Publications

Journal

Hein, Dennis; Bozorgpour, Afshin; Merhof, Dorit; Wang, Ge
Physics-inspired Generative Models in Medical Imaging: A Review
Annual Review of Biomedical Engineering, 2025 (accepted)

Conference

Karimijafarbigloo, Sanaz; Kolahi, Sina Ghorbani; Azad, Reza; Bagci, Ulas; Merhof, Dorit
Frequency-Domain Refinement of Vision Transformers for Robust Medical Image Segmentation under Degradation
IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 2025 (accepted)

Journal

Azad, Reza; Aghdam, Ehsan Khodapanah; Rauland, Amelie; Jia, Yiwei; Avval, Atlas Haddadi; Bozorgpour, Afshin; Karimijafarbigloo, Sanaz; Cohen, Joseph Paul; Adeli, Ehsan; Merhof, Dorit
Medical Image Segmentation Review: The Success of U-Net
IEEE Transactions on Pattern Analysis and Machine Intelligence, 2024 (accepted)

Schäfer, Raphael; Nicke, Till; Höfener, Henning; Lange, Annkristin; Merhof, Dorit; Feuerhake, Friedrich; Schulz, Volkmar; Lotz, Johannes; Kiessling, Fabian
Overcoming Data Scarcity in Biomedical Imaging with a Foundational Multi-Task Model
Nature Communications, 2024

Schueler, Jan; Kuenzel, Jonas; Thuesing, Anna; Pion, Eric; Behncke, Rose Yinghan; Haegerling, Rene; Fuchs, Dieter; Kraus, Andre; Buchholz, Bjoern; Huang, Boqiang; Merhof, Dorit; Werner, Jens M.; Schmidt, Katharina M.; Hackl, Christina; Aung, Thiha; Härteis, Silke
Ultra high frequency ultrasound enables real-time visualization of blood supply from chorioallantoic membrane to human autosomal dominant polycystic kidney tissue
Scientific Reports, 2024

Munk, Anna; Philippi, Vanessa; Buchecker, Verena; Bankstahl, Marion; Glasenapp, Aylina; Blutke, Andreas; Michelakaki, Effrosyni; Talbot, Steven Roger; Huwyler, Jörg; Jirkof, Paulin; Kopaczka, Marcin; Merhof, Dorit; Palme, Rupert; Potschka, Heidrun
Refinement of pain management: multimodal analgesia for neurosurgical approaches in mice
Scientific Reports, 2024 (accepted)

Azad, Reza; Lenßen, Pia; Jia, Yiwei; Strauch, Martin; Bener, Berk Alperen; Merhof, Dorit; Wöll, Dominik
Modeling the Temperature-Dependent Size Change of Polydisperse Nano-objects using a Deep Generative Model
NanoLetters, 2024

Merhof, Dorit
Automatisierte, KI-basierte Analyse von Bilddaten
Blick in die Wissenschaft, 2024

Azad, Reza; Jia, Yiwei; Aghdam, Ehsan K.; Cohen-Adad, Julien; Merhof, Dorit
TransCeption: Enhancing Medical Image Segmentation with Inception-like Transformer Design for Efficient Feature Fusion
Computational Visual Media, 2024

Spehr, Marc; Hamacher, Christoph; Degen, Rudolf; Franke, Melissa; Switacz, Victoria K.; Fleck, David; Katreddi, Raghu Ram; Hernandez-Clavijo, Andres; Strauch, Martin; Horio, Nao; Hachgenei, Enno; Spehr, Jennifer; Liberles, Stephen D.; Merhof, Dorit; Forni, Paolo E.; Zimmer-Bensch, Geraldine; Ben-Shaul, Yoram
A revised conceptual framework for mouse vomeronasal pumping and stimulus sampling
Current Biology, 2024

