Check out the overview of the hackathon results: https://forum.image.sc/t/outcomes-of-the-next-generation-bioimage-analysis-workflows-hackathon/88733
Date: November 6th - November 8th, 2023
Location: Irchel Campus, Y55L06/08, Winterthurerstrasse 190, 8057 Zürich
Bioimage analysis is evolving to address challenges of big data, dealing with complex modalities like 3D and time-resolved imaging and working towards more FAIR image data and image analysis workflows. A big driver for standardization is the development of OME-NGFF, the open, next generation file format for bioimaging data. This poses the questions: Can we also standardize more in doing open-source, next generation image analysis workflows? How will bioimage analysis workflows of the future look? And how do we make those workflows FAIR?
To get the leading people together that are currently pushing the boundaries of next-generation image analysis workflows, we are organizing a hackathon: The “next generation bioimage analysis workflows hackathon”, this November (6th - 8th) in Zurich, Switzerland.
The hackathon will be followed by a 2 day symposium of the BioVisionCenter (launch symposium of the BioVisionCenter) from November 9th to November 10th. Details & sign up for the symposium will be announced later.
| Time | Content | Comment |
|---|---|---|
| Day 1: November 6th | ||
| 9:30 - 10:00 | Coffee | |
| 10:00 - 11:30 | Welcome | |
| Hackathon goals | 1-2 min introduction by people | |
| 11:30 - 13:00 | Invited presentations: Workflows | |
| Nextflow (Christian Tischer) | ||
| Galaxy (Leonid Kostrykin) | ||
| Java-based ImgLib2 workflows (Stephan Saalfeld) | ||
| Prefect (Tim-Oliver Buchholz) | ||
| Omero slurm runners (Torec Luik) | ||
| Fractal (Joel Lüthi) |
Discussion on workflow interoperability | Invited talks à 5-10 min to set stage | | 13:00 - 14:00 | Lunch | At UZH Cafeteria | | 14:00 - 15:00 | Invited presentations: Specs & tools OME-NGFF Spec (Josh Moore) Validating structured Zarr containers (Davis Bennet) Spatial Data (Kevin Yamauchi) Cellprofiler (Nodar Gogoberidze) | Invited talks à 5-10 min to set stage | | 15:30 - 16:30 | Invited presentations: usecases Light-sheet (Konrad Rokicki) Stitching of NGFF datasets (Marvin Albert) Measurements from high-content imaging (Max Hess) Deep learning workflows with OME-Zarrs (Joran Deschamps) | Invited talks à 5-10 min to set stage | | 16:30 - 17:00 | Group forming | Split participants into groups to work on a given topic | | 17:00 - 18:00 | Hackathon Session 1 | | | 18:00 - 18:30 | Summary of the day | What do groups plan to work on | | 19:00 - open | Group Dinner | | | | | | | Day 2: November 7th | | | | 9:00 | Welcome back | | | 9:15 - 12:30 | Hackathon Session 2 | | | 12:30 - 13:30 | Lunch Also: Seminar by Ivo Sbalzarini: Bioimage Informatics: Quo Vadis? | At UZH Cafeteria Y35-F-32 (just a few floors down) | | 13:30 - open | Hackathon Session 3 | | | 17:00 - 18:30 | Summaries of the day | By all groups a short presentation | | 18:30 - 19:30 | Local dinner | Catering: sandwiches brought to the room | | 19:30 - open | Continue hacking | | | | | | | Day 3: November 8th | | | | 9:00 - 12:30 | Hackathon Session 4 | | | 13:00 - 14:00 | Lunch | | | 14:00 - 15:30 | Hackathon Session 5 | | | 15:30 - 17:00 | Summaries of the day | By all groups a short presentation |
We have 30 spots available for the hackathon. Sign-ups happen on a first come, first served basis.
Sign up opens on September 15th and closes on October 15th.