FI
Fabian Isensee
cs.CVeess.IVcs.LGcs.AIImage Processing, Computer-AssistedAlgorithmsDeep learningArtificial IntelligenceBrain NeoplasmsTomography, X-Ray Computed
On Valency
published · living versionsW_m9v2fqa5·v1 · currentpublished
nnInteractive Agent: General-Purpose AI Agents as 3D Image Annotators
with Constantin Ulrich Harsy, Maximilian Rokuss, Benjamin Hamm, Philipp Vollmuth +1
1 version
Preprints & journals
114 papers in the corpus · 2016–2026nnInteractive Agent: General-Purpose AI Agents as 3D Image Annotators2610.31080v1 · Fabian Isensee, Constantin Ulrich Harsy, Maximilian Rokuss et al.2026 · 0 citationsarXivon Valency
nnFoundation: 3D Foundation Models for Radiology2609.26924v1 · Constantin Ulrich Harsy, Tassilo Wald, Karol Gotkowski et al.2026 · 0 citationsarXiv
MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography.42711494 · Lamm, Lorenz, Zufferey, Simon, Zhang, Hanyi et al.2026 · 152 citationsNature methods. 2026
ToothSeg: Robust Tooth Instance Segmentation and Numbering in CBCT Using Deep Learning and Self-Correction.41477803 · Nistelrooij, Niels van, Kramer, Lars, Kempers, Steven et al.2026 · 3 citationsIEEE journal of biomedical and health informatics. 2026;30(8):6801-6812
Multi-class segmentation of aortic branches and zones in computed tomography angiography: The AortaSeg24 challenge.42413466 · Imran, Muhammad, Krebs, Jonathan R, Sivaraman, Vishal Balaji et al.2026 · 2 citationsMedical image analysis. 2026;113:104188
Gut decisions based on the liver: prediction of colorectal neoplasia using AI-based liver analysis of routine CT scans.42318460 · Hinterberger, Anna, Bohn, Jonas, Trofimova, Darya et al.2026 · 0 citationsFrontiers in oncology. 2026;16:1842743
Lost in the Folds: When Cross-Validation Is Not a Deep Ensemble for Uncertainty Estimation2605.18329v2 · Tristan Kirscher, Markus Bujotzek (DKFZ), Yannick Kirchhoff (DKFZ) et al.2026 · 0 citations29th International Conference On Medical Image Computing And Computer Assisted Intervention, Sep 2026, Strasbourg, France
TriALS: Triphasic-Aided Liver Lesion Segmentation Benchmark in Non-Contrast CT2605.16572v1 · Marawan Elbatel, Mohamed Ghonim, Jiaji Mao et al.2026 · 0 citationsarXiv
The autoPET3 Challenge: Automated Lesion Segmentation in Whole-Body PET/CT $\unicode{x2013}$ Multitracer Multicenter Generalization2605.05775v2 · Jakob Dexl, Katharina Jeblick, Andreas Mittermeier et al.2026 · 1 citationarXiv
Incorporating functional soft tissue deformations in AI model training for spatially accurate prostate cancer detection.42097246 · Kovacs, Balint, Zhang, Kevin Sun, Baumgartner, Michael et al.2026 · 0 citationsMagnetic resonance imaging. 2026;131:110698
Benchmark of Segmentation Techniques for Pelvic Fracture in CT and X-Ray: Summary of the PENGWIN 2024 Challenge.41477796 · Sang, Yudi, Liu, Yanzhen, Yibulayimu, Sutuke et al.2026 · 2 citationsIEEE transactions on medical imaging. 2026;45(5):2212-2228
Multi-structure segmentation in CBCT volumes: The ToothFairy2 challenge.42102640 · Bolelli, Federico, Lumetti, Luca, van Nistelrooij, Niels et al.2026 · 3 citationsMedical image analysis. 2026;112:104095
AutoPET Challenge on Fully Automated Lesion Segmentation in Oncologic PET/CT Imaging, Part 2: Domain Generalization.41469162 · Dexl, Jakob, Gatidis, Sergios, Früh, Marcel et al.2026 · 14 citationsJournal of nuclear medicine : official publication, Society of Nuclear Medicine. 2026;67(3):481-488
Explainable AI-based analysis of human pancreas sections identifies traits of type 2 diabetes.41663377 · Klein, Lukas, Ziegler, Sebastian, Gerst, Felicia et al.2026 · 6 citationsNature communications. 2026;17(1):1558
