Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish. - Johannes Stegmaier; Maryam Shahid; Masanari Takamiya; Lixin Yang; Sepand Rastegar; Markus Reischl; Uwe Strähle; Ralf Mikut (Bioinform., 2014)

Generating semi-synthetic validation benchmarks for embryomics. - Johannes Stegmaier; Julian Arz; Benjamin Schott; Jens C. Otte; Andrei Kobitski; G. Ulrich Nienhaus; Uwe Strähle; Peter Sanders 001; Ralf Mikut (ISBI, 2016)

Automation strategies for large-scale 3D image analysis. - Johannes Stegmaier; Benjamin Schott; Eduard Hübner; Manuel Traub; Maryam Shahid; Masanari Takamiya; Andrei Kobitski; Volker Hartmann; Rainer Stotzka; Jos van Wezel; Achim Streit; G. Ulrich Nienhaus; et al. (Autom., 2016)

XPIWIT - an XML pipeline wrapper for the Insight Toolkit. - Andreas Bartschat; Eduard Hübner; Markus Reischl; Ralf Mikut; Johannes Stegmaier (Bioinform., 2016)

Challenges of Integrating A Priori Information Efficiently in the Discovery of Spatio-Temporal Objects in Large Databases. - Benjamin Schott; Johannes Stegmaier; Masanari Takamiya; Ralf Mikut (CoRR, 2016)

New Methods to Improve Large-Scale Microscopy Image Analysis with Prior Knowledge and Uncertainty. - Johannes Stegmaier (CoRR, 2016)

Fuzzy-based Propagation of Prior Knowledge to Improve Large-Scale Image Analysis Pipelines. - Johannes Stegmaier; Ralf Mikut (CoRR, 2016)

3D Cell Nuclei Segmentation with Balanced Graph Partitioning. - Julian Arz; Peter Sanders 001; Johannes Stegmaier; Ralf Mikut (CoRR, 2017)

The MATLAB Toolbox SciXMiner: User's Manual and Programmer's Guide. - Ralf Mikut; Andreas Bartschat; Wolfgang Doneit 001; Jorge Ángel González Ordiano; Benjamin Schott; Johannes Stegmaier; Simon Waczowicz; Markus Reischl (CoRR, 2017)

New Methods to Improve Large-Scale Microscopy Image Analysis with Prior Knowledge and Uncertainty. - Johannes Stegmaier (KIT Scientific Publishing, 2017)

SEGMENT3D: A web-based application for collaborative segmentation of 3D images used in the shoot apical meristem. - Thiago Vallin Spina; Johannes Stegmaier; Alexandre X. Falcão; Elliot Meyerowitz; Alexandre Cunha (ISBI, 2018)

Cell segmentation in 3D confocal images using supervoxel merge-forests with CNN-based hypothesis selection. - Johannes Stegmaier; Thiago Vallin Spina; Alexandre X. Falcão; Andreas Bartschat; Ralf Mikut; Elliot Meyerowitz; Alexandre Cunha (ISBI, 2018)

Transfer Learning with Human Corneal Tissues: An Analysis of Optimal Cut-Off Layer. - Nadezhda Prodanova; Johannes Stegmaier; Stephan Allgeier; Sebastian Bohn; Oliver Stachs; Bernd Köhler; Ralf Mikut; Andreas Bartschat (CoRR, 2018)

EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos. - Benjamin Schott; Manuel Traub; Cornelia Schlagenhauf; Masanari Takamiya; Thomas Antritter; Andreas Bartschat; Katharina Löffler; Denis Blessing; Jens C. Otte; Andrei Kobitski; G. Ulrich Nienhaus; Uwe Strähle; et al. (PLoS Comput. Biol., 2018)

CNN-Based Preprocessing to Optimize Watershed-Based Cell Segmentation in 3D Confocal Microscopy Images. - Dennis Eschweiler; Thiago Vallin Spina; Rohan C. Choudhury; Elliot Meyerowitz; Alexandre Cunha; Johannes Stegmaier (ISBI, 2019)

Combined Learning for Similar Tasks with Domain-Switching Networks. - Daniel Bug; Dennis Eschweiler; Qianyu Liu; Justus Schock; Leon Weninger; Friedrich Feuerhake; Julia Schüler; Johannes Stegmaier; Dorit Merhof (MICCAI (5), 2019)

