2017-04-18 Tuesday Team Meeting
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
Accepting minutes from last meeting
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.
Project Timelines (2-3 minutes each)
Spaces
-
Files/Formats/OME Files (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)
-
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
-
OMERO 5.3.1 (J-M)
- Major share bug
- Release scheduled for Thursday 20/04
- Include other smaller bugfixes
- Pushed 5.3.2 release to 16/05, include thumbnails work
-
OMERO 5.4.0-m1 (Mark)
-
can*
methods work done-
fixed Petr's failing
can*
test -
Mark added
canChgrp
,canChown
-
fixed Petr's failing
-
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
- existing session / security changes already conflict with bringing read-only work to IDR
- further work here will create further conflicts
-
the triggers approach of
-
in OmeroWeb integration tests a couple of failures
- Will to help Mark understand them
-
rare group-related flakiness in import
- may preexist 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
-
-
Outreach
- Planning nightshade user training with new features, analysis tools
-
Files/Formats/OME Files (Sebastien)
Other releases/upgrades:
-
Figure
- release 3.0.0 scheduled 19/04
- Testing deployment from testPypi today
- Will try new commercial tool for pypi testing & release after release
-
Iviewer
- Browser testing - issues in IE
-
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, anyone should feel free to contribute, there's a gdoc for drafting 'Getting Started' suggestions
-
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.
-
Figure
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.
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.
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