---
tags: NGFF, community-call
---
# OME-NGFF community call: 2025-02-21

Please paste this into the Zoom chat as new people join:
:::warning
Welcome to the community call. Live notes for the session are available in https://hackmd.io/HdRQgm3oT1aCGxBXhL1f3Q Where possible, help to structure the notes for later publication rather than commenting in Zoom's chat. Thanks!
:::

## Code of conduct
The OME community is open to everybody and built upon mutual respect. Please take the time to review the code of conduct below.

https://github.com/ome/.github/blob/master/CODE_OF_CONDUCT.md

## Preliminary agenda (not for notes)

| [discourse thread](https://forum.image.sc/t/ome-ngff-community-call-starting-2025-right/108431) | [zulip thread](https://imagesc.zulipchat.com/#narrow/channel/328251-NGFF/topic/Community.20call.20reminder.3A.20tomorrow.20Friday.2020th.20of.20February) |

- Updates (30 minutes) - [slides](https://docs.google.com/presentation/d/1J0_axLXrkA32NRL3AIlBygfU9nTGybVIidpq_Dn0Hhs/edit?usp=sharing)
- Zarr v3
- OME-Zarr RFCs
- OME-Zarr 1.0
- Community (calls, etc.)
- Open discussion (30 minutes)
- ... Please list items here before the meeting 📝 ...

----

<details><summary>First session</summary>

## OME-NGFF community call (10:00 CET; 21 Feb 2025)

### "User registration" Session 1

| Name | Institute | Bluesky Handle | Mastodon Handle | GitHub Handle |
|---------------|-----------|----------------|-----------------|---------------|
| Copy | and | paste | me | |
| Josh Moore | German BioImaging, e.V. | @joshmoore.bsky.social | | joshmoore |
| Sébastien Besson | Glencoe Software | | | sbesson |
| Jan Eglinger | FMI Basel | @imagejan.bsky.social | | imagejan
| Norman Rzepka | scalable minds | @normanrz.com | normanrz.mastodon.social | normanrz |
| Davis Bennett | independent | | | d-v-b |
| Jens Wendt | NFDI4Bioimage | | | JensWendt|
| Tom Boissonnet | HHU Düsseldorf | @tom-bssnnt.bsky.social | | Tom-TBT |
| Koji Kyoda |RIKEN BDR|||openssbd|
| Florian Aymanns | EPFL | | | |
| Ken Ho | Crick | drkenho.bsky.social |@[e-mail] ||
| NOT HERE | :smile: | | | |

### Session 1 Notes

* Presentation (10:05-10:15)
* Open Discussion
- Joost:
- engagement e.g. on image.sc -- more clarity on how people can contribute. What's needed? Purpose for people to join
- How the RFCs and the documents are published on github -- you have to be tech savvy to read them. A rendered URL. ... but specific change page. (perhaps a list). Would make it easier for "outside" contributors who have ideas what to contribute but are not as deeply familiar with the tech-stack as the folks who are already involved in the project.
- Virginie: interested to here crowds opinion on how people can contribute. alternatively, interested in having these meetings be much more welcoming: beyond the technical things but here is what the community is, come and meet people.
- just focusing on contributions pre-selects for a certain group of people
- e.g. people who need to convert their data
- Norman: agreed. these meetings could be more than specification related. More room now to use the format
- +1 for increasing the frequency to quaterly or every other month. actively invite people to share.
- an hour, 20 minutes to showcase work or whatever. still spec talks but they don't have to fill the meeting.
- Josh: challenge was more like a working group. Similar to meshes.
- Seb: showcase shows what's *possible* rather than focusing on what's missing. Pat on the back. (user story)
- Norman: agreed, we need to stop talking (only) about the problems
- Josh: OME-Zarr figures as a quick showcase
- Koji: meeting with Nikon developers. Could ask about OME-Zarr support?
- Very conservative
- Timeline?
- Commenting on 1.0 RFC
- https://forum.image.sc/t/ome-zarr-reading-writing-with-c-libraries/89932
- Davis: tensorstore may be a big ask (also doesn't write Zarr groups)
- Joost: OSS control for EM "SBEMImage" (https://github.com/SBEMimage/SBEMimage) written in Python
- now support OME-TIFF. Could also support OME-Zarr through that.
- Seb: Glencoe looking at private data (almost exclusively)
- nice image.sc blog post about which viewers support private access ("plug your credentials")
- how do we handle access control? one bucket with one password!
- our tool ends up making it easy to start accessing data I shouldn't (server has credentials)
- not specific to OME-Zarr but might end up as an RFC ("accessing data through a server")
- is there a way to put mapped token to prove you have rights to access data?
- Norman: happy to chat about it. have definitely dealt with it.
- Josh: another ongoing project
- https://oscars-project.eu/projects/bio-codes-enhancing-ai-readiness-bioimaging-data-content-based-identifiers
- https://core.iscc.codes/
- capture a checksum (semantics+metadata+data)
- Norman: Collections
- hackmd to capture user stories (motivations)
- does anyone have user stories? Get in touch with Norman on Zulip
- next we start writing it up.
- breaking change
- FYI: Hackathon organization with internal projects -- https://github.com/BioImageTools/
- FYI: mental note for hackathon in Zürich in November
- End: 10:50

