Jun.-Prof. Dr.-Ing.
Johannes Stegmaier
105
+49 241 80 22901
Johannes.Stegmaier@lfb.rwth-aachen.de
Johannes Stegmaier
Junior Professor
105
+49 241 80 22901
Johannes.Stegmaier@lfb.rwth-aachen.de
Curriculum Vitae
| Oct 2022 – Sep 2024 |
Interim professor (W3) at the Chair of Imaging and Computer Vision, RWTH Aachen University, Germany |
| Apr 2018 – Oct 2025 | Junior professor (W1) for Biomedical Image Analysis, RWTH Aachen University, Germany |
| Oct 2016 – Jan 2017 | Postdoc at the Center for Advanced Methods in Biological Image Analysis, Caltech, CA, USA |
| Feb 2015 – Dec 2017 | Postdoc at the Institute for Applied Computer Science, Karlsruhe Chair of Technology, Germany |
| Jun 2016 | Doctorate (Dr.-Ing.) from the Department of Mechanical Engineering, Karlsruhe Chair of Technology, Germany. Thesis: “New Methods to Improve Large-Scale Microscopy Image Analysis with Prior Knowledge and Uncertainty” |
| Jan 2014 – May 2014 | Short Term Scholar at Howard Hughes Medical Institute’s Janelia Research Campus, Ashburn, VA, USA |
| Feb 2012 – Jan 2015 | PhD student at the Institute for Applied Computer Science, Karlsruhe Chair of Technology, Germany |
| Oct 2009 – Dec 2011 | Master of Science in Bioinformatics and Systems Biology, University of Freiburg, Germany |
| Oct 2006 – Sep 2009 | Bachelor of Science in Bioinformatics, University of Tübingen, Germany |
Thesis Topics
Publications
Books and Book Chapters
2022
D. Eschweiler, I. Laube and J. Stegmaier
Spatiotemporal Image Generation for Embryomics Applications
In: Biomedical Image Synthesis and Simulation: Methods and Applications
Spatiotemporal Image Generation for Embryomics Applications
In: Biomedical Image Synthesis and Simulation: Methods and Applications
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
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
New Methods to Improve Large-Scale Microscopy Image Analysis with Prior Knowledge and Uncertainty
In: KIT Scientific Publishing
Journal Publications
2025
Rüveyda Yilmaz, Julian Thull, Johannes Stegmaier and Volkmar Schulz
Diffusion-based Sinogram Interpolation for Limited Angle PET
In: arXiv preprint arXiv:2511.09383
Diffusion-based Sinogram Interpolation for Limited Angle PET
In: arXiv preprint arXiv:2511.09383
F. Khader, G. Müller-Franzes, S. Tayebi Arasteh, T. Han, C. Haarburger, M. Schulze-Hagen, P. Schad, S. Engelhardt, B. Baeßler, S. Foersch, J. Stegmaier, C. Kuhl, S. Nebelung, J. N. Kather and D. Truhn
Denoising Diffusion Probabilistic Models for 3D Medical Image Generation
In: Scientific Reports 13 (1)
Denoising Diffusion Probabilistic Models for 3D Medical Image Generation
In: Scientific Reports 13 (1)
F. Khader, J. N. Kather, G. Müller-Franzes, T. Wang, T. Han, S. Tayebi Arasteh, K. Hamesch, K. Bressem, C. Haarburger, J. Stegmaier, C. Kuhl, S. Nebelung and D. Truhn
Medical Transformer for Multimodal Survival Prediction in Intensive Care: Integration of Imaging and Non-Imaging Data
In: Scientific Reports 13 (1)
Medical Transformer for Multimodal Survival Prediction in Intensive Care: Integration of Imaging and Non-Imaging Data
In: Scientific Reports 13 (1)
2023
Sammy Hermans, Jacob Pilon, Dennis Eschweiler, Johannes Stegmaier, Carmen AH Severens-Rijvers, Salwan Al-Nasiry, Marc van Zandvoort and Dimitrios Kapsokalyvas
Definition and Quantification of Three-Dimensional Imaging Targets to Phenotype Pre-Eclampsia Subtypes: An Exploratory Study
In: International Journal of Molecular Sciences 24 (4)
Definition and Quantification of Three-Dimensional Imaging Targets to Phenotype Pre-Eclampsia Subtypes: An Exploratory Study
In: International Journal of Molecular Sciences 24 (4)
2022
S. Strauss, A. Runions, B. Lane, D. Eschweiler, N. Bajpai, N. Trozzi, A.-L. Routier-Kierzkowska, S. Yoshida, S. R. da Silveira, A. Vijayan and M. Majda R. Tofanelli
Using Positional Information to Provide Context for Biological Image Analysis with MorphoGraphX 2.0
In: eLife 11
Using Positional Information to Provide Context for Biological Image Analysis with MorphoGraphX 2.0
In: eLife 11
2021
Y.-F. Zhang, L. V. Cifuentes, K. N. Wright, J. P. Bhattarai, J. Mohrhardt, D. Fleck, E. Janke, C. Jiang, S. L. Cranfill, N. Goldstein, M. Schreck, A. H. Moberly, Y. Yu, B. R. Arenkiel, J. N. Betley, W. Luo, J. Stegmaier, D. W. Wesson, M. Spehr, M. V. Fuccillo and M. Ma
