Image-Based Biomedical Modeling (IBBM)
Prof. Dr. Bjoern MenzeResearch
The research objective of the Image-Based Biomedical Modeling group is to develop computational algorithms at the interface of- medical computer vision & machine learning
- image-based modeling & disease progression modeling
- machine learning for magnetic resonance signal processing.
Available Student Projects
Currently, active projects include but not limited to:- Currently available Master thesis on Shape Analysis on Meshes or Point Clouds from Medical Data
- Currently available Master thesis on Recommender Systems in collaboration with the Munich based Startup Venn
- Currently available Transformer-Based Pipeline for Pre-Processing MR Spectroscopic Imaging Data
- Available from August 2021 Organs at Risk Detection and Localization for Radiation Therapy Planning using Transformers
- Currently available Transformer-Based Regression Model for Metabolite Quantification in MR Spectroscopic Imaging
- Currently available MA: MR-CT Domain Translation of Spine Data
- Currently available Various projects on (unsupervised) anomaly detection and/or segmentation (at deepc)
- Currently available 3D vessel tracking using transformer
- Currently available Mesh CNN for vessel annomaly detection
- Currently available Deep Learning to Solve sedimentation diffussion
- Currently available Multiple M.Sc/B.Sc thesis, guided research, IDP projects are available in Bayesian inference, generative modeling, federated learning
- Currently available Graph synthesis for medical applications
- Currently available Reinforcement Learning for Biomechanical Modeling
- Currently available Learning-based modeling of cancer progression
- Currently available Cardiac MRI segmentation (at the Children's Hospital of the Harvard Medical School)
People
IBBM group in February 2018 (Please find Jana and Lina in the last picture). Group picture in February 2015 here.
Faculty and Staff
- Fernando Navarro(located in Zürich)
- Hongwei (Bran) Li
- Chinmay Prabhakar (located in Zürich)
- Anjany Sekuboyina (with TUM Neuroradiology, located in Zürich)
- Giles Tetteh (with TUM Neuroradiology)
- Amir Hossein Bayat (with TUM Neuroradiology)
- Timo Löhr (with TUM Neuroradiology)
- Florian Kofler (IGSSE Fellow)
- Carolin Pirkl (IGSSE Fellow)
- Diana Waldmannstetter (IGSSE Fellow)
- Rami Al-Maskari (with ITERM Helmholtz Zentrum München)
- Izabela Horvath (with ITERM Helmholtz Zentrum München)
- Judith Zimmermann (with ICM at Charite Berlin)
- John LaMaster (DAAD Fellow)
- Sebastian Endt (with TUM Physics)
- Sarthak Pati (with University of Pennsylvania)
Students
Guests and Affiliates
- Dr. Chen Niu (CSC Fellow)
- Dr. Kun Zhang (CSC Fellow)
- Dr. Marie Piraud
- Prof. Dr. Koen Van Leemput (August-Wilhelm Scheer Visiting Professor 2015)
- Dr. Alexander Valentinitsch (TUM Neuroradiologie)
Graduates and Alumni
- Dr. Oliver Schoppe (PhD, 2021)
- Dr. Marie Piraud (Postdoc, 2016-2018)
- Dr. Pedro Gómez Damián
- Dr. Miguel Molina Romero
- Dr. Augusto F. Sanches
- Dr. Dhritiman Das (PhD, 2020)
- Jihye Jang (with Harvard BIDMC)
- Dr. Yu Zhao (CSC Fellow)
- Dr. Xin Liu (BERTI Fellow)
- Dr. Jana Lipkova (PhD, 2019)
- Cagdas Ulas (MACSENET Fellow)
- Yusuf Yilmaz (with Universitat Zurich)
- Patrick Bilic (CDTM Fellow)
- Dr. Vasileios Zografos (Postdoc, 2014-15)
- Dr. Esther Alberts (PhD, 2019)
- Dr. Markus Rempfler (PhD, 2019)
- Dr. Lina Xu (PhD, 2018)
- Dr. Miguel Molina Romero (PhD, 2018)
- Dr. Patrick Christ (PhD, 2017)
- Dr. Marie Bieth (PhD, 2017)
- Linus Kreitner (BSc, 2021)
- Nils Börner (BSc, 2021)
- Stefan Gerl (MSc, 2020)
- Alexander Unger (BSc, 2020)
- Philipp Kaeß (BSc, 2020)
- Oliver Kugel (MSc, 2020)
- Vindhya Singh (MSc, 2020)
- Javier Coronel (MSc, 2020)
- Dmitrii Pethukov(MSc, 2019)
- Arno Hilke (MSc, 2019)
- Prashanth Swaminathan (MSc, 2019)
- Berkan Lafci (MSc, 2019)
- Jake Burton (MSc, 2019)
- Rami al-Maskari (MSc, 2019)
- Johannes C. Paetzold (MSc, 2018)
- Avinash Mishra (MSc, 2018)
- Vitaly Nikolaev (MSc, 2018)
