2017-02-21 Tuesday Team Meeting
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
Accepting minutes from last meeting
Project Timelines (2-3 minutes each)
Spaces
Files/Formats/OME Files (Sebastien)
- Bio-Formats 5.3.4 release yesterday
-
OME Files 0.3.1 releasing “as we speak”.
- Bugfix from mitocheck dataset (see below)
-
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
Metadata (Josh)
- Move to extcloud05 - cloud migration at EBI. network & volume issues.
- Thumbnail improvements
-
Upcoming datasets
- 1 ready to go, 2 in preparation
-
Analysis & scaling
- Splitting web to different server from OMERO etc
- Plenty to do up until POTN
OMERO 5.3.0 (J-M)
-
Web API final adjustment
- 2 PRs open, 1 more to come
- omero-marshal release for 5.3.0
- New Role: Probably a last DB change
- Feature freeze next week
-
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
- Docs for roles etc. progressing well
-
Web API final adjustment
-
- Report from Neubias/Lisbon (Josh) Nice weather, nice city!
-
Tagathon (tagging tools)
- Move to using ontologies instead of tags.
- OMERO Might need to tackle OWL, RDF soon
-
Working group 5, Graeme Ball
- Other servers, cytomine (node.js based)
-
Catmaid ‘onto’ tile server.
- Annotated sample image location
- Chris Bakal is hosting Cytomining in London, June 28-30
- Also cyto-hacking (http://cytohack.com/)
- CALL4HELP & Software Lounge sessions (also prizes)
- Short presentations of problems with suggestions for solutions
- New Icy-OMERO plugin coming (5.2)
- stitching in spark…
- KNIME popular, new hires
- Involvement: STSM, Link from website, etc.
- Deep learning, of course. Need lots of examples and GPUs
Other releases/upgrades:
- Figure
-
Iviewer
- Lots of PRs etc.
- Sysadmin
Glencoe Update (Chris)
- ongoing scalability work
- Read-only server
- Pathviewer improvements, multi-channel, stitching tools
User meeting update
- Lining-up speakers, Glencoe update
- May not repeat ‘un-meeting’ this year.
- Helping users, doing work.
AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)