Road to OME-Zarr 1.0

Photo by Diego Jimenez on Unsplash Welcome File format enthusiasts?! Welcome, Road to 1.0 Josh Moore, technical director German BioImaging e.V. NFDI4BIOIMAGE Photo by Tom Shamberger on Unsplash 200 formats | 20 year repository of data | 2 developers Photo by Colin Lloyd on Unsplash Started by making the difficult feasible They don’t tell you how far away the clouds are Photo by Benton Sherman on Unsplash // cc-by https://bit.ly/40hnF50 Image “Monolithic vs. chunked” by Henning Falk https://github.com/zarr-developers/zarr-illustrations-falk-2022 ©2022 NumFOCUS (CC BY 4.0 license) Def. (n) directory-like layout of data rather than a single file, header information is available in formats like JSON or YAML. ‣See Zarr. Pros: ‣natively supports parallel writes ‣server-less access to contents ‣much more web-like access ‣can avoid costly downloads, e.g. when on S3 Cons: ‣many more files on disk ‣no easy way to lock on update ‣reduced desktop support Chunked file formats 7 https://zarr.dev/adopters // cc-by 8 example/ ├── s0 # Full-sized ├── s1 └── s2 # Smallest example/ ├── 0 # Full-sized ├── 1 └── 2 # Smallest example/ ├── 0 # Smallest ├── 1 └── 2 # Full-sized { “multiscales”: [ { “datasets” : [ {"path": “…”}, {"path": “…”}, {“path": “…”} ] } } https://ngff.openmicroscopy.org/ Starts with agreeing (e.g., metadata)… 8 “Largest image on the internet” (~2012) Stitched Zebrafish EM 500 GB, 1 frame Data credit: Faas et al., IDR (idr0053) https://www.youtube.com/watch?v=K8G_ZN8xXE0 https://bit.ly/4nQ5sDJ Photo by Jonathan Letniak on Unsplash Runway to 1.0 // cc-by 17 example/ ├── s0 # Full-sized ├── s1 └── s2 # Smallest example/ ├── 0 # Full-sized ├── 1 └── 2 # Smallest example/ ├── 0 # Smallest ├── 1 └── 2 # Full-sized { “multiscales”: [ { “datasets” : [ {"path": “…”}, {"path": “…”}, {“path": “…”} ] } } https://ngff.openmicroscopy.org/ Starts with agreeing (e.g., metadata)… 17 // cc-by …towards a FAIR standard Moore et. al: Histochemistry and Cell Biology (2023) https://doi.org/10.1007/s00418-023-02209-1 18 Photo by Hieu on Unsplash Avoiding action — turn left immediately! Ausweichmanöver — sofort nach links drehen! Photo by Rob Vesseur on Unsplash Request for Comments (RFC) https://ngff.openmicroscopy.org/rfc // cc-by A proposed way forward: OME-Zarr 1.0 21 QUARTER RFC DESCRIPTION LEAD STATUS Through Q3 2025 RFC-2 Zarr v3 scalableminds Done Q4 2025 RFC-3 5D+ Monash In progress RFC-5 Transforms Janelia / GerBI In progress RFC-6 Simplify multiscales scalableminds In progress RFC-8 Collections scalableminds In progress RFC-9 Zips SciLifeLab In progress Q1 2026 RFC-7 Provenance Broad Drafting RFC-10* Roadmap + Editorial Board GerBI Drafting RFC-11* Core concepts BioVisionCenter Discussion Q2 2026 RFC-12* Metadata GerBI Discussion RFC-13* Clean-up Allen Discussion RFC-14* v1.ALPHA TBD Discussion *: number is not yet assigned // cc-by Where are we now? USE CASES Developers Big data (i.e. connectomics) Repositories (archival) Image processing (i.e. AI-based analysis) Enthusiasts All users Initial development (2017-2020) + + Scale-up (2020-2023) + + + + Stabilization (2024-2026) + + + + + Ready-to-use standard (2027 and beyond) + + + + + + 22 Photo by Niklas Jonasson on Unsplash • 0.6: ASAP • 1.0: First prototype in 2026 • LTS: “Long-term support” What’s next? Much, much more this week. Photo by Rita Candeias on Unsplash Glencoe Software NGFF Roadmap •NGFF specification contributions (Q1 2026) •NGFF tools: bioformats2raw/ raw2ometiff/NGFFConverter •NGFF in OMERO and OMERO Plus https://forum.image.sc/t/glencoes-roadmap-for-ngff-in2026/117500 Slide courtesy Sébastien Besson Standardization enthusiasts! Let’s take off. The skies the limit. Welcome, Standardization enthusiasts! Let’s take off. The skies the limit. Welcome, Hosted by: doi: 10.5281/zenodo. 17564219 joshuaallenmoore Stickers next time. Sorry!