- Christoph Dehner (MSc, 2018)
- Ruchik Yajnik (MSc, 2018)
- Paula Oriuela (MSc, 2017)
- Satish Balakrishnan (MSc, 2017)
- Johannes Rausch (MSc, 2017)
- Diana Waldmannstaedter (MSc, 2017)
- Anna Lysitsina (MSc, 2017)
- Florian Ettliner (MSc, 2017)
- Irene Mayoral (MSc, 2016)
- Azhar Sultan (MSc, 2016)
- Poulami Chakrabarti (MSc, 2016)
- Sindhushree Jayasankar (MSc, 2016)
- Patmaa Sridharan (MSc, 2016)
- Mohamed Ezz (MSc, 2016)
- Hang Xu (MSc, 2016)
- Christine Eilers (BSc, 2018)
- Yeshaswini Nagaraj (MSc, 2016)
- Cristina Precup (MSc, 2016)
- Stefano Trebeschi (MSc, 2016)
- Sophie Ratcliffe (MSc, 2016)
- Ahmed El Fiky (MSc, 2016)
- Patrick Bilic (MSc, 2016)
- David Dao (MSc, 2016)
- Fateme Nejatbakhsh (MSc, 2015)
- Marc Bickel (MSc, 2015)
- Jairo Socarras Fernandez (MSc, 2015)
- Udhayaraj Sivalingam (MSc, 2015)
- Alexandra Derntl (MSc, 2015)
- Jun Shen (MSc, 2015)
- Pedro Gomez (MSc, 2014)
- Daniel Andreasen (Visiting graduate student, 2015)
- Subramoniam Aiyappan (Guest, 2014-15)
- Pavel Dvořák (Visiting graduate student, 2014-15)
- Mansour Alshanawani (Guest, 2014)
Teaching
- WS 2020: Lecture & Exercises 'Informatik I fuer Ingenieurwissenschaften' (MSE) (IN8011) (0MED100702)
- WS 2020: IBBM reading group (IN2122)
- WS 2020: IBBM research seminar (IN2137)
- WS 2020: Marie Sklodowska-Curie ITN "Translational Brain Imaging Training Network" ( TRABIT) Winter School
- SS 2020: Computational physiology for medical image computing lecture (IN2319)
- SS 2020: IBBM reading group (IN2122)
- SS 2020: IBBM research seminar (IN2137)
- WS 2019: Image-based biomedical modeling seminar (IN2107)
- WS 2019: Lecture & Exercises 'Informatik I fuer Ingenieurwissenschaften' (MSE) (IN8011) (0MED100702)
- WS 2019: Imagine neurooncology seminar (0MED100702)
- WS 2019: IBBM reading group (IN2122)
- WS 2019: IBBM research seminar (IN2137)
- SS 2019: Computational physiology for medical image computing lecture (IN2319)
- SS 2019: IBBM reading group (IN2122)
- SS 2019: IBBM research seminar (IN2137)
- WS 2018: Image-based biomedical modeling seminar (IN2107)
- WS 2018: Lecture & Exercises 'Informatik I fuer Ingenieurwissenschaften' (MSE) (IN8011) (0MED100702)
- WS 2018: Imagine neurooncology seminar (0MED100702)
- WS 2018: IBBM reading group (IN2122)
- WS 2018: IBBM research seminar (IN2137)
- WS 2018: Marie Sklodowska-Curie ITN "Translational Brain Imaging Training Network" (TRABIT) Summer School
- SS 2018: Computational physiology for medical image computing lecture (IN2319)
- SS 2018: IBBM reading group (IN2122)
- SS 2018: IBBM research seminar (IN2137)
- WS 2017: Image-based biomedical modeling seminar (IN2107)
- WS 2017: Lecture & Exercises 'Informatik I fuer Ingenieurwissenschaften' (MSE) (IN8011) (0MED100702)
- WS 2017: Imagine neurooncology seminar (0MED100702)
- WS 2017: IBBM reading group (IN2122)
- WS 2017: IBBM research seminar (IN2137)
- SS 2017: Computational physiology for medical image computing lecture (IN2319)
- SS 2017: IBBM reading group (IN2122)
- SS 2017: IBBM research seminar (IN2137)
- WS 2016: Image-based biomedical modeling seminar (IN2107)
- WS 2016: Exercises for 'Informatik I fuer Ingenieurwissenschaften' (MSE) (IN8011) (0MED100702)
- WS 2016: Imagine neurooncology seminar (0MED100702)
- WS 2016: IBBM reading group (IN2122)
- WS 2016: IBBM research seminar (IN2137)
- SS 2016: Computational physiology for medical image computing lecture (IN2319)
- SS 2016: IBBM reading group (IN2122)
- SS 2016: IBBM research seminar (IN2137)
- WS 2015: Image-based biomedical modeling seminar (IN2107)
- WS 2015: Imagine neurooncology seminar (0MED100702)
- WS 2015: IBBM reading group (IN2122)
- WS 2015: IBBM research seminar (IN2137)
- SS 2015: Medical image analysis lecture (IN3200)
- SS 2015: IBBM reading group (IN2122)
- SS 2015: IBBM research seminar (IN2137)
- SS 2015: Medical Image Processing Lecture (with Koen Van Leemput)
- WS 2014: IBBM reading group (IN2122)
- WS 2014: IBBM research seminar (IN2137)
- SS 2014: Image-based biomedical modeling seminar (IN2107)
