Bastian Wittmann

I am a PhD student at the University of Zurich, under the supervision of Prof. Dr. Bjoern Menze. In addition, I am associated with the ETH AI Center. My research focuses on advancing (bio)medical image analysis through artificial intelligence, with a particular emphasis on vascular imaging. I aim to provide novel insights into vascular disorders and diseases by leveraging state-of-the-art deep learning methods and translating them into clinical practice.

Prior to my PhD, I obtained an MSc in "Robotics, Cognition, Intelligence" from the Technical University of Munich and a BSc in automotive engineering through a dual degree program offered by MAN Truck & Bus SE.

📍 I'm currently based in Zürich, Switzerland.

✉️ Email: firstname.lastname@uzh.ch

News and Highlights

02/2026 — Our work on generalist CT foundation models got accepted at Nature Biomedical Engineering.

07/2025 — I presented my work on foundation models for universal 3D blood vessel segmentation at CVPR.

Selected Research

Full list: Google Scholar

First Authorships

vesselFM: A Foundation Model for Universal 3D Blood Vessel Segmentation

B. Wittmann, Y. Wattenberg, T. Amiranashvili, S. Shit, B. Menze

CVPR, 2025.

Paper Code

BibTeX

@inproceedings{
    wittmann_cvpr25,
    author    = {Wittmann, Bastian and Wattenberg, Yannick and Amiranashvili, Tamaz and Shit, Suprosanna and Menze, Bjoern},
    title     = {vesselFM: A Foundation Model for Universal 3D Blood Vessel Segmentation},
    booktitle = {Proceedings of the Computer Vision and Pattern Recognition Conference (CVPR)},
    month     = {June},
    year      = {2025},
    pages     = {20874-20884}
}

VesselFM

Simulation-based segmentation of blood vessels in cerebral 3D OCTA images

B. Wittmann, L. Glandorf, J. C Paetzold, T. Amiranashvili, T. Wälchli, D. Razansky, B. Menze

MICCAI, 2024.

Paper Code

BibTeX

@inproceedings{
    wittmann_miccai24,
    title={Simulation-Based Segmentation of Blood Vessels in Cerebral 3D OCTA Images},
    author={Wittmann, Bastian and Glandorf, Lukas and Paetzold, Johannes C and Amiranashvili, Tamaz and W{\"a}lchli, Thomas and Razansky, Daniel and Menze, Bjoern},
    booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
    pages={645--655},
    year={2024},
    organization={Springer}
}

OCTA

Link Prediction for Flow-Driven Spatial Networks

B. Wittmann, J. C. Paetzold, C. Prabhakar, D. Rueckert, B. Menze

WACV, 2024.

Paper Code

BibTeX

@inproceedings{
    wittmann_wacv24,
    author    = {Wittmann, Bastian and Paetzold, Johannes C. and Prabhakar, Chinmay and Rueckert, Daniel and Menze, Bjoern},
    title     = {Link Prediction for Flow-Driven Spatial Networks},
    booktitle = {Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision (WACV)},
    month     = {January},
    year      = {2024},
    pages     = {2472-2481}
}

GAV

Focused Decoding Enables 3D Anatomical Detection by Transformers

B. Wittmann, F. Navarro, S. Shit, B. Menze

MELBA, 2023.

Paper Code

BibTeX

@article{
    wittmann_melba23,
    title = "Focused Decoding Enables 3D Anatomical Detection by Transformers",
    author = "Wittmann, Bastian and Navarro, Fernando and Shit, Suprosanna and Menze, Bjoern",
    journal = "Machine Learning for Biomedical Imaging",
    volume = "2",
    issue = "February 2023 issue",
    year = "2023",
    pages = "72--95",
    issn = "2766-905X",
    doi = "https://doi.org/10.59275/j.melba.2023-35e6",
    url = "https://melba-journal.org/2023:003"
}

Transoar

SwinFPN: Leveraging Vision Transformers for 3D Organs-At-Risk Detection

B. Wittmann, S. Shit, J. C. Peeken, S. E. Combs, B. Menze

MIDL, 2022.

Paper Code

BibTeX

@inproceedings{
    wittmann_midl22,
    title={SwinFPN: Leveraging Vision Transformers for 3D Organs-At-Risk Detection},
    author={Wittmann, Bastian and Shit, Suprosanna and Navarro, Fernando and Peeken, Jan C and Combs, Stephanie E and others},
    booktitle={Medical Imaging with Deep Learning},
    year={2022} 
}

SwinFPN

Co-Authorships

Generalist foundation models from a multimodal dataset for 3D computed tomography

I. E. Hamamci, S. Er, C. Wang, F. Almas, A. G. Simsek, S. N. Esirgun, I. Dogan, O. F. Durugol, B. Hou, S. Shit, W. Dai, M. Xu, H. Reynaud, M. F. Dasdelen, B. Wittmann, T. Amiranashvili, E. Simsar, M. Simsar, E. B. Erdemir, A. Alanbay, A. Sekuboyina, B. Lafci, A. Kaplan, Z. Lu, M. Polacin, B. Kainz, C. Bluethgen, K. Batmanghelich, M. K. Ozdemir, B. Menze

Nature Biomedical Engineering, 2026.

