Dundee: Petr, June, Dom, Balaji, JM, Mark C, Simone, Ola, Simon, Kenny, Jason, Roger
Remote: Josh, Seb, Eleanor, Kevin E., Wilma, Liza, Will, Melissa, Andreas, Curtis, Alison, Chris
# Agenda - 2:00pm Start #
1. Accepting minutes from [last meeting](https://www.openmicroscopy.org/site/community/minutes/conference-calls/2017/2017-04-11-tuesday-team-meeting)
1. Alison Walter (UW Madison) - converting ROI from ImageJ to OMERO
- Masters at LOCI
- 1) Add ROIs to ImgLib2
- 2) ImageJ-OMERO ROI support
- ImgLib2 ROIs. Add OMERO equivalent ROIs.
- Use Real space
- Binary/Unary operations, affine transforms
- Contains() implementation
- Currently visible in BigDataViewer without needing major changes
- Curtis: ImgLib2 hackathon discussed ROIs. Good progress
- Wrap OMERO ROIs in IJ.
- Saving to OMERO - simply add new ROIs instead of updating existing ROIs
- Consistent boundary behavior - OMERO doesn’t specify behavior. Insight (awt) inconsistent.
- Could configure options for inclusion algorithm.
- IJ -> OMERO ROIs - add annotations to document inclusion behavior
- Jason: IJ inclusion behaviour inconsistent (different plugins)?
- Alison: no
- Curtis: e.g. ‘Open rectangle’ in IJ -> OMERO with annotation to specify ‘open’
- Chris: transforms in real space. Need consistent handling of edges with affine transform.
- Implementation-dependent wrt performance.
- Alison: ImgLib2 does have consistent handling of affine transforms
- Curtis: use cases don’t need to go back and forth Integer space <-> real space.
- Won’t support OMERO label shapes initially
- Jason: can use this on IDR data?
- Josh: e.g. mitocheck 50000 polygons in timelapse movie.
- IDR has 1.2 million polygons
- Curtis: see trackmate for high performance handling of many ROIs
- Chris: would be useful to select shapes within region of an image (big images).
- Alison: probably doable with image ops
- Curtis: BigDataViewer only loads ROIs as needed for viewed region/resolution.
- Josh: OMERO can have extra metadata/annotations - how to handle this in IJ ROIs? E.g. filter ROI display by metadata.
- Curtis: will point us to code etc when ready for testing etc.
1. Project Timelines (2-3 minutes each)
1. [Files/Formats](https://trello.com/b/IBHfAIMP/bio-formats-5-x)/[OME Files](https://trello.com/b/WFYWCvoV/ome-files-0-4-0) (Sebastien)
- OIR testing of new reader (Balaji)
- Assess this week to decide on next steps/release
- Paper discussion -
- 5.4.1 release last week, bug fixes and docs
- Discussing bringing tiling API in C++ (same as for Java)
1. [Metadata](https://trello.com/c/XQXwX6jj/6-metadata) (Josh)
- Paper needs to be in by Friday
- Demo 35 released today (1 new dataset - need to fix rendering settings before tweeting).
- Would be nice to allow authors to set settings (without sending yaml files)
- Wnd-Charm features being generated for users’ meeting
- Several PRs rebased to OMERO 5.3. But maybe target 5.4.
- IDR testing server available with public login
1. [OMERO 5.3.1](https://trello.com/b/2V7YCJKj/omero-5-3-1) (J-M)
- Major [share bug](https://trello.com/c/sMxu4Rwi/1-bug-fix-shares)
- Release scheduled for Thursday 20/04
- Include other smaller bugfixes
- Pushed 5.3.2 release to 16/05, include thumbnails work
1. [OMERO 5.4.0-m1](https://trello.com/b/VkiONV40/omero-5-4-0-m1-new-role) (Mark)
- `can*` methods work done
- fixed Petr’s failing `can*` test
- Mark added `canChgrp`, `canChown`
- still to improve performance
- the triggers approach of `OMERO5.4DEV__1` database could be extended to move more permissions checking code from Java to PL/pgSQL
- in server code [could cache more with session](https://trello.com/c/HRJyHGHh)
- existing session / security changes already conflict with [bringing read-only work to IDR](https://github.com/openmicroscopy/openmicroscopy/pull/5213)
- further work here will create further conflicts
- in OmeroWeb integration tests [a couple of failures](https://trello.com/c/nWvUzN5t)
- Will to help Mark understand them
- rare group-related [flakiness in import](https://trello.com/c/DfulHH2y)
- [may preexist](https://github.com/openmicroscopy/openmicroscopy/pull/4957) roles work but could be triggered more by it
- thorny issue, may require Josh’s help to diagnose
- trying another optimistic fix in tomorrow’s merge build
- Jason: want to try a demo of clients to highlight remaining issues?
- Petr: happy to do one, but clients are looking pretty good
- Planning nightshade user training with new features, analysis tools
1. Other releases/upgrades:
- release 3.0.0 scheduled 19/04
- Testing deployment from testPypi today
- Will try new commercial tool for pypi testing & release after release
- Browser testing - issues in IE
1. new website
- Liza working on graphics, team working on content
- Liza has added the new navigation to allow extra pages in the OMERO developer section
- next content priorities are developer focused and marked with orange labels on the ‘content to dos’ list of the [new website trello board](https://trello.com/b/Y8BzIDEB/new-website), anyone should feel free to contribute, there’s a gdoc for drafting ‘Getting Started’ suggestions
1. Sysadmin (current board and recent PRs)
- Nightshade major version upgrade.
- Pre-upgrade check delayed due to web de-coupling investigation
- 5.3.0 upgrade planned for this evening
- OMERO.web running from separate VM, stable. Ready for upgrade this evening.
- Mark: docs could be improved.
1. Glencoe Update (Chris)
- Olympus work up now for review
- couple PRs related to session handling up for review in the next couple of days
- Working on preparing for OMERO Plus 5.3 / Bio-Formats 5.4
- webinar at the end of the month.
1. User meeting update
- Workshop confirmations
- Will need to start prepping soon
- First night at DCA, with chairs!
- 2nd night - wine tasting in “The Street” with food.
1. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)
- Curtis: would be good to have OME presence at IJ hackathon - several coming up http://imagej.net/Hackathon