2017-04-18

18th April

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. Spaces

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

1. [Outreach](https://trello.com/b/Da6OAWam/outreach)

- Planning nightshade user training with new features, analysis tools

1. Other releases/upgrades:

1. Figure

- release 3.0.0 scheduled 19/04

- Testing deployment from testPypi today

- Will try new commercial tool for pypi testing & release after release

1. Iviewer

- 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