2022

D. Eschweiler, I. Laube, J. Stegmaier
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

2016

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

2024

Dennis Eschweiler, Rüveyda Yilmaz, Matisse Baumann, Ina Laube, Rijo Roy, Abin Jose, Daniel Brückner and Johannes Stegmaier
Denoising Diffusion Probabilistic Models for Generation of Realistic Fully-Annotated Microscopy Image Data Sets
In: PLOS Computational Biology 20 (2)

2023

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, D. Truhn
Denoising Diffusion Probabilistic Models for 3D Medical Image Generation
In: Scientific Reports 13 (1)

2023

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, D. Truhn
Medical Transformer for Multimodal Survival Prediction in Intensive Care: Integration of Imaging and Non-Imaging Data
In: Scientific Reports 13 (1)

2023

A. Dievernich, J. Stegmaier, P. Achenbach, S. Warkentin, T. Braunschweig, U. P. Neumann, U. Klinge
A Deep-Learning-Computed Cancer Score for the Identification of Human Hepatocellular Carcinoma Area Based on a Six-Colour Multiplex Immunofluorescence Panel
In: Cells 12 (7)

2023

Sammy Hermans, Jacob Pilon, Dennis Eschweiler, Johannes Stegmaier, Carmen AH Severens-Rijvers, Salwan Al-Nasiry, Marc van Zandvoort, 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)

2022

D. Moreno-Andrés, A. Bhattacharyya, A. Scheufen, J. Stegmaier
LiveCellMiner: A New Tool to Analyze Mitotic Progression
In: PLOS ONE (in press)

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, R. Tofanelli, M. Majda, E. Echevin, C. Le Gloanec, H. Bertrand-Rakusova, M. Adibi, K. Schneitz, G. Bassel, D. Kierzkowski, J. Stegmaier, M. Tsiantis, R. S. Smith
Using Positional Information to Provide Context for Biological Image Analysis with MorphoGraphX 2.0
In: eLife 11

2022

R. Windoffer, N. Schwarz, S. Yoon, T. Piskova, M. Scholkemper, J. Stegmaier, A. Bönsch, J. Di Russo, R. Leube
Quantitative Mapping of Keratin Networks in 3D
In: eLife 11

2022

U. Klinge, A. Dievernich and J. Stegmaier
Quantitative Characterization of Macrophage, Lymphocyte and Neutrophil Subtypes within the Foreign Body Granuloma of Human Mesh Explants by 5 Marker Multiplex Fluorescence Microscopy
In: Frontiers in Medicine

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, M. Ma
Ventral Striatal Islands of Calleja Neurons Control Grooming in Mice
In: Nature Neuroscience

2021

Dennis Eschweiler, Malte Rethwisch, Mareike Jarchow, Simon Koppers and Johannes Stegmaier
3D fluorescence microscopy data synthesis for segmentation and benchmarking
In: PLOS ONE 16 (12)

2021

S. Rubin, A. Agrawal, J. Stegmaier, S. Krief, N. Felsenthal, J. Svorai, Y. Addadi, P. Villoutreix, T. Stern, E. Zelzer
Application of 3D MAPs Pipeline Identifies the Morphological Sequence Chondrocytes Undergo and the Regulatory Role of GDF5 in this Process
In: Nature Communications 12 (1)

2021

S. Bhide, D. Gombalova, G. Mönke, J. Stegmaier, V. Zinchenko, A. Kreshuk, J. M. Belmonte, M. Leptin
Mechanical Competition Alters the Cellular Interpretation of an Endogenous Genetic Program
In: Journal of Cell Biology 220 (11)

2020

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, T. Dickmeis
MondoA Regulates Gene Expression in Cholesterol Biosynthesis-Associated Pathways Required for Zebrafish Epiboly
In: Elife 9

2020

T. Scherr, K. Streule, A. Bartschat, M. Böhland, K. Löffler, J. Stegmaier, M. Reischl, V. Orian-Rousseau, R. Mikut
BeadNet: Automated Bead Detection and Counting in Low-Resolution Microscopy Images
In: Bioinformatics 36 (17)

2020

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)

2020

J. Gierten, C. Pylatiuk, O. T. Hammouda, C. Schock, J. Stegmaier, J. Wittbrodt, J. Gehrig and F. Loosli
Automated High-Throughput Heartbeat Quantification in Medaka and Zebrafish Embryos under Physiological Conditions
In: Scientific Reports 10 (1)

