Structure-Preserving Multi-domain Stain Color Augmentation Using Style-Transfer with Disentangled Representations. - Sophia J. Wagner; Nadieh Khalili; Raghav Sharma; Melanie Boxberg; Carsten Marr; Walter de Back; Tingying Peng (MICCAI (8), 2021)

Multi-Modality Microscopy Image Style Transfer for Nuclei Segmentation. - Ye Liu; Sophia J. Wagner; Tingying Peng (CoRR, 2021)

Local Attention Graph-Based Transformer for Multi-target Genetic Alteration Prediction. - Daniel Reisenbüchler; Sophia J. Wagner; Melanie Boxberg; Tingying Peng (MICCAI (2), 2022)

S5CL: Unifying Fully-Supervised, Self-supervised, and Semi-supervised Learning Through Hierarchical Contrastive Learning. - Manuel Tran; Sophia J. Wagner; Melanie Boxberg; Tingying Peng (MICCAI (2), 2022)

Multi-Modality Microscopy Image Style Augmentation for Nuclei Segmentation. - Ye Liu; Sophia J. Wagner; Tingying Peng (J. Imaging, 2022)

Approaching Peak Ground Truth. - Florian Kofler; Johannes Wahle; Ivan Ezhov; Sophia J. Wagner; Rami Al-Maskari; Emilia Gryska; Mihail I. Todorov; Christina Bukas; Felix Meissen; Tingying Peng; Ali Ertürk; Daniel Rueckert; et al. (ISBI, 2023)

B-Cos Aligned Transformers Learn Human-Interpretable Features. - Manuel Tran; Amal Lahiani; Yashin Dicente Cid; Melanie Boxberg; Peter Lienemann; Christian Matek; Sophia J. Wagner; Fabian J. Theis; Eldad Klaiman; Tingying Peng (MICCAI (8), 2023)

Fully transformer-based biomarker prediction from colorectal cancer histology: a large-scale multicentric study. - Sophia J. Wagner; Daniel Reisenbüchler; Nicholas P. West; Jan Moritz Niehues; Gregory Patrick Veldhuizen; Philip Quirke; Heike Irmgard Grabsch; Piet A. van den Brandt; Gordon G. A. Hutchins; Susan D. Richman; Tanwei Yuan; Rupert Langer; et al. (CoRR, 2023)

From Whole-slide Image to Biomarker Prediction: A Protocol for End-to-End Deep Learning in Computational Pathology. - Omar S. M. El Nahhas; Marko van Treeck; Georg Wölflein; Michaela Unger; Marta Ligero; Tim Lenz; Sophia J. Wagner; Katherine Jane Hewitt; Firas Khader; Sebastian Foersch; Daniel Truhn; Jakob Nikolas Kather (CoRR, 2023)

Low-Resource Finetuning of Foundation Models Beats State-of-the-Art in Histopathology. - Benedikt Roth; Valentin Koch; Sophia J. Wagner; Julia A. Schnabel; Carsten Marr; Tingying Peng (ISBI, 2024)

DinoBloom: A Foundation Model for Generalizable Cell Embeddings in Hematology. - Valentin Koch; Sophia J. Wagner; Salome Kazeminia; Ece Sancar; Matthias Hehr; Julia A. Schnabel; Tingying Peng; Carsten Marr (MICCAI (12), 2024)

HEST-1k: A Dataset For Spatial Transcriptomics and Histology Image Analysis. - Guillaume Jaume; Paul Doucet; Andrew H. Song; Ming Yang Lu; Cristina Almagro-Pérez; Sophia J. Wagner; Anurag Vaidya; Richard J. Chen; Drew F. K. Williamson; Ahrong Kim; Faisal Mahmood 001 (NeurIPS, 2024)

Using histopathology latent diffusion models as privacy-preserving dataset augmenters improves downstream classification performance. - Jan Moritz Niehues; Gustav Müller-Franzes; Yoni Schirris; Sophia J. Wagner; Michael Jendrusch; Matthias Kloor; Alexander T. Pearson; Hannah Sophie Muti; Katherine Jane Hewitt; Gregory Patrick Veldhuizen; Laura Zigutyte; Daniel Truhn; et al. (Comput. Biol. Medicine, 2024)

Multimodal Whole Slide Foundation Model for Pathology. - Tong Ding; Sophia J. Wagner; Andrew H. Song; Richard J. Chen; Ming Y. Lu; Andrew Zhang; Anurag J. Vaidya; Guillaume Jaume; Muhammad Shaban; Ahrong Kim; Drew F. K. Williamson; Bowen Chen; et al. (CoRR, 2024)

Molecular-driven Foundation Model for Oncologic Pathology. - Anurag Vaidya; Andrew Zhang; Guillaume Jaume; Andrew H. Song; Tong Ding; Sophia J. Wagner; Ming Y. Lu; Paul Doucet; Harry Robertson; Cristina Almagro-Pérez; Richard J. Chen; Dina ElHarouni; et al. (CoRR, 2025)

Navigating Through Whole Slide Images With Hierarchy, Multi-Object, and Multi-Scale Data. - Manuel Tran; Sophia J. Wagner; Wilko Weichert; Christian Matek; Melanie Boxberg; Tingying Peng (IEEE Trans. Medical Imaging, 2025)

A Foundation Model for Spatial Proteomics. - Muhammad Shaban; Yuzhou Chang; Huaying Qiu; Yao Yu Yeo; Andrew H. Song; Guillaume Jaume; Yuchen Wang; Luca L. Weishaupt; Tong Ding; Anurag Vaidya; Abdallah Lamane; Daniel Shao; et al. (CoRR, 2025)