Finally Outshining the Random Baseline: A Simple and Effective Solution for Active Learning in 3D Biomedical Imaging2601.13677v1 · Carsten T. Luth, Jeremias Traub, Kim-Celine Kahl et al.2026 · 0 citationsarXiv
MedNeXt-v2: Scaling 3D ConvNeXts for Large-Scale Supervised Representation Learning in Medical Image Segmentation2512.17774v1 · Saikat Roy, Yannick Kirchhoff, Constantin Ulrich et al.2025 · 0 citationsarXiv
VoxTell: Free-Text Promptable Universal 3D Medical Image Segmentation2511.11450v1 · Maximilian Rokuss, Moritz Langenberg, Yannick Kirchhoff et al.2025 · 0 citationsarXiv
Gut decisions based on the liver: A radiomics approach to boost colorectal cancer screening2510.23687v1 · Anna Hinterberger, Jonas Bohn, Dasha Trofimova et al.2025 · 0 citationsarXiv
Promptable Longitudinal Lesion Segmentation in Whole-Body CT2509.00613v1 · Yannick Kirchhoff, Maximilian Rokuss, Fabian Isensee et al.2025 · 0 citationsarXiv
Towards Interactive Lesion Segmentation in Whole-Body PET/CT with Promptable Models2508.21680v1 · Maximilian Rokuss, Yannick Kirchhoff, Fabian Isensee et al.2025 · 0 citationsarXiv
Benchmarking the CoW with the TopCoW Challenge: Topology-Aware Anatomical Segmentation of the Circle of Willis for CTA and MRA.38235066 · Yang, Kaiyuan, Musio, Fabio, Ma, Yihui et al.2026 · 19 citationsArXiv. 2025
Towards fair decentralized benchmarking of healthcare AI algorithms with the Federated Tumor Segmentation (FeTS) challenge.40628696 · Zenk, Maximilian, Baid, Ujjwal, Pati, Sarthak et al.2025 · 16 citationsNature communications. 2025;16(1):6274
Large Scale Supervised Pretraining For Traumatic Brain Injury Segmentation2504.06741v1 · Constantin Ulrich, Tassilo Wald, Fabian Isensee et al.2025 · 1 citationarXiv
nnLandmark: A Self-Configuring Method for 3D Medical Landmark Detection2504.06742v3 · Alexandra Ertl, Stefan Denner, Robin Peretzke et al.2025 · 0 citationsProceedings of The 9th International Conference on Medical Imaging with Deep Learning, PMLR 315:894-927, 2026
nnInteractive: Redefining 3D Promptable Segmentation2503.08373v1 · Fabian Isensee, Maximilian Rokuss, Lars Kramer et al.2025 · 13 citationsarXiv
Primus: Enforcing Attention Usage for 3D Medical Image Segmentation2503.01835v2 · Tassilo Wald, Saikat Roy, Fabian Isensee et al.2025 · 2 citationsarXiv
Bridging vision language model (VLM) evaluation gaps with a framework for scalable and cost-effective benchmark generation2502.15563v1 · Tim Radsch, Leon Mayer, Simon Pavicic et al.2025 · 0 citationsarXiv
A Fully Automated Artificial Intelligence-Based Approach to Predict Renal Function After Radical or Partial Nephrectomy.39914676 · Abdallah, Nour, Rathi, Nityam, Heller, Nicholas et al.2025 · 6 citationsUrology. 2025;200:97-104
Code and Pixels: Multi-Modal Contrastive Pre-training for Enhanced Tabular Data Analysis2501.07304v1 · Kankana Roy, Lars Kramer, Sebastian Domaschke et al.2025 · 0 citationsarXiv
Expectation-Maximization as the Engine of Scalable Medical Intelligence2501.03410v2 · Wenxuan Li, Pedro R. A. S. Bassi, Tianyu Lin et al.2025 · 0 citationsarXiv
Comparative benchmarking of failure detection methods in medical image segmentation: Unveiling the role of confidence aggregation.39657400 · Zenk, Maximilian, Zimmerer, David, Isensee, Fabian et al.2025 · 20 citationsMedical image analysis. 2025;101:103392
