Johannes Stegmaier

95 papers A* 2B 4Misc 1Journal 56Unranked 31

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	A Pragmatic Note on Evaluating Generative Models with Fréchet Inception Distance for Retinal Image Synthesis. CoRR Yuli Wu, Fucheng Liu, Rüveyda Yilmaz, Henning Konermann, Peter Walter, Johannes Stegmaier
2025	—	`conf`	Atlas-Augmented Semantic Segmentation for Robust Ultra-Low-Field Pediatric Brain Imaging. LISA@MICCAI Kostiantyn Lavronenko, Rüveyda Yilmaz, Zhu Chen, Johannes Stegmaier, Volkmar Schulz
2025	—	`conf`	Cascaded Diffusion Models for 2D and 3D Microscopy Image Synthesis to Enhance Cell Segmentation. ISBI Rüveyda Yilmaz, Kaan Keven, Yuli Wu, Johannes Stegmaier
2025	—	`conf`	CellStyle: Improved Zero-Shot Cell Segmentation via Style Transfer. MICCAI (5) Rüveyda Yilmaz, Zhu Chen, Yuli Wu, Johannes Stegmaier
2025	J	`jnl`	CellStyle: Improved Zero-Shot Cell Segmentation via Style Transfer. CoRR Rüveyda Yilmaz, Zhu Chen, Yuli Wu, Johannes Stegmaier
2025	—	`conf`	Comparative Analysis of Unsupervised and Supervised Autoencoders for Nuclei Classification in Clear Cell Renal Cell Carcinoma Images. ISBI Fatemeh Javadian, Zahra Aminparast, Johannes Stegmaier, Abin Jose
2025	J	`jnl`	Comparative Analysis of Unsupervised and Supervised Autoencoders for Nuclei Classification in Clear Cell Renal Cell Carcinoma Images. CoRR Fatemeh Javadian, Zahra Aminparast, Johannes Stegmaier, Abin Jose
2025	J	`jnl`	Diffusion-based Sinogram Interpolation for Limited Angle PET. CoRR Rüveyda Yilmaz, Julian Thull, Johannes Stegmaier, Volkmar Schulz
2025	J	`jnl`	Evaluating Cross-Subject and Cross-Device Consistency in Visual Fixation Prediction. CoRR Yuli Wu, Henning Konermann, Emil Mededovic, Peter Walter, Johannes Stegmaier
2025	J	`jnl`	Eye on the Target: Eye Tracking Meets Rodent Tracking. CoRR Emil Mededovic, Yuli Wu, Henning Konermann, Marcin Kopaczka, Mareike Schulz, René Tolba, Johannes Stegmaier
2025	—	`conf`	HoloPointNet: A Deep Learning Framework for Efficient 3D Point Cloud Holography. MICCAI (11) Ankit Amrutkar, Ahmet Nazlioglu, Björn Kampa, Volkmar Schulz, Johannes Stegmaier, Markus Rothermel, Dorit Merhof
2025	A*	`conf`	LogicAD: Explainable Anomaly Detection via VLM-based Text Feature Extraction. AAAI Er Jin, Qihui Feng, Yongli Mou, Gerhard Lakemeyer, Stefan Decker, Oliver Simons, Johannes Stegmaier
2025	J	`jnl`	LogicAD: Explainable Anomaly Detection via VLM-based Text Feature Extraction. CoRR Er Jin, Qihui Feng, Yongli Mou, Stefan Decker, Gerhard Lakemeyer, Oliver Simons, Johannes Stegmaier
2025	A*	`conf`	Minimalist Concept Erasure in Generative Models. ICML Yang Zhang, Er Jin, Yanfei Dong, Yixuan Wu, Philip Torr, Ashkan Khakzar, Johannes Stegmaier, Kenji Kawaguchi
2025	J	`jnl`	Minimalist Concept Erasure in Generative Models. CoRR Yang Zhang, Er Jin, Yanfei Dong, Yixuan Wu, Philip Torr, Ashkan Khakzar, Johannes Stegmaier, Kenji Kawaguchi
