum: 105
- Telefon: +49 241 80 22901
- E-Mail: Johannes.Stegmaier@lfb.rwth-aachen.de
Curriculum Vitae
| Okt 2022 – Sep 2024 |
Professurvertretung (W3) am Lehrstuhl für Bildgebung und Bildverarbeitung, RWTH Aachen |
| Apr 2018 – Okt 2025 | Juniorprofessor (W1) für biomedizinische Bildverarbeitung, RWTH Aachen |
| Okt 2016 – Jan 2017 | Postdoc am Center for Advanced Methods in Biological Image Analysis, Caltech, CA, USA |
| Feb 2015 – Dez 2017 | Postdoc am Institut für Angewandte Informatik, Karlsruher Institut für Technologie |
| Jun 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” |
| Jan 2014 – Mai 2014 | Short Term Scholar am Janelia Research Campus, Ashburn, VA, USA |
| Feb 2012 – Jan 2015 | Wissenschaftlicher Mitarbeiter am Institut für Angewandte Informatik, Karlsruher Institut für Technologie |
| Okt 2009 – Dez 2011 | Master of Science in Bioinformatik und Systembiologie, Albert-Ludwidgs-Universität Freiburg i. Br. |
| Okt 2006 – Sep 2009 | Bachelor of Science in Bioinformatik an der Eberhard-Karls-Universität Tübingen |
Abschlussarbeiten
Veröffentlichungen
Bücher und Buchkapitel
Spatiotemporal Image Generation for Embryomics Applications
In: Biomedical Image Synthesis and Simulation: Methods and Applications, S. (in press)
-
2018
Zebrafish: A Pharmacogenetic Model for Anesthesia
In: Methods in Enzymology
-
2016
New Methods to Improve Large-Scale Microscopy Image Analysis with Prior Knowledge and Uncertainty
In: KIT Scientific Publishing
Journal-Veröffentlichungen
Anatomical effects of ablation of the anterior retina in small animal eyes
In: BMC Ophthalmology 26 (1), S. 184
- 2026
Advancing Retina Implant Concepts: Assessing the Design and Validation of Origami-Type Epiretinal Implants by Computational Modeling
In: physica status solidi (a) 223 (14), S. e202600002
- 2025
Diffusion-based Sinogram Interpolation for Limited Angle PET
In: arXiv preprint arXiv:2511.09383
Definition and Quantification of Three-Dimensional Imaging Targets to Phenotype Pre-Eclampsia Subtypes: An Exploratory Study
In: International Journal of Molecular Sciences 24 (4), S. 3240
Using Positional Information to Provide Context for Biological Image Analysis with MorphoGraphX 2.0
In: eLife 11, S. e72601
Ventral Striatal Islands of Calleja Neurons Control Grooming in Mice
In: Nature Neuroscience, S. 1--12, Nature Publishing Group
BeadNet: Automated Bead Detection and Counting in Low-Resolution Microscopy Images
In: Bioinformatics 36 (17), S. 4668--4670, Oxford University Press
Microfluidic Chips for Life Sciences—A Comparison of Low Entry Manufacturing Technologies
In: Small 15, S. 1901956
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), S. dev172510, Oxford University Press for The Company of Biologists Limited
Fuzzy Tissue Detection for Real-Time Focal Control in Corneal Confocal Microscopy
In: at Automatisierungstechnik 67 (10), S. 879--888, De Gruyter Oldenbourg
-
2017
Fuzzy-based Propagation of Prior Knowledge to Improve Large-Scale Image Analysis Pipelines
In: PLOS ONE
-
2017
An Objective Comparison of Cell Tracking Algorithms
In: Nature Methods
-
2017
TIDE is a Simple and Effective Method to Assess Efficiency of Guide RNAs in Zebrafish
In: Zebrafish
-
2016
Automation Strategies for Large-Scale 3D Image Analysis
In: at-Automatisierungstechnik
-
2016
Zebrafish Biosensor for Toxicant Induced Muscle Hyperactivity
In: Scientific Reports
-
2016
Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos
In: Developmental Cell
-
2016
XPIWIT – An XML Pipeline Wrapper for the Insight Toolkit
In: Bioinformatics
-
2015
An Ensemble-Averaged Digital Model of Zebrafish Embryo Development based on High-Speed Light-Sheet Microscopy at Single-Cell Resolution
In: Scientific Reports
-
2014
Fast Segmentation of Stained Nuclei in Terabyte-Scale, Time Resolved 3D Microscopy Image Stacks
In: PLOS ONE
-
2014
Automated Prior Knowledge-Based Quantification of Neuronal Patterns in the Spinal Cord of Zebrafish
In: Bioinformatics
-
2013
Robust Optimal Design of Experiments for Model Discrimination using an Interactive Software Tool
In: PLOS ONE
Konferenz-Veröffentlichungen
- 2026
Focus on the Fog: Leveraging Student Uncertainty for Guided Knowledge Distillation in Semantic Segmentation
In: 2026 IEEE International Conference on Image Processing (ICIP)
Training-Free Stimulus Encoding for Retinal Implants via Sparse Projected Gradient Descent
In: 2026 IEEE International Conference on Image Processing (ICIP), S. 1--6, IEEE
- 2026
PET-Adapter: Test-Time Domain Adaptation for Full and Limited-Angle PET Image Reconstruction
In: Medical Image Computing and Computer Assisted Intervention (MICCAI), S. 381--391
