A workshop which builds on the Universal Musculoskeletal Ultrasonography Database (UMUD) – an open, FAIR-aligned platform developed in collaboration with researchers from the University of Basel (Paul Ritsche, Oliver Faude, Gerardo Romeny Francesco Santini), ETH Zurich (Christoph Leitner), University of Padova (Fabio Sarto, Martino Franchi), University of Jyväskylä (Neil Cronin, Taija Finni) and the Norwegian School of Sport Sciences (Olivier Seynnes). UMUD provides structured access to musculoskeletal ultrasound datasets and aims to promote best practices in image analysis, reproducibility and data sharing across the community.
The session covers topics such as:
- Relationship of muscle geometry, function and health
- Common challenges and solutions in MSK ultrasound image analysis
- Benchmarking and reproducibility of analysis algorithms
- How to prepare and publish ultrasound datasets (FAIR, anonymisation, licensing)
- Practical tools and workflows for researchers
A hands-on, interactive format with contributions from both technical and applied researchers involved in the project.
Speakers:
- Paul Ritsche – University of Basel
- Fabio Sarto – University of Harvard
- Oliver Faude – University of Basel
- Dominic Farris – University of Exeter
- Romina Ledergerber – University of Basel
- Christoph Leitner – ETH Zurich
- Alberto Guzzi – University of Basel
- Francesco Santini – University of Basel
Programme:
The workshop will be a combination of input lectures and practical sessions. Participants are encouraged to bring their own images / videos of MSK ultrasound parameters. Sample data will be provided in any case. Please download the following software prior to the workshop, the installation procedures will NOT be covered:
- DL_Track_US: https://paulritsche.github.io/DL_Track_US/latest/installation / OR UltraTimTrack: https://github.com/timvanderzee/UltraTimTrack
- DeepACSA: https://deepacsa.readthedocs.io/en/latest/installation.html
- FIJI: https://imagej.net/software/fiji/downloads
While we acknowledge that the list of software is not comprehensive, we will highlight further available software during the presentations.
| Time | Activity | Speakers |
| 14:00 | Welcome & Introduction | Paul Ritsche, Fabio Sarto, Oliver Faude |
| 14:05 | Lecture: MSK ultrasound parameters and their relation to performance / health across different populations | Dominic Farris, Romina Ledergerber |
| 14:40 | Lecture: Wearable ultrasound – applications and future possibilities | Christoph Leitner |
| 15:05 | Lecture: Analysis of muscle and tendon image – current challenges and solutions | Dominic Farris, Paul Ritsche |
| 15:35 | Practical: How to analyze your data using manual and automated approaches | Paul Ritsche, Alberto Guzzi |
| 16:20 | Lecture: Reproducible and Fair imaging data management | Francesco Santini |
| 16:40 | Practical: Data sharing best practices using UMUD and ORMIR | Francesco Santini, Paul Ritsche |
| 17:15 | Closing / Wrap-up |
Paul Ritsche, Fabio Sarto, Oliver Faude |
Date: Monday, 6 July
Time: 14:00 – 17:15
Location: UNIL campus, Geopolis Building, Room 2207
Metro station: Unil-Mouline (M1)
Contact:
Paul Ritsche
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