2025	—	`conf`	No Free Lunch in Annotation Either: An Objective Evaluation of Foundation Models for Streamlining Annotation in Animal Tracking. ISBI Emil Mededovic, Valdy Laurentius, Yuli Wu, Marcin Kopaczka, Zhu Chen, Mareike Schulz, René Tolba, Johannes Stegmaier
2025	J	`jnl`	No Free Lunch in Annotation either: An objective evaluation of foundation models for streamlining annotation in animal tracking. CoRR Emil Mededovic, Valdy Laurentius, Yuli Wu, Marcin Kopaczka, Zhu Chen, Mareike Schulz, René Tolba, Johannes Stegmaier
2025	—	`conf`	SIS-Challenge: Event-Based Spatio-Temporal Instance Segmentation Challenge at the CVPR 2025 Event-Based Vision Workshop. ICCVW Friedhelm Hamann, Emil Mededovic, Fabian Gülhan, Yue Wu, Johannes Stegmaier, Jing He, Yiqing Wang, Kexin Zhang, Lingling Li, Licheng Jiao, Mengru Ma, Hongxiang 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, Guillermo Gallego
2025	J	`jnl`	SIS-Challenge: Event-based Spatio-temporal Instance Segmentation Challenge at the CVPR 2025 Event-based Vision Workshop. CoRR Friedhelm Hamann, Emil Mededovic, Fabian Gülhan, Yue Wu, Johannes Stegmaier, Jing He, Yiqing Wang, Kexin Zhang, Lingling Li, Licheng Jiao, Mengru Ma, Hongxiang 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, Guillermo Gallego
2025	—	`conf`	Segment Anything for Cell Tracking. MedAGI Zhu Chen, Mert Edgü, Er Jin, Johannes Stegmaier
2025	J	`jnl`	Segment Anything for Cell Tracking. CoRR Zhu Chen, Mert Edgü, Er Jin, Johannes Stegmaier
2025	J	`jnl`	SelfMOTR: Revisiting MOTR with Self-Generating Detection Priors. CoRR Fabian Gülhan, Emil Mededovic, Yue Wu, Johannes Stegmaier
2025	J	`jnl`	Towards Robust and Generalizable Gerchberg Saxton based Physics Inspired Neural Networks for Computer Generated Holography: A Sensitivity Analysis Framework. CoRR Ankit Amrutkar, Björn Kampa, Volkmar Schulz, Johannes Stegmaier, Markus Rothermel, Dorit Merhof
2025	J	`jnl`	Unconsciously Forget: Mitigating Memorization; Without Knowing What is being Memorized. CoRR Er Jin, Yang Zhang, Yongli Mou, Yanfei Dong, Stefan Decker, Kenji Kawaguchi, Johannes Stegmaier
2025	J	`jnl`	Unsupervised Learning for Feature Extraction and Temporal Alignment of 3D+t Point Clouds of Zebrafish Embryos. CoRR Zhu Chen, Ina Laube, Johannes Stegmaier
2025	—	`conf`	Visual Fixation-Based Retinal Prosthetic Simulation. ISBI Yuli Wu, Do Dinh Tan Nguyen, Henning Konermann, Rüveyda Yilmaz, Peter Walter, Johannes Stegmaier
2024	—	`conf`	Annotated Biomedical Video Generation Using Denoising Diffusion Probabilistic Models and Flow Fields. SASHIMI@MICCAI Rüveyda Yilmaz, Dennis Eschweiler, Johannes Stegmaier
2024	J	`jnl`	Annotated Biomedical Video Generation using Denoising Diffusion Probabilistic Models and Flow Fields. CoRR Rüveyda Yilmaz, Dennis Eschweiler, Johannes Stegmaier
2024	J	`jnl`	Cascaded Diffusion Models for 2D and 3D Microscopy Image Synthesis to Enhance Cell Segmentation. CoRR Rüveyda Yilmaz, Kaan Keven, Yuli Wu, Johannes Stegmaier
