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2020 – today
- 2025
[c26]Er Jin, Qihui Feng, Yongli Mou, Gerhard Lakemeyer, Stefan Decker, Oliver Simons, Johannes Stegmaier:
LogicAD: Explainable Anomaly Detection via VLM-based Text Feature Extraction. AAAI 2025: 4129-4137- [d1]Yuli Wu
, Henning Konermann, Emil Mededovic, Peter Walter, Johannes Stegmaier:
Dataset for Cross-Device and Cross-Subject Consistency Evaluation in Visual Fixation Prediction. IEEE DataPort, 2025
- [i40]Er Jin, Qihui Feng, Yongli Mou, Stefan Decker, Gerhard Lakemeyer, Oliver Simons, Johannes Stegmaier:
LogicAD: Explainable Anomaly Detection via VLM-based Text Feature Extraction. CoRR abs/2501.01767 (2025) - [i39]Emil Mededovic, Valdy Laurentius, Yuli Wu, Marcin Kopaczka, Zhu Chen, Mareike Schulz, René Tolba, Johannes Stegmaier:
No Free Lunch in Annotation either: An objective evaluation of foundation models for streamlining annotation in animal tracking. CoRR abs/2502.03907 (2025) - [i38]Yuli Wu, Henning Konermann, Emil Mededovic, Peter Walter, Johannes Stegmaier:
Evaluating Cross-Subject and Cross-Device Consistency in Visual Fixation Prediction. CoRR abs/2502.05554 (2025) - [i37]Zhu Chen, Ina Laube, Johannes Stegmaier:
Unsupervised Learning for Feature Extraction and Temporal Alignment of 3D+t Point Clouds of Zebrafish Embryos. CoRR abs/2502.06543 (2025) - [i36]Yuli Wu, Fucheng Liu, Rüveyda Yilmaz, Henning Konermann, Peter Walter, Johannes Stegmaier:
A Pragmatic Note on Evaluating Generative Models with Fréchet Inception Distance for Retinal Image Synthesis. CoRR abs/2502.17160 (2025) - [i35]Rüveyda Yilmaz, Zhu Chen, Yuli Wu, Johannes Stegmaier:
CellStyle: Improved Zero-Shot Cell Segmentation via Style Transfer. CoRR abs/2503.08603 (2025) - [i34]Emil Mededovic, Yuli Wu, Henning Konermann, Marcin Kopaczka, Mareike Schulz, René Tolba, Johannes Stegmaier:
Eye on the Target: Eye Tracking Meets Rodent Tracking. CoRR abs/2503.10305 (2025) - 2024
- [j8]Dennis Eschweiler, Rüveyda Yilmaz, Matisse Baumann, Ina Laube, Rijo Roy, Abin Jose, Daniel Brückner, Johannes Stegmaier:
Denoising diffusion probabilistic models for generation of realistic fully-annotated microscopy image datasets. PLoS Comput. Biol. 20(2) (2024) - [c25]Yuli Wu, Weidong He, Dennis Eschweiler, Ningxin Dou, Zixin Fan, Shengli Mi, Peter Walter, Johannes Stegmaier:
Retinal OCT Synthesis with Denoising Diffusion Probabilistic Models for Layer Segmentation. ISBI 2024: 1-5 - [c24]Rüveyda Yilmaz, Dennis Eschweiler, Johannes Stegmaier:
Annotated Biomedical Video Generation Using Denoising Diffusion Probabilistic Models and Flow Fields. SASHIMI@MICCAI 2024: 197-207 - [i33]Raphael van Kempen, Tim Rehbronn, Abin Jose, Johannes Stegmaier, Bastian Lampe, Timo Woopen, Lutz Eckstein:
Enhancing Lidar-based Object Detection in Adverse Weather using Offset Sequences in Time. CoRR abs/2401.09049 (2024) - [i32]Yuli Wu, Julian Wittmann, Peter Walter, Johannes Stegmaier:
Optimizing Retinal Prosthetic Stimuli with Conditional Invertible Neural Networks. CoRR abs/2403.04884 (2024) - [i31]Rüveyda Yilmaz, Dennis Eschweiler, Johannes Stegmaier:
Annotated Biomedical Video Generation using Denoising Diffusion Probabilistic Models and Flow Fields. CoRR abs/2403.17808 (2024) - [i30]Yuli Wu, Do Dinh Tan Nguyen, Henning Konermann, Rüveyda Yilmaz, Peter Walter, Johannes Stegmaier:
Visual Fixation-Based Retinal Prosthetic Simulation. CoRR abs/2410.11688 (2024) - [i29]Rüveyda Yilmaz, Kaan Keven, Yuli Wu, Johannes Stegmaier:
Cascaded Diffusion Models for 2D and 3D Microscopy Image Synthesis to Enhance Cell Segmentation. CoRR abs/2411.11515 (2024) - [i28]Yang Zhang, Er Jin, Yanfei Dong, Ashkan Khakzar, Philip Torr, Johannes Stegmaier, Kenji Kawaguchi:
Effortless Efficiency: Low-Cost Pruning of Diffusion Models. CoRR abs/2412.02852 (2024) - 2023
- [c23]Abin Jose, Rijo Roy, Johannes Stegmaier:
Weakly-supervised Temporal Segmentation of Cell-cycle Stages with Center-cell Focus using Recurrent Neural Networks. Bildverarbeitung für die Medizin 2023: 212-219 - [c22]Yuli Wu, Ivan Karetic, Johannes Stegmaier, Peter Walter, Dorit Merhof:
A Deep Learning-based in silico Framework for Optimization on Retinal Prosthetic Stimulation. EMBC 2023: 1-4 - [c21]Abin Jose, Rijo Roy, Dennis Eschweiler, Ina Laube, Reza Azad, Daniel Moreno-Andrés, Johannes Stegmaier:
End-to-End Classification of Cell-Cycle Stages with Center-Cell Focus Tracker Using Recurrent Neural Networks. ICASSP 2023: 1-5 - [c20]Long Chen, Yuli Wu, Johannes Stegmaier, Dorit Merhof:
SortedAP: Rethinking evaluation metrics for instance segmentation. ICCV (Workshops) 2023: 3925-3931 - [c19]Firas Khader, Gustav Müller-Franzes, Soroosh Tayebi Arasteh, Tianyu Han, Jakob Nikolas Kather, Johannes Stegmaier, Sven Nebelung, Daniel Truhn:
Vector-Quantized Latent Flows for Medical Image Synthesis and Out-Of-Distribution Detection. ISBI 2023: 1-5 - [c18]Firas Khader, Johannes Stegmaier, Sven Nebelung, Daniel Truhn:
Multi-View Abnormality Detection in Clinical Knee MRI Studies Using Transformers. ISBI 2023: 1-4 - [c17]Firas Khader, Gustav Müller-Franzes, Tianyu Han, Sven Nebelung, Christiane Kuhl, Johannes Stegmaier, Daniel Truhn:
Transformers for CT Reconstruction from Monoplanar and Biplanar Radiographs. SASHIMI@MICCAI 2023: 1-10 - [c16]Zhu Chen, Ina Laube, Johannes Stegmaier:
Unsupervised Learning for Feature Extraction and Temporal Alignment of 3D+t Point Clouds of Zebrafish Embryos. MICCAI (8) 2023: 603-612 - [c15]Firas Khader, Jakob Nikolas Kather, Tianyu Han, Sven Nebelung, Christiane Kuhl, Johannes Stegmaier, Daniel Truhn:
Cascaded Cross-Attention Networks for Data-Efficient Whole-Slide Image Classification Using Transformers. MLMI@MICCAI (2) 2023: 417-426 - [i27]Dennis Eschweiler, Johannes Stegmaier:
Denoising Diffusion Probabilistic Models for Generation of Realistic Fully-Annotated Microscopy Image Data Sets. CoRR abs/2301.10227 (2023) - [i26]Yuli Wu, Ivan Karetic, Johannes Stegmaier, Peter Walter, Dorit Merhof:
A Deep Learning-based in silico Framework for Optimization on Retinal Prosthetic Stimulation. CoRR abs/2302.03570 (2023) - [i25]Firas Khader, Jakob Nikolas Kather, Tianyu Han, Sven Nebelung, Christiane Kuhl, Johannes Stegmaier, Daniel Truhn:
Cascaded Cross-Attention Networks for Data-Efficient Whole-Slide Image Classification Using Transformers. CoRR abs/2305.06963 (2023) - [i24]Firas Khader, Gustav Müller-Franzes, Tianyu Han, Sven Nebelung, Christiane Kuhl, Johannes Stegmaier, Daniel Truhn:
Transformers for CT Reconstruction From Monoplanar and Biplanar Radiographs. CoRR abs/2305.06965 (2023) - [i23]Long Chen, Yuli Wu, Johannes Stegmaier, Dorit Merhof:
SortedAP: Rethinking evaluation metrics for instance segmentation. CoRR abs/2309.04887 (2023) - [i22]Yuli Wu, Weidong He, Dennis Eschweiler, Ningxin Dou, Zixin Fan, Shengli Mi, Peter Walter, Johannes Stegmaier:
Retinal OCT Synthesis with Denoising Diffusion Probabilistic Models for Layer Segmentation. CoRR abs/2311.05479 (2023) - 2022
- [c14]Dennis Eschweiler, Richard S. Smith, Johannes Stegmaier:
Robust 3d Cell Segmentation: Extending The View Of Cellpose. ICIP 2022: 191-195 - [c13]Abin Jose, Qi Mei, Dennis Eschweiler, Ina Laube, Johannes Stegmaier:
Linear Discriminant Analysis Metric Learning Using Siamese Neural Networks. ICIP 2022: 3641-3645 - [c12]Dennis Eschweiler, Justus Schock, Johannes Stegmaier:
Probabilistic Image Diversification to Improve Segmentation in 3D Microscopy Image Data. SASHIMI@MICCAI 2022: 24-33 - [i21]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:
Medical Diffusion - Denoising Diffusion Probabilistic Models for 3D Medical Image Generation. CoRR abs/2211.03364 (2022) - [i20]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:
Medical Diagnosis with Large Scale Multimodal Transformers: Leveraging Diverse Data for More Accurate Diagnosis. CoRR abs/2212.09162 (2022) - 2021
- [c11]Dennis Bähr, Dennis Eschweiler, Anuk Bhattacharyya, Daniel Moreno-Andrés, Wolfram Antonin, Johannes Stegmaier:
Cellcyclegan: Spatiotemporal Microscopy Image Synthesis Of Cell Populations Using Statistical Shape Models And Conditional Gans. ISBI 2021: 15-19 - [c10]Dennis Eschweiler, Malte Rethwisch, Simon Koppers, Johannes Stegmaier:
Spherical Harmonics For Shape-Constrained 3d Cell Segmentation. ISBI 2021: 792-796 - [c9]Canyu Yang, Dennis Eschweiler, Johannes Stegmaier:
Semi- and Self-supervised Multi-view Fusion of 3D Microscopy Images Using Generative Adversarial Networks. MLMIR@MICCAI 2021: 130-139 - [i19]Dennis Eschweiler, Johannes Stegmaier:
Robust 3D Cell Segmentation: Extending the View of Cellpose. CoRR abs/2105.00794 (2021) - [i18]Dennis Eschweiler, Malte Rethwisch, Mareike Jarchow, Simon Koppers, Johannes Stegmaier:
3D fluorescence microscopy data synthesis for segmentation and benchmarking. CoRR abs/2107.10180 (2021) - [i17]Canyu Yang, Dennis Eschweiler, Johannes Stegmaier:
Semi- and Self-Supervised Multi-View Fusion of 3D Microscopy Images using Generative Adversarial Networks. CoRR abs/2108.02743 (2021) - 2020
- [j7]Tim Scherr, Karolin Streule, Andreas Bartschat, Moritz Böhland, Johannes Stegmaier, Markus Reischl, Véronique Orian-Rousseau, Ralf Mikut:
BeadNet: deep learning-based bead detection and counting in low-resolution microscopy images. Bioinform. 36(17): 4668-4670 (2020) - [j6]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:
A Multi-Organ Nucleus Segmentation Challenge. IEEE Trans. Medical Imaging 39(5): 1380-1391 (2020) - [c8]Sourabh Bhide, Ralf Mikut, Maria Leptin, Johannes Stegmaier:
Semi-Automatic Generation Of Tight Binary Masks And Non-Convex Isosurfaces For Quantitative Analysis Of 3d Biological Samples. ICIP 2020: 2820-2824 - [c7]Manuel Traub, Johannes Stegmaier:
Towards Automatic Embryo Staging in 3D+t Microscopy Images Using Convolutional Neural Networks and PointNets. SASHIMI@MICCAI 2020: 153-163 - [i16]Sourabh Bhide, Ralf Mikut, Maria Leptin, Johannes Stegmaier:
Semi-Automatic Generation of Tight Binary Masks and Non-Convex Isosurfaces for Quantitative Analysis of 3D Biological Samples. CoRR abs/2001.11469 (2020) - [i15]Tobias Brudermueller, Dennis L. Shung, Loren Laine, Adrian J. Stanley, Stig B. Laursen, Harry R. Dalton, Jeffrey Ngu, Michael Schultz, Johannes Stegmaier, Smita Krishnaswamy:
Making Logic Learnable With Neural Networks. CoRR abs/2002.03847 (2020) - [i14]Dennis Bähr, Dennis Eschweiler, Anuk Bhattacharyya, Daniel Moreno-Andrés, Wolfram Antonin, Johannes Stegmaier:
CellCycleGAN: Spatiotemporal Microscopy Image Synthesis of Cell Populations using Statistical Shape Models and Conditional GANs. CoRR abs/2010.12011 (2020) - [i13]Dennis Eschweiler, Malte Rethwisch, Simon Koppers, Johannes Stegmaier:
Spherical Harmonics for Shape-Constrained 3D Cell Segmentation. CoRR abs/2010.12369 (2020)
2010 – 2019
- 2019
- [j5]Andreas Bartschat, Stephan Allgeier, Tim Scherr, Johannes Stegmaier, Sebastian Bohn, Klaus-Martin Reichert, Arjan Kuijper, Markus Reischl, Oliver Stachs, Bernd Köhler, Ralf Mikut:
Fuzzy tissue detection for real-time focal control in corneal confocal microscopy. Autom. 67(10): 879-888 (2019) - [c6]Dennis Eschweiler, Thiago Vallin Spina, Rohan C. Choudhury, Elliot Meyerowitz, Alexandre Cunha, Johannes Stegmaier:
CNN-Based Preprocessing to Optimize Watershed-Based Cell Segmentation in 3D Confocal Microscopy Images. ISBI 2019: 223-227 - [c5]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. SASHIMI@MICCAI 2019: 81-89 - [c4]Daniel Bug, Dennis Eschweiler, Qianyu Liu, Justus Schock, Leon Weninger, Friedrich Feuerhake, Julia Schüler, Johannes Stegmaier, Dorit Merhof:
Combined Learning for Similar Tasks with Domain-Switching Networks. MICCAI (5) 2019: 565-572 - [i12]Dennis Eschweiler, Johannes Stegmaier:
Algorithms used for the Cell Segmentation Benchmark Competition at ISBI 2019 by RWTH-GE. CoRR abs/1904.06890 (2019) - [i11]Manuel Traub, Johannes Stegmaier:
Towards Automatic Embryo Staging in 3D+T Microscopy Images using Convolutional Neural Networks and PointNets. CoRR abs/1910.00443 (2019) - 2018
- [j4]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:
EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos. PLoS Comput. Biol. 14(4) (2018) - [c3]Johannes Stegmaier, Thiago Vallin Spina, Alexandre X. Falcão, Andreas Bartschat, Ralf Mikut, Elliot Meyerowitz, Alexandre Cunha:
Cell segmentation in 3D confocal images using supervoxel merge-forests with CNN-based hypothesis selection. ISBI 2018: 382-386 - [c2]Thiago Vallin Spina, Johannes Stegmaier, Alexandre X. Falcão, Elliot Meyerowitz, Alexandre Cunha:
SEGMENT3D: A web-based application for collaborative segmentation of 3D images used in the shoot apical meristem. ISBI 2018: 391-395 - [i10]Nadezhda Prodanova, Johannes Stegmaier, Stephan Allgeier, Sebastian Bohn, Oliver Stachs, Bernd Köhler, Ralf Mikut, Andreas Bartschat:
Transfer Learning with Human Corneal Tissues: An Analysis of Optimal Cut-Off Layer. CoRR abs/1806.07073 (2018) - [i9]Dennis Eschweiler, Thiago Vallin Spina, Rohan C. Choudhury, Elliot Meyerowitz, Alexandre Cunha, Johannes Stegmaier:
CNN-based Preprocessing to Optimize Watershed-based Cell Segmentation in 3D Confocal Microscopy Images. CoRR abs/1810.06933 (2018) - 2017
- [b1]Johannes Stegmaier:
New Methods to Improve Large-Scale Microscopy Image Analysis with Prior Knowledge and Uncertainty. Karlsruhe Institute of Technology, Germany, KIT Scientific Publishing 2017 - [i8]Julian Arz, Peter Sanders, Johannes Stegmaier, Ralf Mikut:
3D Cell Nuclei Segmentation with Balanced Graph Partitioning. CoRR abs/1702.05413 (2017) - [i7]Ralf Mikut, Andreas Bartschat, Wolfgang Doneit, Jorge Ángel González Ordiano, Benjamin Schott, Johannes Stegmaier, Simon Waczowicz, Markus Reischl:
The MATLAB Toolbox SciXMiner: User's Manual and Programmer's Guide. CoRR abs/1704.03298 (2017) - [i6]Johannes Stegmaier, Thiago Vallin Spina, Alexandre X. Falcão, Andreas Bartschat, Ralf Mikut, Elliot Meyerowitz, Alexandre Cunha:
Cell Segmentation in 3D Confocal Images using Supervoxel Merge-Forests with CNN-based Hypothesis Selection. CoRR abs/1710.06608 (2017) - [i5]Thiago Vallin Spina, Johannes Stegmaier, Alexandre X. Falcão, Elliot Meyerowitz, Alexandre Cunha:
SEGMENT3D: A Web-based Application for Collaborative Segmentation of 3D images used in the Shoot Apical Meristem. CoRR abs/1710.09933 (2017) - 2016
- [j3]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:
Automation strategies for large-scale 3D image analysis. Autom. 64(7): 555-566 (2016) - [j2]Andreas Bartschat, Eduard Hübner, Markus Reischl, Ralf Mikut, Johannes Stegmaier:
XPIWIT - an XML pipeline wrapper for the Insight Toolkit. Bioinform. 32(2): 315-317 (2016) - [c1]Johannes Stegmaier, Julian Arz, Benjamin Schott, Jens C. Otte, Andrei Kobitski, G. Ulrich Nienhaus, Uwe Strähle, Peter Sanders, Ralf Mikut:
Generating semi-synthetic validation benchmarks for embryomics. ISBI 2016: 684-688 - [i4]Benjamin Schott, Johannes Stegmaier, Masanari Takamiya, Ralf Mikut:
Challenges of Integrating A Priori Information Efficiently in the Discovery of Spatio-Temporal Objects in Large Databases. CoRR abs/1602.02938 (2016) - [i3]Johannes Stegmaier, Julian Arz, Benjamin Schott, Jens C. Otte, Andrei Kobitski, G. Ulrich Nienhaus, Uwe Strähle, Peter Sanders, Ralf Mikut:
Generating Semi-Synthetic Validation Benchmarks for Embryomics. CoRR abs/1604.04906 (2016) - [i2]Johannes Stegmaier, Ralf Mikut:
Fuzzy-based Propagation of Prior Knowledge to Improve Large-Scale Image Analysis Pipelines. CoRR abs/1608.01276 (2016) - [i1]Johannes Stegmaier:
New Methods to Improve Large-Scale Microscopy Image Analysis with Prior Knowledge and Uncertainty. CoRR abs/1608.08471 (2016) - 2014
- [j1]Johannes Stegmaier, Maryam Shahid, Masanari Takamiya, Lixin Yang, Sepand Rastegar, Markus Reischl, Uwe Strähle, Ralf Mikut:
Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish. Bioinform. 30(5): 726-733 (2014)
Coauthor Index
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