Conference

Bassi, Pedro R. A. S.; Li, Wenxuan; Tang, Yucheng; Isensee, Fabian; Wang, Zifu; Chen, Jieneng; Chou, Yu-Cheng; Wald, Tassilo; Ulrich, Constantin; Baumgartner, Michael; Roy, Saikat; Maier-Hein, Klaus; Jaeger, Paul; Ye, Yiwen; Xie, Yutong; Zhang, Jianpeng; Chen, Ziyang; Xia, Yong; Kirchhoff, Yannick; Rokuss, Maximilian R.; Shi, Pengcheng; Ma, Ting; Du, Yuxin; Bai, Fan; Huang,  Tiejun; Zhao, Bo; Xing, Zhaohu; Zhu, Lei; Gupta, Saumya; Wang, Haonan; Li, Xiaomeng; Huang, Ziyan; Ye, Jin; He, Junjun; Sadegheih, Yousef; Bozorgpour, Afshin; Kumari, Pratibha; Azad, Reza; Merhof, Dorit; Gu, Hanxue; Dong, Haoyu; Yang, Jichen; Mazurowski, Maciej; Wu, Linshan; Zhuang, Jia-Xin; Chen, Hao; Roth, Holger; Xu, Daguang; Blaschko, Matthew; Decherchi, Sergio; Cavalli, Andrea; Yuille, Alan; Zhou, Zongwei
Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Image Segmentation?
Conference on Neural Information Processing Systems (NeurIPS), Datasets and Benchmarks Track, 2024 (accepted)

Kolahi, Sina Ghorbani; Chaharsooghi, Seyed Kamal; Khatibi, Toktam; Bozorgpour, Afshin; Azad, Reza; Heidari, Moein; Hacihaliloglu, Ilker; Merhof, Dorit
MSA2NET: Multi-scale Adaptive Attention-guided Network for Medical Image Segmentation
British Machine Vision Conference (BMVC), 2024 (accepted)

Kumari, Pratibha; Reisenbüchler, Daniel; Luttner, Lucas; Schaadt, Nadine S.; Feuerhake, Friedrich; Merhof, Dorit
Continual Domain Incremental Learning for Privacy-aware Digital Pathology
International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2024 (accepted)

Reisenbüchler, Daniel; Luttner, Lucas; Schaadt, Nadine S.; Feuerhake, Friedrich; Merhof, Dorit
Unsupervised Latent Stain Adaption for Digital Pathology
International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2024 (accepted)

Sadegheih, Yousef; Merhof, Dorit
Segmentation of Brain Metastases in MRI: A Two-Stage Deep Learning Approach with Modality Impact Study
MICCAI Workshop on PRedictive Intelligence in MEdicine (PRIME), 2024 (accepted)

Karimijafarbigloo, Sanaz; Azad, Reza; Merhof, Dorit
Self-Supervised Contrastive Learning for Consistent Few-Shot Image Representations
MICCAI Workshop on PRedictive Intelligence in MEdicine (PRIME), 2024 (accepted)

Chen, Long; Merhof, Dorit
Learning Instance-Discriminative Pixel Embeddings Using Pixel Triplets
MICCAI Workshop on Machine Learning in Medical Imaging (MLMI), 2024 (accepted)

Karimijafarbigloo, Sanaz; Azad, Reza; Kazerouni, Amirhossein; Merhof, Dorit
Reducing Uncertainty in 3D Medical Image Segmentation under Limited Annotations through Contrastive Learning
Medical Imaging with Deep Learning (MIDL), 2024

Karimijafarbigloo, Sanaz; Kazerouni, Amirhossein; Azad, Reza; Velichko, Yury; Bagci, Ulas; Merhof, Dorit
Leveraging Unlabeled Data for 3D Medical Image Segmentation through Self-Supervised Contrastive Learning
International Symposium on Biomedical Imaging (ISBI), 2024

Bozorgpour, Afshin; Azad, Babak; Azad, Reza; Velichko, Yury; Bagci, Ulas; Merhof, Dorit
HCA-Net: Hierarchical Context Attention Network for Intervertebral Disc Semantic Labeling
International Symposium on Biomedical Imaging (ISBI), 2024

Kazerouni, Amirhossein; Karimijafarbigloo, Sanaz; Azad, Reza; Velichko, Yury; Bagci, Ulas; Merhof, Dorit
FuseNet: Self-Supervised Dual-Path Network for Medical Image Segmentation
International Symposium on Biomedical Imaging (ISBI), 2024

Huang, Boqiang; Ying, Jiayu; Lyu, Ruizhi; Schaadt, Nadine; Klinkhammer, Barbara; Boor, Peter; Lotz, Johannes; Feuerhake, Friedrich; Merhof, Dorit
UTNetPara: A Hybrid CNN-Transformer Architecture with Multi-Scale Fusion for Wole-Slide Image Segmentation
International Symposium on Biomedical Imaging (ISBI), 2024