</details>

## OME-NGFF community call (17:00 CET; 21 Feb 2025)

### "User registration" Session 2

| Name | Institute | Bluesky Handle | Mastodon Handle | GitHub Handle |
|---------------|-----------|----------------|-----------------|---------------|
| Copy | and | paste | me | |
| Josh Moore | German BioImaging, e.V. | @joshmoore.bsky.social | | joshmoore |
| Will Moore | Dundee Uni / OME | will-j-moore | | |
| Ian Hunt-Isaak | earthmover | ianhi | |ianhi|
| Eric Perlman | | @perlman.bsky.social | @[e-mail] |
| Joel Lüthi | BioVisionCenter, UZH, CH | @joelluethi.bsky.social | | jluethi |
| Dan Toloudis | Allen Institute for Cell Science | | | toloudis |
| Ken Ho | The Francis Crick Institute | drkenho.sky.social| @[e-mail]| DrKenHo-crick |
| Kiya Govek | The Jackson Laboratory | | | govekk |
| Fernando Cervantes | The Jackson Laboratory | | | fercer |
| Kabilar Gunalan | Massachusetts Institute of Technology | @kabilar.bsky.social | | kabilar |
| Erick Ratamero | The Jackson Laboratory | @ratamero.microscopy.codes | idlethumbs.social/@ratamero | erickmartins |
| Cameron Fraser | Allen Institute for Cell Science | | | frasercl |
| John Bogovic | HHMI Janelia | @bogovicj.bsky.social | | bogovicj |
| David Ackerman | HHMI Janelia | | davidackerman
| Marwan Zouinkhi | HHMI Janelia | @mzouink.bsky.social | | mzouink |
| Melissa Linkert | Glencoe Software | | | melissalinkert |
| Rebecca Vorimo | HHMI Janelia | | | rinva|
| Mark Kittisopikul | HHMI Janelia | @markkitti.bsky.social | https://fosstodon.org/@markkitti | mkitti |
| Diyi Chen | HHMI Janelia | | | dchen116 |
| Damir Sudar | Quantitative Imaging Systems LLC | @dsudar.bsky.social | | dsudar |

### Session 2 Notes

- Erick: https://www.bioimagingnorthamerica.org/events/ome-2025-community-meeting/
- Mark: 1.0 prerequisites
- Zarr v3 complaints
- "Under construction" needs to go away. Yup. See https://github.com/zarr-developers/zarr-specs/pull/330
- Cross testing has posed some issues
- e.g. ts writes v2 such zstd isn't readable by other implementations like zarr-python
- Norman: Yes! definitely put on the list 1.0
- zstd becoming a prominent codec (zarr-python v3 default)
- how do we enumerate codecs in OME-Zarr
- Norman: see https://github.com/zarr-developers/zarr-extensions
- Ken: if "more reliable then extensions"?
- Norman: there are different goals. mine:
- every version has been breaking so far
- want to get to the point where we can not break for a long time
- KH: :+1: for something more stable.
- Dan:
- 1. sample implementation that's really robust will go a long way to make it feel serious.
- An "implementation" should codify all the MUSTs, SHOULDs, MAYs etc. from the spec..
- 2. metadata: official way of dealing with more metadata, even if it is just one field that says, "put it here"
- or a statement that "you're on your own"
- 3. thinking a lot about collections, distinction between zarr groups and sources from different filesystems. (perhaps completely required in 1.0)
- David:
- reference implementation in https://ome-zarr-models-py.readthedocs.io
- v0.4 done; working on v0.5. Love that to be a community project.
- outcome of the last hackathon
- Norman:
- discussed collections at the hackathon. working on stories to motivate
- working towards a RFC. definitely part of 1.0
- get in touch on zulip, etc.
- likely to get a WG/meeting series started soon
- Luca: regarding transforms
- with Wouter, contributing an implementation to ome-zarr-models-py
- working other than displacements... (currently without pydantic)
- please say if development needs prioritizing say the word. (April? Yes!)
- Abbas
- as an end user, very interested in transforms. (webknossos, etc.)
- need transforms for stitching
- Luca (in chat): https://github.com/multiview-stitcher/multiview-stitcher
- Joel (in chat): That library is super cool, we've had a lot of fun using it
- don't want to duplicate the large datasets.
- top priority
- John
- thanks Dan + others for reviewing RFC transforms
- currently working on what parts are necessary vs optional for implementation
- currently working on complete set of examples
- Josh
- Displacement field might be something in its own page so fully optional
- Joel
- Community calls are helpful for people to catch up on what's going into RFCs

- Meetings
- Erick: need to change how people view this meeting - wasn't attending because viewed it as heavily technical spec meeting
- Virginie taking over community-facing meeting series

- Misc
- Abbas: infrastructure based on zarr
- Working on new parallelization for chunk-wise compute, but having trouble getting in touch with dask developers
- Davis: DON'T set Dask chunk size to be same as Zarr chunk size. Overhead of 1 millisecond for every task.
- Dask chunks should not be as small as Zarr chunks
- Davis: dask forums aren't very lively, but ping people directly (e.g. Davis) on github repo
- zulip is also a good option for these kinds of questions
- Will: what's the Python reference implementation for working with arrays? is everyone using different things?
- Josh: likely a dozen different tools...
- 2023 hackathon outcomes: https://forum.image.sc/t/outcomes-of-the-next-generation-bioimage-analysis-workflows-hackathon/88733
- David: next steps need to be limited scope - started with validating metadata, before moving on to writing metadata
- would be ok with adding support for reading/writing data to ome-zarr-models-py
- https://ome-zarr-models-py.readthedocs.io/en/stable/
- Ken: Java for getting users to adopt... what's the latest on java development for ome-zarr?
- John: progress on Zurich hackathon last year for reading/writing zarr 3 from java. can expect Fiji support for that "soon"
- smaller community working on java than python, and Fiji maintenance is a big task