2015-02-10 Tuesday Team Meeting
Dundee: Mark, Will, Kenny, Chris, Petr, Emil, Ola, Jean-Marie, June, Simon, Roger, Dominik, Helen, Jason, Balaji Remote: Colin, Sebastien B, Ian, Kelli, Josh M, Wilma, Melissa, Andreas, Curtis, Josh B, Sebastien S, Liza
Agenda - 2:30pm Start
Accepting minutes from last meeting
- accepted
Project Timelines (2-3 minutes each)
Core (incl. CI & QA) - 14:30 UK
-
Units/Maps/Namespaces - getting to developer documentation time (cf. MPorter), also some last UI changes
-
mtools as a test run? Nothing’s broken so far.
- Jean-Marie: Petr will be doing some testing on Friday
- Roger: but new methods may be needed to keep things forward-compatible
-
mtools as a test run? Nothing’s broken so far.
-
Rendering - in progress, PR opened by Melissa
- Josh: some tricky issues, will try to work them out, so not yet time for client work
- libbioformats (Roger) - finishing up OME-TIFF reader; almost complete now
-
Windows testing (Simon)
- Simon: would welcome any available help, getting CI server up and running, etc.
- Kenny: we have a Windows Server 2012R2
-
Jason: would be good to know soon if will be ready for 5.1.0 testing
- Simon: probably not, integration tests haven’t yet even run on Windows
- Josh: would be good to know what is broken, e.g., recent tables fix
- Roger: the Bio-Formats tests pass on Windows
- Chris: has at least been improving over time
- Jason: so, no we won’t
- Roger: note that in usage statistics, 10% of servers are on Windows
-
Next steps?
- m4 this week if possible
-
Finish up Upcoming cards, then start tackling tickets (goal?)
- around another month of development time left to make changes usable
- Weekly-ish latest deploys with a "m5" in 2 weeks
-
5.1.0 board
- can add cards to first column if nowhere better, to make sure they get done for 5.1.0
- include cards noting what new testing must be done
- developer documentation of changes
-
Josh: necromancer to be largely replaced in six days
- many services being migrated
- be patient regarding other sysadmin work
-
Units/Maps/Namespaces - getting to developer documentation time (cf. MPorter), also some last UI changes
Glencoe Update (Chris) - 14:48 UK
-
various HCS improvements in Bio-Formats and OMERO
-
PRs coming in due course, maybe not next week
- already deployed by Glencoe in production
- populate_metadata, populate_roi, etc.: scripts not often tested, and awkward to test, so will be trying to simplify and make more robust
-
PRs coming in due course, maybe not next week
- working with some very large plates, pushing limits, including graphical client / UX
-
Jason: attending digital pathology session at conference
- many vendors, so perhaps many more image formats
-
various HCS improvements in Bio-Formats and OMERO
Virtual Microscope/teaching (Ola) - 14:56 UK
- successfully upgraded to m3, next will be m4 (ndpi, etc.)
- meeting another doctor from Ninewell’s on Friday
-
received tissuegnostics scanner data, so can try importing
- Melissa: prediction: it’s not going to work
FLIMfit/OPT (Ian) - 14:58 UK
- Continuing Matlab 2014b upgrade work
-
working through critical bugs, hoping to release before too long
- 5.1 will probably have to wait for a while yet
Bio-Formats large file sets (Sebastien B) - 14:59 UK
- Woolz libraries finally compiled and set up on all CI nodes/servers
- also Woolz testing scenario under ome-internal
-
questions from Dallas on how to properly check generated OME-TIFF w/ Fiji
- will ask for more information and point at the documentation
- also looking at setting up some QA process for generated OME-TIFF
Other consortium timelines (5 minutes) - 15:01 UK
-
Jean-Marie: discussion with Curtis about ImageJ OMERO
- Balaji now has it running, Curtis will help him get going with issues
- Curtis: planned modularization of Insight will help
-
Jean-Marie: discussion with Curtis about ImageJ OMERO
AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled) - 15:03 UK
-
Meeting report/Heidelberg: CellH5, ontologies, and much much more.
-
Jason: attended two consecutive meetings with Josh
-
systemsmicroscopy.eu: large phenotypic screening effort, HCS metadata standards
-
OME-TIFF / SPW model generally accepted
- also CellH5, though noted that HDF5 is not self-describing
- given variety of image formats, Bio-Formats generally accepted as interface to data
- issues somewhat repeat those Alvis Brazma worked on with microarray data management
- interest in annotating various model objects, especially ROIs
-
interest in ontological terms
- Josh: including environmental factor ontology
-
OME-TIFF / SPW model generally accepted
- second meeting included various efforts to address familiar problems
-
systemsmicroscopy.eu: large phenotypic screening effort, HCS metadata standards
-
Jason: attended two consecutive meetings with Josh
-
Meeting report/Heidelberg: CellH5, ontologies, and much much more.
OMERO.figure update - Will - 15:17 UK
Done 15:56 UK