2024	B	`conf`	Deep Learning Approach for Renal Cell Carcinoma Detection, Subtyping, And Grading. ICIP Maroof Abdul Aziz, Fatemeh Javadian, Sherin Susheel Mathew, Avinash Gopal, Johannes Stegmaier, Sonit Singh, Abin Jose
2024	J	`jnl`	Denoising diffusion probabilistic models for generation of realistic fully-annotated microscopy image datasets. PLoS Comput. Biol. Dennis Eschweiler, Rüveyda Yilmaz, Matisse Baumann, Ina Laube, Rijo Roy, Abin Jose, Daniel Brückner, Johannes Stegmaier
2024	J	`jnl`	Effortless Efficiency: Low-Cost Pruning of Diffusion Models. CoRR Yang Zhang, Er Jin, Yanfei Dong, Ashkan Khakzar, Philip Torr, Johannes Stegmaier, Kenji Kawaguchi
2024	J	`jnl`	Enhancing Lidar-based Object Detection in Adverse Weather using Offset Sequences in Time. CoRR Raphael van Kempen, Tim Rehbronn, Abin Jose, Johannes Stegmaier, Bastian Lampe, Timo Woopen, Lutz Eckstein
2024	J	`jnl`	Optimizing Retinal Prosthetic Stimuli with Conditional Invertible Neural Networks. CoRR Yuli Wu, Julian Wittmann, Peter Walter, Johannes Stegmaier
2024	—	`conf`	Retinal OCT Synthesis with Denoising Diffusion Probabilistic Models for Layer Segmentation. ISBI Yuli Wu, Weidong He, Dennis Eschweiler, Ningxin Dou, Zixin Fan, Shengli Mi, Peter Walter, Johannes Stegmaier
2024	J	`jnl`	Visual Fixation-Based Retinal Prosthetic Simulation. CoRR Yuli Wu, Do Dinh Tan Nguyen, Henning Konermann, Rüveyda Yilmaz, Peter Walter, Johannes Stegmaier
2023	—	`conf`	A Deep Learning-based in silico Framework for Optimization on Retinal Prosthetic Stimulation. EMBC Yuli Wu, Ivan Karetic, Johannes Stegmaier, Peter Walter, Dorit Merhof
2023	J	`jnl`	A Deep Learning-based in silico Framework for Optimization on Retinal Prosthetic Stimulation. CoRR Yuli Wu, Ivan Karetic, Johannes Stegmaier, Peter Walter, Dorit Merhof
2023	—	`conf`	Cascaded Cross-Attention Networks for Data-Efficient Whole-Slide Image Classification Using Transformers. MLMI@MICCAI (2) Firas Khader, Jakob Nikolas Kather, Tianyu Han, Sven Nebelung, Christiane Kuhl, Johannes Stegmaier, Daniel Truhn
2023	J	`jnl`	Cascaded Cross-Attention Networks for Data-Efficient Whole-Slide Image Classification Using Transformers. CoRR Firas Khader, Jakob Nikolas Kather, Tianyu Han, Sven Nebelung, Christiane Kuhl, Johannes Stegmaier, Daniel Truhn
2023	J	`jnl`	Denoising Diffusion Probabilistic Models for Generation of Realistic Fully-Annotated Microscopy Image Data Sets. CoRR Dennis Eschweiler, Johannes Stegmaier
2023	Misc	`conf`	End-to-End Classification of Cell-Cycle Stages with Center-Cell Focus Tracker Using Recurrent Neural Networks. ICASSP Abin Jose, Rijo Roy, Dennis Eschweiler, Ina Laube, Reza Azad, Daniel Moreno-Andrés, Johannes Stegmaier
2023	—	`conf`	Enhancing Lidar-Based Object Detection in Adverse Weather Using Offset Sequences in Time. ICECET Raphael van Kempen, Tim Rehbronn, Abin Jose, Johannes Stegmaier, Bastian Lampe, Timo Woopen, Lutz Eckstein
