2020-10-20
Attending:
Will, Seb, Jason, Josh, Petr, Simon, Dominik, Frances, June, Emil, David, Erin, Melissa, Wilma, Kevin, Ola, Chris, Andreas
Start: 2:00 pm UK
Project Status
(2-3 minutes each)
- IDR
- Next release end of the month
- idr0088 to go ahead - big screen.
- Started import ahead of time (takes a long time)
- idr0095 - don’t expect any problems
- Seb: 2 talks and 2 posters at the CSHL conference.
- 6 registered to attend
- Josh: will discuss more on Monday but.. getting close to having ‘Fire’ access at ebi s3
- Not public but it is backed-up etc.
- Seb: can we use it for uploads?
- Josh: assume we’d need something in front of it?
- NGFF
- Labels: needs some marketing - spec is out but no comments from the community.
- Jason: could write a paper - Josh: just need screenshots, or video would be nice
- Post on image.sc and try to get feedback
- HCS: progress and target demo
- Target early next week to show something working.
- 3 PRs:
- Dom: generate zarr from omero-cli-zarr
- Josh: ome-zarr-py to consume plate
- Will: view in vizarr
- Oct 29th meeting (OME2020 follow-up meeting), see image.sc
- Adding Erin, Chris etc to list
- Josh: several tangents. Try to get a handful of lightning talks. 5 mins each.
- e.g. TileDB from Glencoe, HCS, labels, etc.
- More content the better
- Jason: consider a paper on all the work going back to zarr conversion etc.
- e.g. Nature Methods paper - 300 words?
- Josh: Trevor asking what reference to cite zarr work.
- Paper too slow. Post to preprint archive?
- Chris: will work on tiledb, etc. bioformats2raw HCS layout
- Josh: also have a PR suggestion for Saalfeld re: N5+S3+Zarr
- Bio-Formats 6.6
- Release delayed. Infrastructure changes discussed at meeting.
- Mostly all merged etc.
- SA:
- Seb: Everything recovered from last week, as far as we know.
- Some infrastructure improvements in progress
- Website updates faster - not tied to UoD
- Glencoe:
- see NGFF as well.
- More labels in tileDB
- Windows fixes - few PRs.
- Conversions for plates in prep
- Labelled objects into OMERO.tables. HCS data.
- Community
- CSHL preparation 4th Nov
- See calendar for run-throughs
- Ola: imported images with histograms etc in yaml
- Moving to public instance soon
- Josh: maybe want to add omero-zarr-ms microservice for public use?
- Or could export as zarr to s3 etc.
- Ola: OK, will get back to you
- I2K meeting workshops - Nov 30th - Dec 2.
- Link: https://www.janelia.org/you-janelia/conferences/from-images-to-knowledge-with-imagej-friends
- Josh: see hackMD with info
- Heidelberg interested
- E.g use BigData viewer or napari, vizarr
- Illustrate that data is BIG. E.g. McDole data.
- Show how to create data (save for the end - not follow-along)
- Submission by the end of the week.
- What about other IDR / OMERO work?
- Seb: workshops up to 4hrs max.
- Petr: we have other workshops in the week before.
- Not much time to create new workflow by then, but will do for GBI in Jan
- Jason: can we re-use workflows, eg. idr0021?
- Petr: big change to use IDR server instead of workshop server
- Jason: I’ll work with Petr on submission text. Josh to cover other workshop submission.
- Petr: Jim Proctor also actively promoting work to make our training resources more “asyncronous”
- Human Cell Atlas: interested in our work
AOB
(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
Main Topic
(20-25 minutes plus 15 minutes questions max)
