Johannes Stegmaier

ORCID

Publication Activity (10 Years)

Years Active: 2014-2024
Publications (10 Years): 60

Top Venues

Karlsruhe Institute of Technology, Germany (PHD)

Education History

Karlsruhe Institute of Technology, Germany

PHD

Publications

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 (2024)
Yuli Wu, Julian Wittmann, Peter Walter, Johannes Stegmaier
Optimizing Retinal Prosthetic Stimuli with Conditional Invertible Neural Networks. CoRR (2024)
Rüveyda Yilmaz, Dennis Eschweiler, Johannes Stegmaier
Annotated Biomedical Video Generation using Denoising Diffusion Probabilistic Models and Flow Fields. CoRR (2024)
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)
Firas Khader, Johannes Stegmaier, Sven Nebelung, Daniel Truhn
Multi-View Abnormality Detection in Clinical Knee MRI Studies Using Transformers. ISBI (2023)
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)
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 (2023)
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)
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 (2023)
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)
Long Chen, Yuli Wu, Johannes Stegmaier, Dorit Merhof
SortedAP: Rethinking evaluation metrics for instance segmentation. ICCV (Workshops) (2023)
Long Chen, Yuli Wu, Johannes Stegmaier, Dorit Merhof
SortedAP: Rethinking evaluation metrics for instance segmentation. CoRR (2023)
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)
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)
Dennis Eschweiler, Johannes Stegmaier
Denoising Diffusion Probabilistic Models for Generation of Realistic Fully-Annotated Microscopy Image Data Sets. CoRR (2023)
Yuli Wu, Ivan Karetic, Johannes Stegmaier, Peter Walter, Dorit Merhof
A Deep Learning-based in silico Framework for Optimization on Retinal Prosthetic Stimulation. CoRR (2023)
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)
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)
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 (2023)
Dennis Eschweiler, Justus Schock, Johannes Stegmaier
Probabilistic Image Diversification to Improve Segmentation in 3D Microscopy Image Data. SASHIMI@MICCAI (2022)
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 (2022)
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 (2022)
Abin Jose, Qi Mei, Dennis Eschweiler, Ina Laube, Johannes Stegmaier
Linear Discriminant Analysis Metric Learning Using Siamese Neural Networks. ICIP (2022)
Dennis Eschweiler, Richard S. Smith, Johannes Stegmaier
Robust 3d Cell Segmentation: Extending The View Of Cellpose. ICIP (2022)
Dennis Eschweiler, Malte Rethwisch, Mareike Jarchow, Simon Koppers, Johannes Stegmaier
3D fluorescence microscopy data synthesis for segmentation and benchmarking. CoRR (2021)
Canyu Yang, Dennis Eschweiler, Johannes Stegmaier
Semi- and Self-supervised Multi-view Fusion of 3D Microscopy Images Using Generative Adversarial Networks. MLMIR@MICCAI (2021)
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)
Dennis Eschweiler, Johannes Stegmaier
Robust 3D Cell Segmentation: Extending the View of Cellpose. CoRR (2021)
Canyu Yang, Dennis Eschweiler, Johannes Stegmaier
Semi- and Self-Supervised Multi-View Fusion of 3D Microscopy Images using Generative Adversarial Networks. CoRR (2021)
Dennis Eschweiler, Malte Rethwisch, Simon Koppers, Johannes Stegmaier
Spherical Harmonics For Shape-Constrained 3d Cell Segmentation. ISBI (2021)
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 (2020)
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 (2020)
Manuel Traub, Johannes Stegmaier
Towards Automatic Embryo Staging in 3D+t Microscopy Images Using Convolutional Neural Networks and PointNets. SASHIMI@MICCAI (2020)
Dennis Eschweiler, Malte Rethwisch, Simon Koppers, Johannes Stegmaier
Spherical Harmonics for Shape-Constrained 3D Cell Segmentation. CoRR (2020)
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)
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) (2020)
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 (2020)
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) (2020)
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)
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) (2019)
Manuel Traub, Johannes Stegmaier
Towards Automatic Embryo Staging in 3D+T Microscopy Images using Convolutional Neural Networks and PointNets. CoRR (2019)
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)
Dennis Eschweiler, Johannes Stegmaier
Algorithms used for the Cell Segmentation Benchmark Competition at ISBI 2019 by RWTH-GE. CoRR (2019)
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)
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 (2018)
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)
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)
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 (2018)
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)
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 (2017)
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 (2017)
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 (2017)
Julian Arz, Peter Sanders, Johannes Stegmaier, Ralf Mikut
3D Cell Nuclei Segmentation with Balanced Graph Partitioning. CoRR (2017)
Andreas Bartschat, Eduard Hübner, Markus Reischl, Ralf Mikut, Johannes Stegmaier
XPIWIT - an XML pipeline wrapper for the Insight Toolkit. Bioinform. 32 (2) (2016)
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) (2016)
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 (2016)
Johannes Stegmaier
New Methods to Improve Large-Scale Microscopy Image Analysis with Prior Knowledge and Uncertainty. CoRR (2016)
Johannes Stegmaier, Ralf Mikut
Fuzzy-based Propagation of Prior Knowledge to Improve Large-Scale Image Analysis Pipelines. CoRR (2016)
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)
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 (2016)
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) (2014)

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Publication Activity (10 Years)

Top Topics

Top Venues

Johannes Stegmaier