Azad, Reza; Niggemeier, Leon; Hüttemann, Michael; Kazerouni, Amirhossein; Aghdam, Ehsan Khodapanah; Velichko, Yuri; Bagci, Ulas; Merhof, Dorit
Beyond self-attention: deformable large kernel attention or medical image segmentation
IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 2024

Kazerouni, Amirhossein; Azad, Reza; Hosseini, Alireza; Merhof, Dorit; Bagci, Ulas
INCODE: Implicit neural conditioning with prior knowledge embeddings
IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 2024

Journal

Weninger, Leon; Ecke, Jarek; Jütten, Kerstin; Clusmann, Hans; Wiesmann, Martin; Merhof, Dorit; Na, Chuh-Hyoun
Diffusion MRI anomaly detection in glioma patients
Scientific Reports, 13, 20366, 2023

Sadegheih, Yousef; Weninger, Leon; Merhof, Dorit
Novel deep learning approaches for analyzing diffusion imaging data
KI - Künstliche Intelligenz, Springer, KUIN-D-23-00083, 2023

Kazerouni, Amirhossein; Aghdam, Ehsan Khodapanah; Heidari, Moein; Azad, Reza; Fayyaz, Mohsen; Hacihaliloglu, Ilker; Merhof, Dorit
Diffusion models in medical imaging: A comprehensive survey
Medical Image Analysis, 102846, 2023

Berijanian, Maryam; Schaadt, Nadine S; Huang, Boqiang; Lotz, Johannes; Feuerhake, Friedrich; Merhof, Dorit
Unsupervised many-to-many stain translation for histological image augmentation to improve classification accuracy
Journal of Pathology Informatics, 14, 100195, 2023

Torow, Natalia; Li, Ronghui; Hitch, Thomas Charles Adrian; … Gadermayr, Michael; … Merhof, Dorit; … Hornef, Mathias Walter
M cell maturation and cDC activation determine the onset of adaptive immune priming in the neonatal Peyer’s patch
Immunity, 2023

Zentrich, Eva; Wassermann, Laura; Struve, Birgitta; Selke, Kristin; Buettner, Manuela; Keubler, Lydia Maria; Reifenrath, Janin; Angrisani, Nina; Kempfert, Merle; Krause, Annika; Bellmann, Olaf; Kopaczka, Marcin; Merhof, Dorit; Bankstahl, Marion; Bleich, André; Häger, Christine
Postoperative Severity Assessment in Sheep
European Surgical Research, 64(1)27-36, 2023

Mösch, Lucas; Kunzcik, Janosch Frederick; Breuer, Lukas; Merhof, Dorit; Gass, Peter; Potschka, Heidrun; Zechner, Dietmar; Vollmar, Brigitte; Tolba, René; Häger, Christine; Bleich, André; Czaplik, Michael; Barbosa Pereira, Carina
Towards substitution of invasive telemetry: An integrated home cage concept for unobstrusive monitoring of objective physiological parameters in rodents
PLOS ONE, PONE-D-23-14127R1, 2023 (accepted)

Gupta, Anubha; Gehlot, Shiv; Goswami, Shubham; Motwani, Sachin; Gupta, Ritu; Faura, Álvaro García; Štepec, Dejan; Martinčič, Tomaž; Azad, Reza; Merhof, Dorit; Bozorgpour, Afshin; Azad, Babak; Sulaiman, Alaa; Pandey, Deepanshu; Gupta, Pradyumna;  Bhattacharya, Sumit; Sinha, Aman; Agarwal, Rohit; Qiu, Xinyun; Zhang; Yucheng; Fan, Ming; Park, Yoonbeom; Lee, Daehong; Park, Joon Sik; Lee, Kwangyeol; Ye, Jaehyung
SegPC-2021: A challenge & dataset on segmentation of Multiple Myeloma plasma cells from microscopic images
Medical Image Analysis, 83, 102677, 2023

Aja-Fernández, Santiago; Martín-Martín, Carmen; Planchuelo-Gómez, Álvaro; … Rauland, Amelie; Merhof, Dorit; … Pieciak, Tomasz
Validation of Deep Learning techniques for quality augmentation in diffusion MRI for clinical studies
NeuroImage: Clinical,103483, 2023

Bilic, Patrick; Christ, Patrick; Li, Hongwei Bran; … Merhof, Dorit; … Rippel, Oliver; … Weninger, Leon; … ; Menze, Bjoern
The liver tumor segmentation benchmark (LITS)
Medical Image Analysis, 84, 102680, 2023

