Dundee: Petr, Kenny, JM, Mark, Simon, Simone, Roger, Ola, Balaji, June, Jason
Remote: Will, Sebastien, Helen, Andreas, Josh, Chris, Melissa, Eleanor, David, Emil, Wilma,
# Agenda - 2:00pm Start #
1. Accepting minutes from [last meeting](https://www.openmicroscopy.org/site/community/minutes/conference-calls/2017/2017-02-14-tuesday-team-meeting)
1. Project Timelines (2-3 minutes each)
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)
1. Bio-Formats 5.3.4 release yesterday
1. OME Files 0.3.1 releasing “as we speak”.
- Bugfix from mitocheck dataset (see below)
1. Benchmark update
- See OME Files paper
- OME files is C++ tool for writing OME-TIFF acquisition/analysis
- Need evidence of ‘performance improvement’ for paper reviewer
- Use 3 Datasets 5D / HCS / metadata rich
- Test in different environments
- Read metadata / pixels -> write OME-XML / OME-TIFF
- Plot results with “Java BF Linux” as reference.
- OME-Files faster in most cases (except Metadata - needs investigation)
- JVM caching/optimisation can have an effect on metadata performance
- Will resubmit paper end of next week
- Jason: need to discuss libs/architecture, use of XML etc
- Design of benchmarking tests is important/tricky
- Roger: serialisation overhead is significant
1. [Metadata](https://trello.com/c/XQXwX6jj/6-metadata) (Josh)
1. Move to extcloud05 - cloud migration at EBI. network & volume issues.
1. Thumbnail improvements
1. Upcoming datasets
- 1 ready to go, 2 in preparation
1. Analysis & scaling
- Splitting web to different server from OMERO etc
- Plenty to do up until POTN
1. [OMERO 5.3.0](https://trello.com/b/FoyfXCaf/omero-5-3-0) (J-M)
1. Web API final adjustment
- 2 PRs open, 1 more to come
- omero-marshal release for 5.3.0
1. New Role: Probably a last DB change
1. Feature freeze next week
1. Post-release: discuss IDR, BF & OMERO 5.3 divergence
- Backport IDR changes on top of OMERO 5.3
- Aim to avoid custom changes in OMERO 5.4
1. Docs for roles etc. progressing well
1. Report from Neubias/Lisbon (Josh) Nice weather, nice city!
1. Tagathon (tagging tools)
- Move to using ontologies instead of tags.
- OMERO Might need to tackle OWL, RDF soon
1. Working group 5, Graeme Ball
1. Other servers, cytomine (node.js based)
1. Catmaid ‘onto’ tile server.
1. Annotated sample image location
1. Chris Bakal is hosting Cytomining in London, June 28-30
- Also cyto-hacking (http://cytohack.com/)
1. CALL4HELP & Software Lounge sessions (also prizes)
- Short presentations of problems with suggestions for solutions
1. New Icy-OMERO plugin coming (5.2)
1. stitching in spark…
1. KNIME popular, new hires
1. Involvement: STSM, Link from website, etc.
1. Deep learning, of course. Need lots of examples and GPUs
1. Other releases/upgrades:
- Lots of PRs etc.
1. Glencoe Update (Chris)
- ongoing scalability work
- Read-only server
- Pathviewer improvements, multi-channel, stitching tools
1. User meeting update
- Lining-up speakers, Glencoe update
- May not repeat ‘un-meeting’ this year.
- Helping users, doing work.
1. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)