Bioimage Hackathon 01: Further developing OME-Zarr specifications and implementations
Dates: 31 January - 6 February 2022 (Monday - Sunday, 7 days)
Location: Milan, Italy at Human Technopole research institute
COVID-19 notice: Due to the ongoing COVID-19 pandemic, the organizational committee is keeping a close eye on the local (Milan/Human Technopole research institute) regulations regarding COVID-19. In case of drastic changes to the travel regulations in Miltan/Human Technopole, the event will be shifted either to a later date or held virtually. Applicants would be notified in case such decision to either postpone the event or hold it virtually is reached.
Applicants should also check travel regulations from their country to Italy at the webpages provided below:
Global BioImaging invites you to participate in a 7-day in-person bioimage hackathon focused on OME-Zarr next generation image file format.
Differences in nomenclature and data formats in the field of bioimaging data inhibit sharing. For users, translating between data formats is imperfect, time-consuming and must be performed repeatedly. Combined with the growing number of formats and advancements in both data volume and complexity, translation is increasingly a bottleneck.
This hackathon will focus on the next-generation format OME-Zarr that aims to enable a one-time conversion of datasets to a common file format as well as the ability to store them on highly-parallel object storage. Such next-generation file format can revolutionize the sharing of bioimaging data by expediting access and driving discovery.
The topics of this hackathon will be about further developing the OME-Zarr specifications and ecosystem, such as:
- implementation of the tables specification (started at the October hackathon)
- begin transformation specification (#28) on top of pixel spacing
- discuss trade-offs in the collection specification (#31)
- improve Fiji integration & usability (e.g., drag-n-drop)
- ...bring your own suggestion (please mentioned these in the application form)
This hackathon is limited to 16 places. Selection of the participants will take place after application deadline.
Scientific committee: Christian Tischer (Centre for Bioimage Analysis, EMBL Heidelberg, Germany) and Josh Moore (Open Microscopy Environment, University of Dundee, United Kingdom)
Apply for the Bioimage Hackathon at the following link (deadline extended until 25 December):
Application for this event is now closed.
- Coding experience is essential
- Prior contributions towards open image file formats and/or open software is considered a plus
- Service provision, e.g., as a core facility staff, image analysis as a service, etc is considered a plus
For more information about the topics, please visit the following page:
Contact person: Gleb Grebnev, gleb.grebnev at embl.de
Please note that participants will need to bring their own laptops for this event.
In addition, travel support is available to cover the costs of transportation and accommodation for persons applying from academia/research institutions/universities around the globe. A maximum of 8 travel grants are available for persons who are based outside Europe to attend this event and a smaller number of travel grants is available for person who are based in Europe.