LungVis 1.0: an automatic AI-powered 3D imaging ecosystem unveils spatial profiling of nanoparticle delivery and acinar migration of lung macrophages.39604430 · Yang, Lin, Liu, Qiongliang, Kumar, Pramod et al.2024 · 24 citationsNature communications. 2024;15(1):10138
Scaling nnU-Net for CBCT Segmentation2411.17213v2 · Fabian Isensee, Yannick Kirchhoff, Lars Kraemer et al.2024 · 8 citationsarXiv
Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation?2411.03670v2 · Pedro R. A. S. Bassi, Wenxuan Li, Yucheng Tang et al.2024 · 5 citationsarXiv
Decoupling Semantic Similarity from Spatial Alignment for Neural Networks2410.23107v1 · Tassilo Wald, Constantin Ulrich, Gregor Kohler et al.2024 · 0 citationsarXiv
Longitudinal Segmentation of MS Lesions via Temporal Difference Weighting2409.13416v1 · Maximilian Rokuss, Yannick Kirchhoff, Saikat Roy et al.2024 · 6 citationsarXiv
Data-Centric Strategies for Overcoming PET/CT Heterogeneity: Insights from the AutoPET III Lesion Segmentation Challenge2409.10120v1 · Balint Kovacs, Shuhan Xiao, Maximilian Rokuss et al.2024 · 0 citationsarXiv
From FDG to PSMA: A Hitchhiker's Guide to Multitracer, Multicenter Lesion Segmentation in PET/CT Imaging2409.09478v2 · Maximilian Rokuss, Balint Kovacs, Yannick Kirchhoff et al.2024 · 5 citationsarXiv
Quality Assured: Rethinking Annotation Strategies in Imaging AI2407.17596v2 · Tim Radsch, Annika Reinke, Vivienn Weru et al.2024 · 9 citationsarXiv
Mitigating False Predictions In Unreasonable Body Regions2404.15718v1 · Constantin Ulrich, Catherine Knobloch, Julius C. Holzschuh et al.2024 · 1 citationarXiv
nnU-Net Revisited: A Call for Rigorous Validation in 3D Medical Image Segmentation2404.09556v2 · Fabian Isensee, Tassilo Wald, Constantin Ulrich et al.2024 · 408 citationsarXiv
Skeleton Recall Loss for Connectivity Conserving and Resource Efficient Segmentation of Thin Tubular Structures2404.03010v2 · Yannick Kirchhoff, Maximilian R. Rokuss, Saikat Roy et al.2024 · 46 citationsarXiv
Revisiting 3D Medical Scribble Supervision: Benchmarking Beyond Cardiac Segmentation2403.12834v2 · Karol Gotkowski, Klaus H. Maier-Hein, Fabian Isensee2024 · 5 citationsarXiv
Understanding metric-related pitfalls in image analysis validation.36945687 · Reinke, Annika, Tizabi, Minu D, Baumgartner, Michael et al.2025 · 233 citationsArXiv. 2024
Fully Automated Versions of Clinically Validated Nephrometry Scores Demonstrate Superior Predictive Utility versus Human Scores.38343198 · Wood, Andrew M, Abdallah, Nour, Heller, Nicholas et al.2024 · 8 citationsBJU international. 2024;133(6):690-698
Metrics reloaded: recommendations for image analysis validation.38347141 · Maier-Hein, Lena, Reinke, Annika, Godau, Patrick et al.2024 · 539 citationsNature methods. 2024;21(2):195-212
Discovering Process Dynamics for Scalable Perovskite Solar Cell Manufacturing with Explainable AI.37904613 · Klein, Lukas, Ziegler, Sebastian, Laufer, Felix et al.2024 · 31 citationsAdvanced materials (Deerfield Beach, Fla.). 2024;36(7):e2307160
Panoptica -- instance-wise evaluation of 3D semantic and instance segmentation maps2312.02608v1 · Florian Kofler, Hendrik Moller, Josef A. Buchner et al.2023 · 2 citationsarXiv
Addressing image misalignments in multi-parametric prostate MRI for enhanced computer-aided diagnosis of prostate cancer.37957250 · Kovacs, Balint, Netzer, Nils, Baumgartner, Michael et al.2023 · 10 citationsScientific reports. 2023;13(1):19805
Look Ma, no code: fine tuning nnU-Net for the AutoPET II challenge by only adjusting its JSON plans2309.13747v2 · Fabian Isensee, Klaus H.Maier-Hein2023 · 2 citationsarXiv
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