2023	—	`conf`	Multi-View Abnormality Detection in Clinical Knee MRI Studies Using Transformers. ISBI Firas Khader, Johannes Stegmaier, Sven Nebelung, Daniel Truhn
2023	J	`jnl`	Retinal OCT Synthesis with Denoising Diffusion Probabilistic Models for Layer Segmentation. CoRR Yuli Wu, Weidong He, Dennis Eschweiler, Ningxin Dou, Zixin Fan, Shengli Mi, Peter Walter, Johannes Stegmaier
2023	—	`conf`	SortedAP: Rethinking evaluation metrics for instance segmentation. ICCV (Workshops) Long Chen, Yuli Wu, Johannes Stegmaier, Dorit Merhof
2023	J	`jnl`	SortedAP: Rethinking evaluation metrics for instance segmentation. CoRR Long Chen, Yuli Wu, Johannes Stegmaier, Dorit Merhof
2023	J	`jnl`	Transformers for CT Reconstruction From Monoplanar and Biplanar Radiographs. CoRR Firas Khader, Gustav Müller-Franzes, Tianyu Han, Sven Nebelung, Christiane Kuhl, Johannes Stegmaier, Daniel Truhn
2023	—	`conf`	Transformers for CT Reconstruction from Monoplanar and Biplanar Radiographs. SASHIMI@MICCAI Firas Khader, Gustav Müller-Franzes, Tianyu Han, Sven Nebelung, Christiane Kuhl, Johannes Stegmaier, Daniel Truhn
2023	—	`conf`	Unsupervised Learning for Feature Extraction and Temporal Alignment of 3D+t Point Clouds of Zebrafish Embryos. MICCAI (8) Zhu Chen, Ina Laube, Johannes Stegmaier
2023	—	`conf`	Vector-Quantized Latent Flows for Medical Image Synthesis and Out-Of-Distribution Detection. ISBI Firas Khader, Gustav Müller-Franzes, Soroosh Tayebi Arasteh, Tianyu Han, Jakob Nikolas Kather, Johannes Stegmaier, Sven Nebelung, Daniel Truhn
2023	—	`conf`	Weakly-supervised Temporal Segmentation of Cell-cycle Stages with Center-cell Focus using Recurrent Neural Networks. Bildverarbeitung für die Medizin Abin Jose, Rijo Roy, Johannes Stegmaier
2022	B	`conf`	Linear Discriminant Analysis Metric Learning Using Siamese Neural Networks. ICIP Abin Jose, Qi Mei, Dennis Eschweiler, Ina Laube, Johannes Stegmaier
2022	J	`jnl`	Medical Diagnosis with Large Scale Multimodal Transformers: Leveraging Diverse Data for More Accurate Diagnosis. CoRR 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
2022	J	`jnl`	Medical Diffusion - Denoising Diffusion Probabilistic Models for 3D Medical Image Generation. CoRR 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, Sven Nebelung, Jakob Nikolas Kather, Daniel Truhn
2022	—	`conf`	Probabilistic Image Diversification to Improve Segmentation in 3D Microscopy Image Data. SASHIMI@MICCAI Dennis Eschweiler, Justus Schock, Johannes Stegmaier
2022	B	`conf`	Robust 3d Cell Segmentation: Extending The View Of Cellpose. ICIP Dennis Eschweiler, Richard S. Smith, Johannes Stegmaier
2021	J	`jnl`	3D fluorescence microscopy data synthesis for segmentation and benchmarking. CoRR Dennis Eschweiler, Malte Rethwisch, Mareike Jarchow, Simon Koppers, Johannes Stegmaier