Towards Annotation-Free Segmentation of Fluorescently Labeled Cell Membranes in Confocal Microscopy Images. - Dennis Eschweiler; Tim Klose; Florian Nicolas Müller-Fouarge; Marcin Kopaczka; Johannes Stegmaier (SASHIMI@MICCAI, 2019)

Fuzzy tissue detection for real-time focal control in corneal confocal microscopy. - Andreas Bartschat; Stephan Allgeier; Tim Scherr; Johannes Stegmaier; Sebastian Bohn; Klaus-Martin Reichert; Arjan Kuijper; Markus Reischl; Oliver Stachs; Bernd Köhler; Ralf Mikut (Autom., 2019)

Algorithms used for the Cell Segmentation Benchmark Competition at ISBI 2019 by RWTH-GE. - Dennis Eschweiler; Johannes Stegmaier (CoRR, 2019)

Semi-Automatic Generation Of Tight Binary Masks And Non-Convex Isosurfaces For Quantitative Analysis Of 3d Biological Samples. - Sourabh Bhide; Ralf Mikut; Maria Leptin; Johannes Stegmaier (ICIP, 2020)

Towards Automatic Embryo Staging in 3D+t Microscopy Images Using Convolutional Neural Networks and PointNets. - Manuel Traub; Johannes Stegmaier (SASHIMI@MICCAI, 2020)

BeadNet: deep learning-based bead detection and counting in low-resolution microscopy images. - Tim Scherr; Karolin Streule; Andreas Bartschat; Moritz Böhland; Johannes Stegmaier; Markus Reischl; Véronique Orian-Rousseau; Ralf Mikut (Bioinform., 2020)

Making Logic Learnable With Neural Networks. - Tobias Brudermueller; Dennis L. Shung; Loren Laine; Adrian J. Stanley; Stig B. Laursen; Harry R. Dalton; Jeffrey Ngu; Michael Schultz; Johannes Stegmaier; Smita Krishnaswamy (CoRR, 2020)

A Multi-Organ Nucleus Segmentation Challenge. - Neeraj Kumar 002; Ruchika Verma; Deepak Anand; Yanning Zhou 001; Omer Fahri Onder; Efstratios Tsougenis; Hao Chen 011; Pheng-Ann Heng; Jiahui Li 005; Zhiqiang Hu; Yunzhi Wang; Navid Alemi Koohbanani; et al. (IEEE Trans. Medical Imaging, 2020)

Cellcyclegan: Spatiotemporal Microscopy Image Synthesis Of Cell Populations Using Statistical Shape Models And Conditional Gans. - Dennis Bähr; Dennis Eschweiler; Anuk Bhattacharyya; Daniel Moreno-Andrés; Wolfram Antonin; Johannes Stegmaier (ISBI, 2021)

Spherical Harmonics For Shape-Constrained 3d Cell Segmentation. - Dennis Eschweiler; Malte Rethwisch; Simon Koppers; Johannes Stegmaier (ISBI, 2021)

Semi- and Self-supervised Multi-view Fusion of 3D Microscopy Images Using Generative Adversarial Networks. - Canyu Yang; Dennis Eschweiler; Johannes Stegmaier (MLMIR@MICCAI, 2021)

Robust 3D Cell Segmentation: Extending the View of Cellpose. - Dennis Eschweiler; Johannes Stegmaier (CoRR, 2021)

3D fluorescence microscopy data synthesis for segmentation and benchmarking. - Dennis Eschweiler; Malte Rethwisch; Mareike Jarchow; Simon Koppers; Johannes Stegmaier (CoRR, 2021)

Robust 3d Cell Segmentation: Extending The View Of Cellpose. - Dennis Eschweiler; Richard S. Smith; Johannes Stegmaier (ICIP, 2022)

Linear Discriminant Analysis Metric Learning Using Siamese Neural Networks. - Abin Jose; Qi Mei; Dennis Eschweiler; Ina Laube; Johannes Stegmaier (ICIP, 2022)

Probabilistic Image Diversification to Improve Segmentation in 3D Microscopy Image Data. - Dennis Eschweiler; Justus Schock; Johannes Stegmaier (SASHIMI@MICCAI, 2022)

Medical Diffusion - Denoising Diffusion Probabilistic Models for 3D Medical Image Generation. - Firas Khader; Gustav Mueller-Franzes; Soroosh Tayebi Arasteh; Tianyu Han; Christoph Haarburger; Maximilian Schulze-Hagen; Philipp Schad; Sandy Engelhardt; Bettina Baeßler; Sebastian Foersch; Johannes Stegmaier; Christiane Kuhl; et al. (CoRR, 2022)

