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OME2024 NGFF Challenge
Front matter
Zoom
Please paste this into the Zoom chat as new people join:
Welcome to the call. Please be aware that this session may be recorded. Live notes for the session are available in https://hackmd.io/3emKqKQsT_2U35vLepzDEQ 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
Check-in (20241009)
Agenda
Session 1
Attending
Notes
- The image file may be corrupted
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Learn More →Session 2
Data status
Challenge feedback
+1
: EP (non-JAX)- The image file may be corrupted
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Learn More →WM: demo of https://deploy-preview-53–ngff-challenge.netlify.app/
EP: how are we collecting feedback from everyone on how it went?
Check-in (20240925)
Agenda
Session 1
Attending
Notes
Session 2
Attending
Notes:
Check-in (20240911)
Agenda
Session 1
Session 2
Attending
Notes
- The image file may be corrupted
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Learn More →Commitment (20240904)
Agenda
Session 1
also: there are updates to the NGFF validator.
Highly recommended to validate any generated data
pip install ome2024-ngff-challenge
andome2024-ngff-challenge resave -h
webknossos
Python packageSession 2
Check-in (20240821)
Agenda
Session 1
- The image file may be corrupted
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Learn More →Session 2
Spec freeze? (20240731)
Agenda
Session 1
@base
specified (not normal). Can add framing.- The image file may be corrupted
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Learn More →- The image file may be corrupted
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Learn More →Session 2
Attendees
Notes
JM->ML
)- The image file may be corrupted
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Learn More →- The image file may be corrupted
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Learn More →- The image file may be corrupted
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Learn More →Status Sync (20240717)
Rough agenda
Please keep an eye on this or add your own.
- The image file may be corrupted
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Learn More →Session 1
Attendees
Notes
Josh: dev2 (binary) is in a fairly good
Seb: zarr2zarr - not on the dev2/rfc-2 format yet. Solely upgrades v2 to v3 (and v3 to v2). (Josh: i.e. dev1).
Aybuke: haven't done conversions yet but will do. Kola is likely to be the person.
Next steps on binary
Metadata/dev3 (Francois)
zarr.json/.zattrs
(but we will need references between them)- The image file may be corrupted
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Learn More →ACTIONS
Session 2
Attendees
Notes
zarr3 driver
compliant with the current specs for sharding? https://google.github.io/tensorstore/driver/zarr3/index.html'Spike 1 (20240703)
Rough agenda
Session 1
Attendees
Notes
dask.from_array()
rather thanfrom_zarr
- The image file may be corrupted
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Learn More →Session 2
Attendees
Notes
Kick-off (20240619)
Rough agenda
Session 1
Attendees
Notes
Introductions, etc.
Tom: not many datasets from HHU. could go fishing but it's not going to be significant (certainly not annotated). happy to be involved with the REMBI/RO-Crate work discussion. Poor understanding of what needs to develop. Python coding.
Joost: also tema 3. Have lots of datasets from 2 projects. Multimodal. Interested in generalizability, including transforms. Python coding at the Crick. Generally interested in the challenge. Would love to see benchmark data. Might not be able to share the Crick data. Have inhouse compute & storage.
Josh: selling point is "self-publication platform", but 'dev' version of the data might be a blocker. Convert to NGFF v0.4 (Zarr v2) might be good first step.
Team 1: v2/v3 (Python-spin)
Javascript
Java
Distribution
TODOs:
Session 2
Attendees
Notes
Hannes: with scalableminds
Kola: getting up to speed
Josh: intro on 3 teams
Kiya: pitching to JAX leadership
Josh: team 1 goal: Write a python script to convert ome-zarr to v3, put that data somewhere
Davis: what's the idea with the ro-crate specification with zarr?
Josh: who's doing something in the next two weeks?
Tom/Kola: RO-Crate tutorial
Josh: neuroglancer example for dev1
Peter & co.: napari release (independently of challenge)
Hannes/Norman: deployment of zarr-java
Josh: send updates, etc.
Kick-off (20240612)
Session 1
Attendees:
Notes
Seb: adjusting calendars now. How much more can change? Josh: not much I assume. An hour earlier for the AM session and an hour later for the PM session is likely the limi
Frances: expected to join both? (Hell) no. :) Choose what works best for you.
Datasets & repositories
Scope
Tools
"Teams":
Notes
Seb: adjusting calendars now. How much more can change? Josh: not much I assume. An hour earlier for the AM session and an hour later for the PM session is likely the limi
Frances: expected to join both? (Hell) no. :) Choose what works best for you.
Datasets & repositories
Scope
Tools
"Teams":
Session 2
Attendees
Notes
Data & repositories
Process & tools
Timeline of challenge