2021	—	`conf`	Cellcyclegan: Spatiotemporal Microscopy Image Synthesis Of Cell Populations Using Statistical Shape Models And Conditional Gans. ISBI Dennis Bähr, Dennis Eschweiler, Anuk Bhattacharyya, Daniel Moreno-Andrés, Wolfram Antonin, Johannes Stegmaier
2021	J	`jnl`	Robust 3D Cell Segmentation: Extending the View of Cellpose. CoRR Dennis Eschweiler, Johannes Stegmaier
2021	J	`jnl`	Semi- and Self-Supervised Multi-View Fusion of 3D Microscopy Images using Generative Adversarial Networks. CoRR Canyu Yang, Dennis Eschweiler, Johannes Stegmaier
2021	—	`conf`	Semi- and Self-supervised Multi-view Fusion of 3D Microscopy Images Using Generative Adversarial Networks. MLMIR@MICCAI Canyu Yang, Dennis Eschweiler, Johannes Stegmaier
2021	—	`conf`	Spherical Harmonics For Shape-Constrained 3d Cell Segmentation. ISBI Dennis Eschweiler, Malte Rethwisch, Simon Koppers, Johannes Stegmaier
2020	J	`jnl`	A Multi-Organ Nucleus Segmentation Challenge. IEEE Trans. Medical Imaging Neeraj Kumar, Ruchika Verma, Deepak Anand, Yanning Zhou, Omer Fahri Onder, Efstratios Tsougenis, Hao Chen, Pheng-Ann Heng, Jiahui Li, Zhiqiang Hu, Yunzhi Wang, Navid Alemi Koohbanani, Mostafa Jahanifar, Neda Zamani Tajeddin, Ali Gooya, Nasir M. Rajpoot, Xuhua Ren, Sihang Zhou, Qian Wang, Dinggang Shen, Cheng-Kun Yang, Chi-Hung Weng, Wei-Hsiang Yu, Chao-Yuan Yeh, Shuang Yang, Shuoyu Xu, Pak-Hei Yeung, Peng Sun, Amirreza Mahbod, Gerald Schaefer, Isabella Ellinger, Rupert Ecker, Örjan Smedby, Chunliang Wang, Benjamin Chidester, That-Vinh Ton, Minh-Triet Tran, Jian Ma, Minh N. Do, Simon Graham, Quoc Dang Vu, Jin Tae Kwak, Akshaykumar Gunda, Raviteja Chunduri, Corey Hu, Xiaoyang Zhou, Dariush Lotfi, Reza Safdari, Antanas Kascenas, Alison O'Neil, Dennis Eschweiler, Johannes Stegmaier, Yanping Cui, Baocai Yin, Kailin Chen, Xinmei Tian, Philipp Grüning, Erhardt Barth, Elad Arbel, Itay Remer, Amir Ben-Dor, Ekaterina Sirazitdinova, Matthias Kohl, Stefan Braunewell, Yuexiang Li, Xinpeng Xie, Linlin Shen, Jun Ma, Krishanu Das Baksi, Mohammad Azam Khan, Jaegul Choo, Adrián Colomer, Valery Naranjo, Linmin Pei, Khan M. Iftekharuddin, Kaushiki Roy, Debotosh Bhattacharjee, Aníbal Pedraza, Maria Gloria Bueno, Sabarinathan Devanathan, Saravanan Radhakrishnan, Praveen Koduganty, Zihan Wu, Guanyu Cai, Xiaojie Liu, Yuqin Wang, Amit Sethi
2020	J	`jnl`	BeadNet: deep learning-based bead detection and counting in low-resolution microscopy images. Bioinform. Tim Scherr, Karolin Streule, Andreas Bartschat, Moritz Böhland, Johannes Stegmaier, Markus Reischl, Véronique Orian-Rousseau, Ralf Mikut
2020	J	`jnl`	CellCycleGAN: Spatiotemporal Microscopy Image Synthesis of Cell Populations using Statistical Shape Models and Conditional GANs. CoRR Dennis Bähr, Dennis Eschweiler, Anuk Bhattacharyya, Daniel Moreno-Andrés, Wolfram Antonin, Johannes Stegmaier