Ventral Striatal Islands of Calleja Neurons Control Grooming in Mice
In: Nature Neuroscience
Ventral Striatal Islands of Calleja Neurons Control Grooming in Mice
In: Nature Neuroscience
M. Weger, B. Weger, A. Schink, M. Takamiya, J. Stegmaier, C. Gobet, A. Parisi, A. Kobitski, J. Mertes, N. Krone, U. Strähle, G. U. Nienhaus, R. Mikut, F. Gachon, P. Gut and T. Dickmeis
MondoA Regulates Gene Expression in Cholesterol Biosynthesis-Associated Pathways Required for Zebrafish Epiboly
In: Elife 9
MondoA Regulates Gene Expression in Cholesterol Biosynthesis-Associated Pathways Required for Zebrafish Epiboly
In: Elife 9
2020
K. Streule T. Scherr
BeadNet: Automated Bead Detection and Counting in Low-Resolution Microscopy Images
In: Bioinformatics 36 (17)
BeadNet: Automated Bead Detection and Counting in Low-Resolution Microscopy Images
In: Bioinformatics 36 (17)
M. Takamiya, J. Stegmaier, A. Y. Kobitski, B. Schott, B. D. Weger, D. Margariti, A. R. C. Delgado, V. Gourain, T. Scherr, L. Yang, S. Sorge, V. Hartmann, J. C. Otte, J. v. Wezel, R. Stotzka, T. Reinhard, G. Schlunk, T. Dickmeis, S. Rastegar, R. Mikut, G. U. Nienhaus and U. Strähle
Pax6 Organizes the Anterior Eye Segment Independently of Optic Cup Patterning by Guiding Two Distinct Neural Crest Waves
In: PLoS Genetics 16 (6)
Pax6 Organizes the Anterior Eye Segment Independently of Optic Cup Patterning by Guiding Two Distinct Neural Crest Waves
In: PLoS Genetics 16 (6)
2019
K. Neeraj, V. Ruchika, A. Deepak, Z. Yanning, F. O. Omer, T. Efstratios, C. Hao, A. H. Pheng, L. Jiahui, H. Zhiqiang, [...], D. Eschweiler, J. Stegmaier and others
A Multi-organ Nucleus Segmentation Challenge
In: IEEE Transactions on Medical Imaging
A Multi-organ Nucleus Segmentation Challenge
In: IEEE Transactions on Medical Imaging
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 15
Microfluidic Chips for Life Sciences—A Comparison of Low Entry Manufacturing Technologies
In: Small 15
2019
V. Gerber, L. Yang, M. Takamiya, V. Ribes, V. Gourain, R. Peravali, J. Stegmaier, R. Mikut, M. Reischl, M. Ferg and 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)
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 and R. Mikut
Fuzzy Tissue Detection for Real-Time Focal Control in Corneal Confocal Microscopy
In: at Automatisierungstechnik 67 (10)
Fuzzy Tissue Detection for Real-Time Focal Control in Corneal Confocal Microscopy
In: at Automatisierungstechnik 67 (10)
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 and 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)
EmbryoMiner: A New Framework for Interactive Knowledge Discovery in Large-Scale Cell Tracking Data of Developing Embryos
In: PLOS Computational Biology 14 (4)
2017
![](https://www.lfb.rwth-aachen.de/wp-content/themes/bootstrap-basic4/img/file-bibtex_icon.png")
J. Stegmaier, R. Mikut
Fuzzy-based Propagation of Prior Knowledge to Improve Large-Scale Image Analysis Pipelines
In: PLOS ONE
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
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
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
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
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
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
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
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
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
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
Robust Optimal Design of Experiments for Model Discrimination using an Interactive Software Tool
In: PLOS ONE
Conference Publications
2025
Rüveyda Yilmaz, Zhu Chen, Yuli Wu and Johannes Stegmaier
CellStyle: Improved Zero-Shot Cell Segmentation via Style Transfer
In: International Conference on Medical Image Computing and Computer-Assisted Intervention
CellStyle: Improved Zero-Shot Cell Segmentation via Style Transfer
In: International Conference on Medical Image Computing and Computer-Assisted Intervention
2025
Ruveyda Yilmaz, Kaan Keven, Yuli Wu and Johannes Stegmaier
Cascaded Diffusion Models for 2D and 3D Microscopy Image Synthesis to Enhance Cell Segmentation
In: 2025 IEEE International Symposium on Biomedical Imaging (ISBI)
Cascaded Diffusion Models for 2D and 3D Microscopy Image Synthesis to Enhance Cell Segmentation
