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. A big next step for OME-NGFF will be the adoption of the Zarr V3 standard to address concerns about file numbers in OME-Zarr files.
Following up on the successful 2023 Next generation bioimage analysis workflows hackathon (see a summary of the results here), we are bringing together leading developers and researchers this fall in Zurich Switzerland. Major topics of the hackathon will be handling OME-Zarrs in Python and in Java, how to build workflows for processing OME-Zarrs and further evolution of the OME-NGFF spec.
The hackathon consists of 3 parts: An optional pre-hackathon meeting on Monday, the main hackathon from Tuesday-Thursday an optional Friday hacking day.
Topics
This year’s hackathon will follow a set of pre-defined topics & the focus areas of the hackathon will be coordinated on in pre-hackathon meetings.
- OME-Zarr in Java, lead by Vladimir Ulman & Norman Rzepka
- OME-Zarr Python ecosystem, lead by Lorenzo Cerrone
- OME-Zarr workflows, lead by Joel Lüthi
You want to lead your own topic at the hackathon? Please reach out!
Program
Optional Monday program: Program is to be confirmed
Optional Friday program: Continue working in your hackathon group
Download the brief participant introduction here.
Target audience
- Your day-to-day work involves image analysis, data management and/or tool development for image analysis
- You are involved in developing tools, making tools accessible to others or shaping image analysis standards
- You are working with OME-NGFF, FAIR image data or standardized workflow managers
Sign Up
We have 30 spots available for the hackathon. Sign-ups happen on a first come, first served basis.
Sign up here
Sign up opens on August 21st.
Travel Grants
We have travel grants available. You must be signed up to the event to qualify for a travel grant. See more details on the travel grants here.
Travel advice
TBD hotel deals
TBD other hotels
TBD travel to Zurich
TBD travel within Zurich
TBD finding the hackathon room
Organizers
- Joel Lüthi, BioVisionCenter (University of Zurich) & SwissBIAS
- Josh Moore, NFDI4BIOIMAGE
- Christian Tischer, Bioimage Analysis Service Team Leader, Data Science Center, EMBL Heidelberg & NFDI4BIOIMAGE
- Vladimir Ulman, CEITEC – Central European Institute of Technology, Masaryk University, Brno, Czech Republic & IT4Innovations National Supercomputing Center at VSB – Technical University of Ostrava, Ostrava, Czech Republic
- Norman Rzepka, scalable minds
- Eric Perlman, Yikes LLC
- Lorenzo Cerrone, Ethel Mendocilla Sato, Virginie Uhlmann, BioVisionCenter (University of Zurich)
Sponsors
This event is made possible through funding by NFDI4Bioimage through German Bioimaging: https://gerbi-gmb.de/
This event has been made possible in part by grant 2024-342803 from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation.
