2016-11-22 Tuesday Team Meeting
Dundee: Kenny, Roger, Petr, Dominik, Will, Michael, Tom, June, Simon, Gus, Helen, Mark, David, Jean-Marie, Simone, Chris, Roger
Remote: Sebastien, Wilma, Eleanor, Andreas, Josh, Melissa,
Agenda - 2:00pm Start
Accepting minutes from last meeting
Project Timelines (2-3 minutes each)
Spaces
Files/Formats/OME Files (Sebastien)
- B-F: cut 5.3.0 m2 release.
- Architecture changes and JPEG-XR work included
- Some follow-ups (documentation, testing)
- Discussing add this to OMERO 5.3 m6
- OME files: next milestone discussion
- C++ 11 as a requirement - cf Roger’s blog post
- MULTIMOT as a driver of the new features (see below)
Metadata (Josh)
-
MULTIMOT
- 12th, 13th dec multimot devs to visit Dundee
- Prep for January meeting
- Similiar to IDR - tabular data with schema
- Record paths / tracks of cell invasion
- Will try to provide API for them to implement
-
“Frictionless data” http://frictionlessdata.io/data-packages/
- Json data
-
IDR paper preparation
- Outages - E.g. multiple searches
- 2 more Datasets in preparation for import
-
MULTIMOT
-
- Potential m6 for JPEG-XR
- Insight to enter maintenance mode soon
- Dom to move to import / web
- Josh - can close all Insight trac tickets!
- Web - discussion about thumbnail caching and using React.js for centre panel
- Design issue on plate names - any feedback, please add
- Chris - need to consult community. E.g. blog post etc. Big impact
- Backport to 5.2 OMERO+ and get feedback from Glencoe customers
-
- Balaji in Edinburgh on Thursday
- Petr: good trip to Germany. Everyone asks “How do we get installed/started?”
- Good workflow & setup. Larger group with smaller time slot but went well.
- Simon: workshop in London
Other releases/upgrades:
- Figure - Balaji re-starting work
- ImageJ
- Learning
- Sysadmin
-
Website redevelopment/redesign (Liza)
- Working on design this week - typography, images etc.
- Helen: working with Gus on 5.3 features, icons
- Another review soon
- Smuggler (Montpellier)
Glencoe Update (Chris)
- CellProfiler completion
- Ohsu & harvard scalability improvements, Server & client
- Thumbnailing caching and invalidation - OMERO.web plugin
- Elasticsearch to improve OMERO search. JCB data-viewer data.
- Then port to OMERO 5.2 (end of this week) and test with IDR
- No work to parallelise searching yet
- Will replace Lucene searching, using same API initially
- Evaluate with both searches running alongside, test with real data
Michael Porter presenting on his Map Annotation app and the issues he's encountered
- New project 6 months ago
- Assay development - lots of variables to track
- Antibodies, media, culture duration, scientists
- Excel spreadsheet not easy to link to data…
- Using map annotations
- Projects - different media, Datasets Well #, Images with different Antibodies
- Matlab tool: dictionary of keys & values. Case sensitivity etc important
- Can browse P/D/I and check existing Key-value pairs.
- Adding to “All images in Dataset” is tricky to undo
- Searching: case sensitive for keys but not for values.
- Whitespace is a problem
- Chris: not tried to index key-value pairs in new search work
- New search should be able to provide existing keys & values to use for auto-complete
- Michael: useful to use colon in search to target map-anns
- Chris: but other bugs with E.g. colons in keys/values, handling other special chars etc.
- Currently no ‘types’ - everything is just a string. Can’t do ‘more than’ etc.
- Michael: working across different user’s data is tricky
- Ola’s mapr might help, but don’t know yet
- Chris: infrastructure can’t support ‘context’ E.g. find image in Dataset with ann
- Petr/Will: what about using tags? Easier to add & query. Organise by tag-set
- Gus: convert map-annotations to tags?
- Chris: yes we’ve done this. Tags don’t work so well with many different values
- Roger: use hql? Chris: works OK but not with larger image counts