In: 2025 IEEE International Symposium on Biomedical Imaging (ISBI)
2025
Friedhelm Hamann, Emil Mededovic, Fabian Gülhan, Yuli Wu, Johannes Stegmaier, Jing He, Yiqing Wang, Kexin Zhang, Lingling Li, Licheng Jiao, Mengru Ma, Honxiang Huang, Yuhao Yan, Hongwei Ren, Xiaopeng Lin, Yulong Huang, Bojun Cheng, Se Hyun Lee, Gyu Sung Ham, Kanghan Oh, Gi Hyun Lim, Boxuan Yang, Bowen Du and Guillermo Gallego
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
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
2025
Yang Zhang, Er Jin, Yanfei Dong, Yixuan Wu, Ashkan Khakzar, Philip Torr, Johannes Stegmaier and Kenji Kawaguchi
Minimalist Concept Erasure in Generative Models
In: Forty-second International Conference on Machine Learning (ICML)
Minimalist Concept Erasure in Generative Models
In: Forty-second International Conference on Machine Learning (ICML)
2025
Yang Zhang*, Er Jin*, Yanfei Dong, Ashkan Khakzar, Philip Torr, Johannes Stegmaier and Kenji Kawaguchi
Effortless Efficiency: Low-Cost Pruning of Diffusion Models
In: First Workshop on Scalable Optimization for Efficient and Adaptive Foundation Models
Effortless Efficiency: Low-Cost Pruning of Diffusion Models
In: First Workshop on Scalable Optimization for Efficient and Adaptive Foundation Models
2025
Yang Zhang*, Er Jin*, Yanfei Dong, Yixuan Wu, Ashkan Khakzar, Philip Torr, Johannes Stegmaier and Kenji Kawaguchi
Minimalist Concept Erasure in Generative Models
In: Forty-second International Conference on Machine Learning (ICML)
Minimalist Concept Erasure in Generative Models
In: Forty-second International Conference on Machine Learning (ICML)
Emil Mededovic, Valdy Laurentius, Yuli Wu, Marcin Kopaczka, Zhu Chen, Mareike Schulz, René Tolba and Johannes Stegmaier
No Free Lunch in Annotation either: An objective evaluation of Foundation models for Streamlining Annotation in Animal Tracking
In: IEEE 22nd International Symposium on Biomedical Imaging (ISBI)
No Free Lunch in Annotation either: An objective evaluation of Foundation models for Streamlining Annotation in Animal Tracking
In: IEEE 22nd International Symposium on Biomedical Imaging (ISBI)
2023
Long Chen, Yuli Wu, Johannes Stegmaier and Dorit Merhof
SortedAP: Rethinking Evaluation Metrics for Instance Segmentation
In: ICCV Workshop on BioImage Computing
SortedAP: Rethinking Evaluation Metrics for Instance Segmentation
In: ICCV Workshop on BioImage Computing
2023
Abin Jose, Rijo Roy, Dennis Eschweiler, Ina Laube, Reza Azad, Daniel Moreno-Andres and Johannes Stegmaier
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)
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)
2022
Abin Jose, Qi Mei, Dennis Eschweiler, Ina Laube and Johannes Stegmaier
Linear Discriminant Analysis Metric Learning Using Siamese Neural Networks
In: International Conference on Image Processing (ICIP)
Linear Discriminant Analysis Metric Learning Using Siamese Neural Networks
In: International Conference on Image Processing (ICIP)
Dennis Eschweiler, Tim Klose, Florian Nicolas Müller-Fouarge, Marcin Kopaczka and Johannes Stegmaier
Towards Annotation-Free Segmentation of Fluorescently Labeled Cell Membranes in Confocal Microscopy Images
In: MICCAI International Workshop on Simulation and Synthesis in Medical Imaging (SASHIMI)
Towards Annotation-Free Segmentation of Fluorescently Labeled Cell Membranes in Confocal Microscopy Images
In: MICCAI International Workshop on Simulation and Synthesis in Medical Imaging (SASHIMI)
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)
Combined Learning for Similar Tasks with Domain-Switching Networks
In: International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI)
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
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
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
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)
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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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
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In: EMBL Symposium ‘Seeing is Believing – Imaging the Processes of Life’, Heidelberg, Germany
04/2013
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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
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