Dundee: Will, Petr, Kenny, Dominik, Jean-Marie, Mark, Simon, Sebastien, Mike-Wicks (EDI), June,
Remote: Josh, Wilma, Emil, Melissa, David
Start: 2:00 pm
(2-3 minutes each)
Merging ongoing, into develop.
Existing work: logs, metrics, Insight GUI PR
Upcoming: no default thumbnails, parallel import CLI
Few other miscellaneous PRs (channel color, etc)
5.4.8 RC build targeted for 31st of August (Friday)
Various testing necessary
Careful to test all Insight & BF changes
workshops, esp if no time to demo import)
Basel: doing import (don’t need help)
Sydney: no import → need help
Okinawa: probably not
Jason: thanks for summer work on import
Discussed holding back release for more import work.
Prod51 set up by Seb
Idr0041 currently being reannotated on prod51 (Seb)
on idr-testing. Now uses %hash% instead of %timestamp% for directory names to avoid clashes when importing in parallel. Import with “skip all”. But still latest import attempt just failed again.
is finished. Still waiting for genotype annotation from J-K, but can be added later in case it’s too late for idr 0.5.1 release.
Mail (Kenny): New mailman server:
behaviour changed. Seems to be working OK over last week.
necessarily a bad thing.
Approx 2-weeks’ work.
Jason: Longterm stable provider? Archiving?
Prefer ome ‘branding’ instead of google.ome etc.
Discourse? (IJ etc)
Usability vv google
New public alternative jupyterhub server.
New www.ome/training pages and ome/apps page
between IDR and training work. JM: recently added Trakmate
OMERO 5.4.8 timeline (see import above)
Pyramids work ongoing
OMERO-metadata PR open. Needs discussion & test fixes
Melissa: Channels ome PR
Chris (away): OMERO.parade PR
#hca (Josh): still waiting on real data.
Will go in _from_hca directory.
the S3 work.
#ome-ssbd is quiet, but will start ramping up
Prep for Sydney, Japan, Cambridge… ~1 a month
(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
(20-25 minutes plus 15 minutes questions max)
Mike Wicks - EDU
Comparative Pathology Workbench (CPW)
HCA (Human Cell Atlas) CZI-funded project, 6-8 Sub Areas
large intestine (not discussed today)
Albert Berger. (mapping model, bioinformatics).
Prototype for pathologists
To Visualise, Arrange, “Annotate”, Analyse their data
Share dta with other pathologists
Grid/Matrix presentation of Data
Before: rows “meant” something. E.g. Mouse / histopathology etc.
Functionality of CPW (typical Pathologist’s workflow)
Biuild a matrix or matrices
Assign data to cells - 1 image per cell
What Data is in a CPW cell? Mostly Images, hence OMERO.
SPA web application
Database back-end to store Matrices, Django
Annotate matrices / cells
Blogging Engine? - collaborative commentary
Free-form grid metaphor.
OMERO flattened tree
Of interest to OME..?
Integration with OMERO
Avoid Reinventing the wheel
SPA with React - NO! Django more suitable