- 2026
SelfMOTR: Revisiting MOTR with Self-Generating Detection Priors
In: European Conference on Computer Vision (ECCV), S. 213--231
Atlas-Augmented Semantic Segmentation for Robust Ultra-Low-Field Pediatric Brain Imaging
In: MICCAI Challenge on Low Field Pediatric Brain Magnetic Resonance Image Segmentation and Quality Assurance, Springer Nature Switzerland
- 2025
CellStyle: Improved Zero-Shot Cell Segmentation via Style Transfer
In: International Conference on Medical Image Computing and Computer-Assisted Intervention, S. 67--77
- 2025
Cascaded Diffusion Models for 2D and 3D Microscopy Image Synthesis to Enhance Cell Segmentation
In: 2025 IEEE International Symposium on Biomedical Imaging (ISBI)
- 2025
SIS-Challenge: Event-based Spatio-temporal Instance Segmentation Challenge at the CVPR 2025 Event-based Vision Workshop
In: Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV) Workshops, S. 4675--4683
- 2025
Minimalist Concept Erasure in Generative Models
In: Forty-second International Conference on Machine Learning (ICML)
- 2025
Effortless Efficiency: Low-Cost Pruning of Diffusion Models
In: First Workshop on Scalable Optimization for Efficient and Adaptive Foundation Models
- 2025
Minimalist Concept Erasure in Generative Models
In: Forty-second International Conference on Machine Learning (ICML), PMLR
- 2025
- 2024
SortedAP: Rethinking Evaluation Metrics for Instance Segmentation
In: ICCV Workshop on BioImage Computing
End-to-end classification of cell-cycle stages with center-cell focus tracker using recurrent neural networks
In: International Conference on Acoustics, Speech and Signal Processing (ICASSP), S. 1--5
Linear Discriminant Analysis Metric Learning Using Siamese Neural Networks
In: International Conference on Image Processing (ICIP), S. 3641--3645
-
2017
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
Automatic Corneal Tissue Classification Using Bag-of-Visual-Words Approaches
In: Forum Bildverarbeitung, Karlsruhe, Germany
-
2016
A Framework for Feedback-based Segmentation of 3D Image Stacks
In: Current Directions in Biomedical Engineering
-
2016
Generating Semi-Synthetic Validation Benchmarks for Embryomics
In: IEEE International Symposium on Biomedical Imaging (ISBI)
-
2016
Robust Individual Circadian Parameter Estimation for Biosignal-based Personalization of Cancer Chronotherapy
In: Proc., Workshop Biosignal Processing, Berlin
-
2015
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
Visualization for Error-controlled Surface Reconstruction from Large Electron Microscopy Image Stacks
In: IEEE Vis, Chicago
-
2012
Challenges of Uncertainty Propagation in Image Analysis
In: Proc., 22. Workshop Computational Intelligence, Dortmund
-
2012
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
Konferenz-Abstracts
-
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
-
Interactive Cell Tracking Analysis of Light-Sheet Microscopy Data in Zebrafish Embryos using EmbryoMiner
In: 10th Anniversary Light-Sheet Fluorescence Microscopy Conference, Dresden, Germany
-
Automated and High-Throughput Screening Platforms for Assessing Early Zebrafish Behavior
In: 5th European Zebrafish Principal Investigator Meeting, Trento, Italy
-
Interactive Knowledge Discovery in Large-Scale 3D+T Cell Tracking Data
In: EMBL Symposium 'Seeing is Believing – Imaging the Processes of Life', Heidelberg, Germany
-
A New Framework for Interactive Knowledge-Discovery in Large-Scale Trajectory Data of Zebrafish Embryos
In: 10th European Zebrafish Meeting, Budapest, Hungary
-
High-Throughput Screening and Analysis of Startle Response Behavior in Zebrafish
In: 10th European Zebrafish Meeting, Budapest, Hungary
-
A Novel Method For Studying 3D Cellular Architecture in the Growth Plate
In: Cartilage Biology & Pathology, Lucca, Italy
-
Automated Approaches to Sample Handling and High-Throughput Behavioral Screening of Zebrafish
In: Zebrafish Genetics, Orlando, USA
-
Automated and High-Throughput Zebrafish Embryonic Behavioral Screening Platforms
In: Measuring Behavior, Dublin, Ireland
-
Exploiting Biological Prior Knowledge and Uncertainty for Large-Scale Image Analysis
In: EMBL Symposium 'Seeing is Believing – Imaging the Processes of Life', Heidelberg, Germany
-
Enhancing Image Analysis Pipelines with Uncertainty Treatment
In: IEEE International Symposium on Biomedical Imaging, New York City, USA
-
Efficient Extraction of Cell Shapes and Nuclei from 3D Light-sheet Microscopy Images
In: BioImage Informatics, Leuven, Belgium
-
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
-
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