2020	J	`jnl`	Making Logic Learnable With Neural Networks. CoRR Tobias Brudermueller, Dennis L. Shung, Loren Laine, Adrian J. Stanley, Stig B. Laursen, Harry R. Dalton, Jeffrey Ngu, Michael Schultz, Johannes Stegmaier, Smita Krishnaswamy
2020	B	`conf`	Semi-Automatic Generation Of Tight Binary Masks And Non-Convex Isosurfaces For Quantitative Analysis Of 3d Biological Samples. ICIP Sourabh Bhide, Ralf Mikut, Maria Leptin, Johannes Stegmaier
2020	J	`jnl`	Semi-Automatic Generation of Tight Binary Masks and Non-Convex Isosurfaces for Quantitative Analysis of 3D Biological Samples. CoRR Sourabh Bhide, Ralf Mikut, Maria Leptin, Johannes Stegmaier
2020	J	`jnl`	Spherical Harmonics for Shape-Constrained 3D Cell Segmentation. CoRR Dennis Eschweiler, Malte Rethwisch, Simon Koppers, Johannes Stegmaier
2020	—	`conf`	Towards Automatic Embryo Staging in 3D+t Microscopy Images Using Convolutional Neural Networks and PointNets. SASHIMI@MICCAI Manuel Traub, Johannes Stegmaier
2019	J	`jnl`	Algorithms used for the Cell Segmentation Benchmark Competition at ISBI 2019 by RWTH-GE. CoRR Dennis Eschweiler, Johannes Stegmaier
2019	—	`conf`	CNN-Based Preprocessing to Optimize Watershed-Based Cell Segmentation in 3D Confocal Microscopy Images. ISBI Dennis Eschweiler, Thiago Vallin Spina, Rohan C. Choudhury, Elliot Meyerowitz, Alexandre Cunha, Johannes Stegmaier
2019	—	`conf`	Combined Learning for Similar Tasks with Domain-Switching Networks. MICCAI (5) Daniel Bug, Dennis Eschweiler, Qianyu Liu, Justus Schock, Leon Weninger, Friedrich Feuerhake, Julia Schüler, Johannes Stegmaier, Dorit Merhof
2019	J	`jnl`	Fuzzy tissue detection for real-time focal control in corneal confocal microscopy. Autom. Andreas Bartschat, Stephan Allgeier, Tim Scherr, Johannes Stegmaier, Sebastian Bohn, Klaus-Martin Reichert, Arjan Kuijper, Markus Reischl, Oliver Stachs, Bernd Köhler, Ralf Mikut
2019	—	`conf`	Towards Annotation-Free Segmentation of Fluorescently Labeled Cell Membranes in Confocal Microscopy Images. SASHIMI@MICCAI Dennis Eschweiler, Tim Klose, Florian Nicolas Müller-Fouarge, Marcin Kopaczka, Johannes Stegmaier
2019	J	`jnl`	Towards Automatic Embryo Staging in 3D+T Microscopy Images using Convolutional Neural Networks and PointNets. CoRR Manuel Traub, Johannes Stegmaier
2018	J	`jnl`	CNN-based Preprocessing to Optimize Watershed-based Cell Segmentation in 3D Confocal Microscopy Images. CoRR Dennis Eschweiler, Thiago Vallin Spina, Rohan C. Choudhury, Elliot Meyerowitz, Alexandre Cunha, Johannes Stegmaier
2018	—	`conf`	Cell segmentation in 3D confocal images using supervoxel merge-forests with CNN-based hypothesis selection. ISBI Johannes Stegmaier, Thiago Vallin Spina, Alexandre X. Falcão, Andreas Bartschat, Ralf Mikut, Elliot Meyerowitz, Alexandre Cunha
2018	J	`jnl`	EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos. PLoS Comput. Biol. 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, Ralf Mikut, Johannes Stegmaier