Paper Code

BibTeX

@article{
    hamamci_bme26,
    title = {Generalist foundation models from a multimodal dataset for {3D} computed tomography},
    issn = {2157-846X},
    url = {https://doi.org/10.1038/s41551-025-01599-y},
    doi = {10.1038/s41551-025-01599-y},
    journal = {Nature Biomedical Engineering},
    author = {Hamamci, Ibrahim Ethem and Er, Sezgin and Wang, Chenyu and Almas, Furkan and Simsek, Ayse Gulnihan and Esirgun, Sevval Nil and Dogan, Irem and Durugol, Omer Faruk and Hou, Benjamin and Shit, Suprosanna and Dai, Weicheng and Xu, Murong and Reynaud, Hadrien and Dasdelen, Muhammed Furkan and Wittmann, Bastian and Amiranashvili, Tamaz and Simsar, Enis and Simsar, Mehmet and Erdemir, Emine Bensu and Alanbay, Abdullah and Sekuboyina, Anjany and Lafci, Berkan and Kaplan, Ahmet and Lu, Zhiyong and Polacin, Malgorzata and Kainz, Bernhard and Bluethgen, Christian and Batmanghelich, Kayhan and Ozdemir, Mehmet Kemal and Menze, Bjoern},
    month = feb,
    year = {2026},       
}

CT Rate

CADS: A Comprehensive Anatomical Dataset and Segmentation for Whole-Body Anatomy in Computed Tomography

M. Xu, T. Amiranashvili, F. Navarro, M. Fritsak, I. E. Hamamci, S. Shit, B. Wittmann, S. Er, S. M. Christ, E. de la Rosa, J. Deseoe, R. Graf, H. Möller, A. Sekuboyina, J. C. Peeken, S. Becker, G. Baldini, J. Haubold, F. Nensa, R. Hosch, N. Mirajkar, S. Khalid, S. Zachow, M.-A. Weber, G. Langs, J. Wasserthal, M. K. Ozdemir, A. Fedorov, R. Kikinis, S. Tanadini-Lang, J. S. Kirschke, S. E. Combs, B. Menze

arXiv preprint, 2025.

arXiv Code

BibTeX

@article{
    xu_arxiv25,
    title={CADS: A Comprehensive Anatomical Dataset and Segmentation for Whole-Body Anatomy in Computed Tomography},
    author={Xu, Murong and Amiranashvili, Tamaz and Navarro, Fernando and Fritsak, Maksym and Hamamci, Ibrahim Ethem and Shit, Suprosanna and Wittmann, Bastian and Er, Sezgin and Christ, Sebastian M and de la Rosa, Ezequiel and others},
    journal={arXiv preprint arXiv:2507.22953},
    year={2025}                       
}

In Vivo Network-Level Cerebrovascular Mapping Reveals the Impact of Flow Topology on Capillary Stalls After Stroke

L. Glandorf, J. Droux, E. Jessen, B. Wittmann, B. Weber, S. Wegener, B. Menze, R. Leitgeb, D. Schillinger, M. El Amki, D. Razansky

bioRxiv preprint, 2025.

bioRxiv

BibTeX

@article{
    glandorf_biorxiv25,
    title={In Vivo Network-Level Cerebrovascular Mapping Reveals the Impact of Flow Topology on Capillary Stalls After Stroke},
    author={Glandorf, Lukas and Droux, Jeanne and Jessen, Etienne and Wittmann, Bastian and Weber, Bruno and Wegener, Susanne and Menze, Bjoern and Leitgeb, Rainer and Schillinger, Dominik and El Amki, Mohamad and others},
    journal={bioRxiv},
    pages={2025--07},
    year={2025},
    publisher={Cold Spring Harbor Laboratory}                               
}

LSA OCTA Seg

Bessel beam optical coherence microscopy enables multiscale assessment of cerebrovascular network morphology and function

L. Glandorf, B. Wittmann, J. Droux, C. Glück, B. Weber, S. Wegener, M. El Amki, R. Leitgeb, B. Menze, D. Razansky

Light: Science & Applications, 2024.

Paper

BibTeX

@article{
    glandorf_lsa24,
    title={Bessel beam optical coherence microscopy enables multiscale assessment of cerebrovascular network morphology and function},
    author={Glandorf, Lukas and Wittmann, Bastian and Droux, Jeanne and Gl{\"u}ck, Chaim and Weber, Bruno and Wegener, Susanne and El Amki, Mohamad and Leitgeb, Rainer and Menze, Bjoern and Razansky, Daniel},
    journal={Light: Science \& Applications},
    volume={13},
    number={1},
    pages={307},
    year={2024},
    publisher={Nature Publishing Group UK London}         
}

LSA OCTA Seg

Relationformer: A Unified Framework for Image-to-Graph Generation

S. Shit*, R. Koner*, B. Wittmann, J. C. Paetzold, I. Ezhov, H. Li, J. Pan, S. Sharifzadeh, G. Kaissis, V. Tresp, B. Menze

ECCV, 2022.

Paper Code

BibTeX

@inproceedings{
    shit_eccv22,
    title={Relationformer: A Unified Framework for Image-To-Graph Generation},
    author={Shit, Suprosanna and Koner, Rajat and Wittmann, Bastian and Paetzold, Johannes and Ezhov, Ivan and Li, Hongwei and Pan, Jiazhen and Sharifzadeh, Sahand and Kaissis, Georgios and Tresp, Volker and others},
    booktitle={European conference on computer vision},
    pages={422--439},
    year={2022},
    organization={Springer}
}

RelationFormer