Medical Diagnosis with Large Scale Multimodal Transformers: Leveraging Diverse Data for More Accurate Diagnosis. - Firas Khader; Gustav Mueller-Franzes; Tianci Wang; Tianyu Han; Soroosh Tayebi Arasteh; Christoph Haarburger; Johannes Stegmaier; Keno K. Bressem; Christiane Kuhl; Sven Nebelung; Jakob Nikolas Kather; Daniel Truhn (CoRR, 2022)

Weakly-supervised Temporal Segmentation of Cell-cycle Stages with Center-cell Focus using Recurrent Neural Networks. - Abin Jose; Rijo Roy; Johannes Stegmaier (Bildverarbeitung für die Medizin, 2023)

A Deep Learning-based in silico Framework for Optimization on Retinal Prosthetic Stimulation. - Yuli Wu 001; Ivan Karetic; Johannes Stegmaier; Peter Walter; Dorit Merhof (EMBC, 2023)

End-to-End Classification of Cell-Cycle Stages with Center-Cell Focus Tracker Using Recurrent Neural Networks. - Abin Jose; Rijo Roy; Dennis Eschweiler; Ina Laube; Reza Azad; Daniel Moreno-Andrés; Johannes Stegmaier (ICASSP, 2023)

SortedAP: Rethinking evaluation metrics for instance segmentation. - Long Chen 014; Yuli Wu 001; Johannes Stegmaier; Dorit Merhof (ICCV (Workshops), 2023)

Enhancing Lidar-Based Object Detection in Adverse Weather Using Offset Sequences in Time. - Raphael van Kempen; Tim Rehbronn; Abin Jose; Johannes Stegmaier; Bastian Lampe; Timo Woopen; Lutz Eckstein (ICECET, 2023)

Vector-Quantized Latent Flows for Medical Image Synthesis and Out-Of-Distribution Detection. - Firas Khader; Gustav Müller-Franzes; Soroosh Tayebi Arasteh; Tianyu Han; Jakob Nikolas Kather; Johannes Stegmaier; Sven Nebelung; Daniel Truhn (ISBI, 2023)

Multi-View Abnormality Detection in Clinical Knee MRI Studies Using Transformers. - Firas Khader; Johannes Stegmaier; Sven Nebelung; Daniel Truhn (ISBI, 2023)

Unsupervised Learning for Feature Extraction and Temporal Alignment of 3D+t Point Clouds of Zebrafish Embryos. - Zhu Chen 002; Ina Laube; Johannes Stegmaier (MICCAI (8), 2023)

Transformers for CT Reconstruction from Monoplanar and Biplanar Radiographs. - Firas Khader; Gustav Müller-Franzes; Tianyu Han; Sven Nebelung; Christiane Kuhl; Johannes Stegmaier; Daniel Truhn (SASHIMI@MICCAI, 2023)

Cascaded Cross-Attention Networks for Data-Efficient Whole-Slide Image Classification Using Transformers. - Firas Khader; Jakob Nikolas Kather; Tianyu Han; Sven Nebelung; Christiane Kuhl; Johannes Stegmaier; Daniel Truhn (MLMI@MICCAI (2), 2023)

Denoising Diffusion Probabilistic Models for Generation of Realistic Fully-Annotated Microscopy Image Data Sets. - Dennis Eschweiler; Johannes Stegmaier (CoRR, 2023)

Deep Learning Approach for Renal Cell Carcinoma Detection, Subtyping, And Grading. - Maroof Abdul Aziz; Fatemeh Javadian; Sherin Susheel Mathew; Avinash Gopal; Johannes Stegmaier; Sonit Singh; Abin Jose (ICIP, 2024)

Retinal OCT Synthesis with Denoising Diffusion Probabilistic Models for Layer Segmentation. - Yuli Wu 001; Weidong He; Dennis Eschweiler; Ningxin Dou; Zixin Fan; Shengli Mi; Peter Walter; Johannes Stegmaier (ISBI, 2024)

Annotated Biomedical Video Generation Using Denoising Diffusion Probabilistic Models and Flow Fields. - Rüveyda Yilmaz; Dennis Eschweiler; Johannes Stegmaier (SASHIMI@MICCAI, 2024)