2018	—	`conf`	SEGMENT3D: A web-based application for collaborative segmentation of 3D images used in the shoot apical meristem. ISBI Thiago Vallin Spina, Johannes Stegmaier, Alexandre X. Falcão, Elliot Meyerowitz, Alexandre Cunha
2018	J	`jnl`	Transfer Learning with Human Corneal Tissues: An Analysis of Optimal Cut-Off Layer. CoRR Nadezhda Prodanova, Johannes Stegmaier, Stephan Allgeier, Sebastian Bohn, Oliver Stachs, Bernd Köhler, Ralf Mikut, Andreas Bartschat
2017	J	`jnl`	3D Cell Nuclei Segmentation with Balanced Graph Partitioning. CoRR Julian Arz, Peter Sanders, Johannes Stegmaier, Ralf Mikut
2017	J	`jnl`	Cell Segmentation in 3D Confocal Images using Supervoxel Merge-Forests with CNN-based Hypothesis Selection. CoRR Johannes Stegmaier, Thiago Vallin Spina, Alexandre X. Falcão, Andreas Bartschat, Ralf Mikut, Elliot Meyerowitz, Alexandre Cunha
2017	—	`—`	New Methods to Improve Large-Scale Microscopy Image Analysis with Prior Knowledge and Uncertainty. Johannes Stegmaier
2017	J	`jnl`	SEGMENT3D: A Web-based Application for Collaborative Segmentation of 3D images used in the Shoot Apical Meristem. CoRR Thiago Vallin Spina, Johannes Stegmaier, Alexandre X. Falcão, Elliot Meyerowitz, Alexandre Cunha
2017	J	`jnl`	The MATLAB Toolbox SciXMiner: User's Manual and Programmer's Guide. CoRR Ralf Mikut, Andreas Bartschat, Wolfgang Doneit, Jorge Ángel González Ordiano, Benjamin Schott, Johannes Stegmaier, Simon Waczowicz, Markus Reischl
2016	J	`jnl`	Automation strategies for large-scale 3D image analysis. Autom. 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, Uwe Strähle, Markus Reischl, Ralf Mikut
2016	J	`jnl`	Challenges of Integrating A Priori Information Efficiently in the Discovery of Spatio-Temporal Objects in Large Databases. CoRR Benjamin Schott, Johannes Stegmaier, Masanari Takamiya, Ralf Mikut
2016	J	`jnl`	Fuzzy-based Propagation of Prior Knowledge to Improve Large-Scale Image Analysis Pipelines. CoRR Johannes Stegmaier, Ralf Mikut
2016	J	`jnl`	Generating Semi-Synthetic Validation Benchmarks for Embryomics. CoRR Johannes Stegmaier, Julian Arz, Benjamin Schott, Jens C. Otte, Andrei Kobitski, G. Ulrich Nienhaus, Uwe Strähle, Peter Sanders, Ralf Mikut
2016	—	`conf`	Generating semi-synthetic validation benchmarks for embryomics. ISBI Johannes Stegmaier, Julian Arz, Benjamin Schott, Jens C. Otte, Andrei Kobitski, G. Ulrich Nienhaus, Uwe Strähle, Peter Sanders, Ralf Mikut
2016	J	`jnl`	New Methods to Improve Large-Scale Microscopy Image Analysis with Prior Knowledge and Uncertainty. CoRR Johannes Stegmaier
2016	J	`jnl`	XPIWIT - an XML pipeline wrapper for the Insight Toolkit. Bioinform. Andreas Bartschat, Eduard Hübner, Markus Reischl, Ralf Mikut, Johannes Stegmaier
2014	J	`jnl`	Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish. Bioinform. Johannes Stegmaier, Maryam Shahid, Masanari Takamiya, Lixin Yang, Sepand Rastegar, Markus Reischl, Uwe Strähle, Ralf Mikut