2017-02-07

7th February

Dundee: Will, Petr, Dominik, June, Simon, Mark, Chris, Helen, Kenny, Balaji, Simone, Roger,

Remote: Sebastien, Jean-Marie, Ola, Josh, Wilma, Melissa, David,

# Agenda - 2:00pm Start #

1. Accepting minutes from [last meeting](https://www.openmicroscopy.org/site/community/minutes/conference-calls/2017/2017-01-31-tuesday-team-meeting)

1. Project Timelines (2-3 minutes each)

1. Spaces

1. [Files/Formats](https://trello.com/b/IBHfAIMP/bio-formats-5-3-x)/[OME Files](https://trello.com/b/wA1T35Ld/ome-files-0-3-0) (Sebastien)

• Going Well!

• 5.3.3. Released last weeks. Congrats all.

• 5.3.4 work started - board open etc.

• Formats meeting - good to know what’s important for 5.3.0

• OME files: benchmarking results being analysed.

  • A couple of critical issues: writing pixels, reading metadata.

  • Request extension of paper. Fix as many bugs fixes as possible.

  • Features for 0.3.0: C++ 11 Tiff compression. Performance

  • Pushing extended metadata work to 0.4.0

• 5.3.x will go into OMERO 5.3.0. If we get to BF 5.4.0 shouldn’t have

  any breaking changes.

• Trying to stick to semver as close as possible

1. [Metadata](https://trello.com/c/XQXwX6jj/6-metadata) (Josh)

1. Ontology deliverable going out

• Euro-BioImaging doc specifying what ontologies we’ve used

1. demo33 deployment

• Still issues with clouds at EBI

• Still annotations to update

1. demo34 planning

• Still planning stage

• Evolving, but focus on analysis and scaling up

1. ITR & NEUBIAS

• Josh to Lisbon on Sunday.

1. [OMERO 5.3.0](https://trello.com/b/FoyfXCaf/omero-5-3-0)

1. [New Roles](https://trello.com/c/t0nT7KYa/133-new-role) (Mark)

* this week reviewing “user management” role to,

* allow group leaders previous powers, like create user in their group

* prevent privilege elevation

* next week hope to look at checking/adding `can*` methods on object permissions so clients more easily know current user’s powers

* these “new roles” changes make the server run somewhat slower: performance needs investigating and improving

1. [Color](https://trello.com/c/sGlYbbvB/213-color-in-shape-settings)

* update script testing

* Test SQL updates

1. Chris Java 9 issues (JavaDoc etc) resolved?

• JM - most issues resolved (server starts) but docs issue not fixed

• JM: can turn off JavaDoc

• BF changes in plate naming need to be tested etc.

1. Probably need a sql script to “migrate” annotation from wellsample/image to wells. Following major changes in UI.

• Chris: not much annotations on Plate now, except Tables.

  • Mostly at Well level rather than Image level.

  • Use OMERO.script to allow users to run as needed (and reverse if

    error!)

  • Some users do have lots of Image annotations

  • Josh - big change for IDR: lots of workflows rely on current

    Well+Image

  • Chris: view Image - need to see Well metadata at same time

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

• Josh to Portugal

• Josh: http://cytohack.com/ London. Cell tracking hackathon

1. Other releases/upgrades:

1. [Figure](https://trello.com/b/BW5fN9Ox/omero-figure-2-0-0)

• Plan to release after 5.3.0 E.g week later.

1. [iviewer](https://trello.com/b/1t6i9daP/omero-5-3-0)

• ROI and other usability improvements in progress

1. Sysadmin

1. Any post patching issues noticed by team?

• We have snapshots but can’t keep for too long

• VMWare nodes being prepared

1. Glencoe Update (Chris)

• Using new BF tiff-writing.

• CyclicIF images. 42 channels in 1 tiff file. Stitching, registering,

  pyramids etc.

• 40GB files!

• Seb: some scalability issues but otherwise OK, tests etc.

• Melissa PR: pyramid tiff reader to support OME metadata and

  multi-channel pyramids.

• Nice to have pre-calculated pyramids in one file.

• Chris: sometimes useful to pre-process before import to more

  performant storage (cf OMERO 4)

• New imaging modalities have tricky data structures with poor

  performance

• Progress on OMERO read-only mode: multiple servers for scalability.

• Roger: used sub IFD tag to read subresolutions from standard TIFF

• Chris: not looked at that approach. Wanted to use as much existing

  code as possible to get working solution.

1. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)

- Help guide pdfs - what do we want to do about these now Gus isn’t here to do them? Is everyone doing work on the help website prepared to edit the pdfs too every time or do we want to move to having pdfs be internal for training and just update them when we need them?

- J-M: a limited number of PDF is used. Getting started, configuration. We already have template to generate pre-training those ones.

- J-M: pdfs not downloaded very much. We only use ‘getting started’ for training.

- Helen: will open PR to remove links to PDFs.

- Helen: would like to move site to Jekyll markdown instead of editing html