Optimizing Retinal Prosthetic Stimuli with Conditional Invertible Neural Networks. - Yuli Wu 001; Julian Wittmann; Peter Walter; Johannes Stegmaier (CoRR, 2024)

Effortless Efficiency: Low-Cost Pruning of Diffusion Models. - Yang Zhang; Er Jin; Yanfei Dong; Ashkan Khakzar; Philip Torr 001; Johannes Stegmaier; Kenji Kawaguchi (CoRR, 2024)

Denoising diffusion probabilistic models for generation of realistic fully-annotated microscopy image datasets. - Dennis Eschweiler; Rüveyda Yilmaz; Matisse Baumann; Ina Laube; Rijo Roy; Abin Jose; Daniel Brückner; Johannes Stegmaier (PLoS Comput. Biol., 2024)

LogicAD: Explainable Anomaly Detection via VLM-based Text Feature Extraction. - Er Jin; Qihui Feng; Yongli Mou; Gerhard Lakemeyer; Stefan Decker; Oliver Simons; Johannes Stegmaier (AAAI, 2025)

Visual Fixation-Based Retinal Prosthetic Simulation. - Yuli Wu 001; Do Dinh Tan Nguyen; Henning Konermann; Rüveyda Yilmaz; Peter Walter; Johannes Stegmaier (ISBI, 2025)

Comparative Analysis of Unsupervised and Supervised Autoencoders for Nuclei Classification in Clear Cell Renal Cell Carcinoma Images. - Fatemeh Javadian; Zahra Aminparast; Johannes Stegmaier; Abin Jose (ISBI, 2025)

No Free Lunch in Annotation Either: An Objective Evaluation of Foundation Models for Streamlining Annotation in Animal Tracking. - Emil Mededovic; Valdy Laurentius; Yuli Wu 001; Marcin Kopaczka; Zhu Chen; Mareike Schulz; René Tolba; Johannes Stegmaier (ISBI, 2025)

Cascaded Diffusion Models for 2D and 3D Microscopy Image Synthesis to Enhance Cell Segmentation. - Rüveyda Yilmaz; Kaan Keven; Yuli Wu 001; Johannes Stegmaier (ISBI, 2025)

Dataset for Cross-Device and Cross-Subject Consistency Evaluation in Visual Fixation Prediction. - Yuli Wu 001; Henning Konermann; Emil Mededovic; Peter Walter; Johannes Stegmaier (IEEE DataPort, 2025)

Evaluating Cross-Subject and Cross-Device Consistency in Visual Fixation Prediction. - Yuli Wu 001; Henning Konermann; Emil Mededovic; Peter Walter; Johannes Stegmaier (CoRR, 2025)

A Pragmatic Note on Evaluating Generative Models with Fréchet Inception Distance for Retinal Image Synthesis. - Yuli Wu 001; Fucheng Liu; Rüveyda Yilmaz; Henning Konermann; Peter Walter; Johannes Stegmaier (CoRR, 2025)

CellStyle: Improved Zero-Shot Cell Segmentation via Style Transfer. - Rüveyda Yilmaz; Zhu Chen; Yuli Wu 001; Johannes Stegmaier (CoRR, 2025)

Eye on the Target: Eye Tracking Meets Rodent Tracking. - Emil Mededovic; Yuli Wu 001; Henning Konermann; Marcin Kopaczka; Mareike Schulz; René Tolba; Johannes Stegmaier (CoRR, 2025)

Towards Robust and Generalizable Gerchberg Saxton based Physics Inspired Neural Networks for Computer Generated Holography: A Sensitivity Analysis Framework. - Ankit Amrutkar; Björn Kampa; Volkmar Schulz; Johannes Stegmaier; Markus Rothermel; Dorit Merhof (CoRR, 2025)

Minimalist Concept Erasure in Generative Models. - Yang Zhang; Er Jin; Yanfei Dong; Yixuan Wu; Philip Torr 001; Ashkan Khakzar; Johannes Stegmaier; Kenji Kawaguchi (CoRR, 2025)

SIS-Challenge: Event-based Spatio-temporal Instance Segmentation Challenge at the CVPR 2025 Event-based Vision Workshop. - Friedhelm Hamann; Emil Mededovic; Fabian Gülhan; Yue Wu 004; Johannes Stegmaier; Jing He; Yiqing Wang; Kexin Zhang 003; Lingling Li 002; Licheng Jiao; Mengru Ma; Hongxiang Huang; et al. (CoRR, 2025)