2021-02-16
Attending: Will, Frances, Petr, David, June, Jean-Marie, Wilma, Dominik, Josh, Sebastien, Melissa, Kevin, Emil, Chris, Jason, Erin, Andreas
Start: 2:00 pm UK
Project Status
(2-3 minutes each)
- IDR:
- Released prod93 on thursday with 3 studies.
- idr0093 problems - need to remove screen while working on a fix
- Deleting plate by plate
- Short downtime, then back up on Thursday.
- Announce on twitter etc.
- Jason: we need to be able to handle these cases in our workflow
- Seb: if we have 1 release per study, submitters could review first, possible to revert
- But not practicable on our current scale
- Frances: this was a new BF reader. Not a common occurence
- Melissa: reader fix nearly done
- NGFF
- 2D Benchmark shaping up, see https://github.com/ome/ngff-latency-benchmark/pull/15
- Josh: 2D looking good now. Benchmarking performance graph looking good
- 3D issues
- Needs work
- David: Trying to modify bf2raw to do 3D chunking while maintaining resolution
- Imaris downsampling in Z problems with BF not recognising these as multiple resolutions (treated as series)
- Seb: could update Imaris reader to ‘do the right thing’ and downsample in Z, but might not work well with OMERO etc.
- Benchmark testing only needs to work on the lowest resolution
- Chris: array access no different between resolutions
- Josh: Do 3D chunking and then throw away other resolutions (series)
- Josh: feedback on graphs appreciated
- NB: zarr was faster than expected - nested storage was failing so blank chuncks being returned (fast)
- NGFF community call next Tuesday. AM and PM time slots
- Invites on image.sc like previous meetings. NO requirement. Everyone welcome
- Will affect standup availability on Tue morning
- AWS (Jason): Access via UoD –> JISC
- Decision use both UoD and Glencoe AWS resources for benchmarking testing
- Chris: future - compare AWS with Azure, Google cloud etc?
- Releases
- preparing insight 5.5.16 (bugs) (ready to go)
- iviewer 0.10.2 (probably tomorrow)
- finalising figure
- web later
- 3rd party project integration
- CellProfiler 4 upgrade in notebooks. Old Pipelines work. cf. zarr discussion
- New API to interface with ilastik
- SA
- all systems patched and passwords rotated
- decisions needed on some older machines
- Glencoe
- label image infrastructure being used and integrated
- iviewer ROI saving issues
- Community
- Training on Thursday and Friday this week McGill
AOB
- UoD day off on Friday
- Jason: Team Meeting runner
- Jason New Role: https://wellcomeleap.org/ (a life sciences DARPA)
- Program director position
- Starts today!
(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
Main Topic
(20-25 minutes plus 15 minutes questions max)