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

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

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 67 (10)

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

2024

Yuli Wu, Julian Wittmann, Peter Walter and Johannes Stegmaier
Optimizing Retinal Prosthetic Stimuli with Conditional Invertible Neural Networks
In: arXiv preprint arXiv:2403.04884

2024

Yuli Wu, Weidong He, Dennis Eschweiler, Ningxin Dou, Zixin Fan, Shengli Mi, Peter Walter and Johannes Stegmaier
Retinal OCT Synthesis with Denoising Diffusion Probabilistic Models for Layer Segmentation
In: IEEE 21st International Symposium on Biomedical Imaging (ISBI)

2023

F. Khader, J. N. Kather, T. Han, S. Nebelung, C. Kuhl, J. Stegmaier, D. Truhn
Cascaded Cross-Attention Networks for Data-Efficient Whole-Slide Image Classification Using Transformers
In: Machine Learning in Medical Imaging Workshop at MICCAI 2023 (accepted paper)

2023

F. Khader, G. Müller-Franzes, S. T. Arasteh, T. Han, J. N. Kather, J. Stegmaier, S. Nebelung, D. Truhn
Vector-Quantized Latent Flows for Medical Image Synthesis and Out-Of-Distribution Detection
In: IEEE 20th International Symposium on Biomedical Imaging (ISBI)

2023

F. Khader, J. Stegmaier, S. Nebelung, D. Truhn
Multi-View Abnormality Detection in Clinical Knee MRI Studies Using Transformers
In: IEEE 20th International Symposium on Biomedical Imaging (ISBI)

2023

A. Jose, R. Roy, J. Stegmaier
Weakly-Supervised Temporal Segmentation of Cell-Cycle Stages with Center-Cell Focus using Recurrent Neural Networks
In: BVM Workshop

2023

Zhu Chen, Ina Laube, Johannes Stegmaier
Unsupervised Learning for Feature Extraction and Temporal Alignment of 3D+t Point Clouds of Zebrafish Embryos
In: International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI)

2023

Long Chen, Yuli Wu, Johannes Stegmaier and Dorit Merhof
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)

2023

Yuli Wu, Ivan Karetic, Johannes Stegmaier, Peter Walter and Dorit Merhof
A Deep Learning-based in silico Framework for Optimization on Retinal Prosthetic Stimulation
In: International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)

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)

2022

Dennis Eschweiler, Justus Schock and Johannes Stegmaier
Probabilistic Image Diversification to Improve Segmentation in 3D Microscopy Image Data
In: MICCAI International Workshop on Simulation and Synthesis in Medical Imaging (SASHIMI)

2022

Dennis Eschweiler, Richard S. Smith and Johannes Stegmaier
Robust 3D Cell Segmentation: Extending the View of Cellpose
In: IEEE International Conference in Image Processing (ICIP)

2021

C. Yang, D. Eschweiler, J. Stegmaier
Semi-and Self-Supervised Multi-View Fusion of 3D Microscopy Images using Generative Adversarial Networks
In: MICCAI Workshop on Machine Learning for Medical Image Reconstruction (MLMIR)

2021

Dennis Eschweiler, Malte Rethwisch, Simon Koppers and Johannes Stegmaier
Spherical Harmonics for Shape-Constrained 3D Cell Segmentation
In: IEEE International Symposium on Biomedical Imaging (ISBI)

2021

D. Bähr, D. Eschweiler, A. Bhattacharyya, D. Moreno-Andrés, W. Antonin and J. Stegmaier
CellCycleGAN: Spatiotemporal Microscopy Image Synthesis of Cell Populations using Statistical Shape Models and Conditional GANs
In: IEEE International Symposium on Biomedical Imaging (ISBI)

2020

M. Traub and J. Stegmaier
Towards Automatic Embryo Staging in 3D+t Microscopy Images using Convolutional Neural Networks and PointNets
In: MICCAI International Workshop on Simulation and Synthesis in Medical Imaging (SASHIMI)

2020

S. Bhide, R. Mikut, M. Leptin and J. Stegmaier
Semi-Automatic Generation of Tight Binary Masks and Non-Convex Isosurfaces for Quantitative Analysis of 3D Biological Samples
In: IEEE International Conference on Image Processing (ICIP)

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 International 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

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