Conference

Azad, Reza; Kazerouni, Amirhossein; Azad, Babak; Aghdam, Ehsan Khodapanah; Velichko, Yuri; Bagci, Ulas; Merhof, Dorit
Laplacian-Former: Overcoming the Limitations of Vision Transformers in Local Texture Detection
International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2023

Azad, Reza; Arimond, René; Aghdam, Ehsan Khodapanah; Kazerouni, Amirhosein; Merhof, Dorit
Dae-former: Dual attention-guided efficient transformer for medical image segmentation
MICCAI Workshop on Predictive Intelligence in Medicine (PRIME), 2023

Karimijafarbigloo, Sanaz; Azad, Reza; Merhof, Dorit
Self-supervised Few-shot Learning for Semantic Segmentation: An Annotation-free Approach
MICCAI Workshop on Predictive Intelligence in Medicine (PRIME), 2023

Bozorgpour, Afshin; Sadegheih, Yousef; Kazerouni, Amirhossein; Azad, Reza; Merhof, Dorit
DermoSegDiff: A Boundary-aware Segmentation Diffusion Model for Skin Lesion Delineation.
MICCAI Workshop on Predictive Intelligence in Medicine (PRIME), 2023

Azad, Reza; Kazerouni, Amirhossein; Sulaiman, Alaa; Bozorgpour, Afshin; Aghdam , Ehsan Khodapanah; Jose, Abin; Merhof, Dorit
Unlocking Fine-Grained Details with Wavelet-based High-Frequency Enhancement in Transformers
MICCAI Workshop on Machine Learning in Medical Imaging (MLMI), 2023

Molaei, Amirali; Aminimehr, Amirhossein; Tavakoli, Armin; Kazerouni, Amirhossein; Azad, Bobby; Azad, Reza; Merhof, Dorit
Implicit Neural Representation in Medical Imaging: A Comparative Survey
ICCV Workshop on Computer Vision for Automated Medical Diagnosis (CVAMD), 2023

Karimijafarbigloo, Sanaz; Azad, Reza; Kazerouni, Amirhossein; Velichko, Yuri; Bagci, Ulas; Merhof, Dorit
Self-supervised Semantic Segmentation: Consistency over Transformation
ICCV Workshop on Computer Vision for Automated Medical Diagnosis (CVAMD), 2023

Chen, Long; Wu, Yuli; Stegmaier, Johannes; Merhof, Dorit
SortedAP: Rethinking Evaluation Metrics for Instance Segmentation
ICCV Workshop on BioImage Computing, 2023

Karimijafarbigloo, Sanaz; Azad, Reza; Kazerouni, Amirhossein; Ebadollahi, Saeed; Merhof, Dorit
MMCFormer: Missing Modality Compensation Transformer for Brain Tumor Segmentation
Medical Imaging with Deep Learning (MIDL), 2023

Karimijafarbigloo, Sanaz; Azad, Reza; Kazerouni, Amirhossein; Merhof, Dorit
MS-Former: Multi-Scale Self-Guided Transformer for Medical Image Segmentation
Medical Imaging with Deep Learning (MIDL), 2023

Heidari, Moein; Kazerouni, Amirhossein; Soltany, Milad; Azad, Reza; Aghdam, Ehsan Khodapanah; Cohen-Adad, Julien; Merhof, Dorit
Hiformer: Hierarchical multi-scale representations using transformers for medical image segmentation
IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 6202-6212, 2023

Wu, Yuli; Karetic, Ivan; Stegmaier, Johannes; Walter, Peter; Merhof, Dorit
A Deep Learning-based in silico Framework for Optimization on Retinal Prosthetic Stimulation
International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), 2023

Rauland, Amelie; Merhof, Dorit
Using Synthetic Training Data in Neural Networks for the Estimation of Fiber Orientation Distribution Functions from Single Shell Data
International Symposium on Biomedical Imaging (ISBI), 2023

Aghdam, Ehsan Khodapanah; Azad, Reza; Zarvani, Maral; Merhof, Dorit
Attention Swin U-Net: Cross-Contextual Attention Mechanism for Skin Lesion Segmentation
International Symposium on Biomedical Imaging (ISBI), 2023

Rippel, Oliver; Merhof, Dorit
Anomaly Detection for Automated Visual Inspection: A Review
Bildverarbeitung in der Automation: Ausgewählte Beiträge des Jahreskolloquiums BVAu 2022, 1-13, 2023