2016-10-04 Tuesday Team Meeting
Dundee: Gus, Mark, Simone, Dominik, Helen, Simon, Roger, Jean-Marie, June, Petr, Balaji, Will, Ola, Jason, Chris Remote: Eleanor, Josh, Seb, Liza, David, Wilma, Andrea F., Melissa, Dominik, Andreas, Emil
Agenda - 2:00pm Start
Accepting minutes from last meeting
- accepted
Project Timelines (2-3 minutes each)
Spaces - 14:04 UK
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Files/Formats/OME Files (Sebastien)
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Bio-Formats 5.2.3 status
- about to release 5.2.3, waiting for last PR, builds this afternoon
- will try to get Boost PR into tag for Roger
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OME Files 0.2.2 status
- Roger working on last piece of code for inclusion in release
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Bio-Formats 5.3.0 plan
- new minor series 5.3.x, propose to move to semantic versioning hereon
- rearchitect Bio-Formats components / dependencies
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APIs: tiling, options
- options because difficult to know which getters/setters are offered by underlying readers
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Roger: options down to OME-Files too?
- Sebastien: maybe
- Roger: would be a big win
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Mark: semver for OMERO too? or be very clear about difference
- Chris: may not yet need to announce change in policy
- Jason: good where we can to have others maintain sets of things like ontology terms; such concerns affect even API for configuring Bio-Formats
- Chris: as well as our enumerations possibly not being exhaustive, there is also a separate issue of defining backward compatibility, definitely an issue in the ontology community
- Roger: also issue of code-generated enums maybe not being enums in the programming language to make changes less breaking
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Bio-Formats 5.2.3 status
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Metadata (Josh)
- working on draft paper, nearly ready for submission
- getting demo-2 good for Jason's coming demo in Singapore
- trying to stabilize mapr UI for demo-3
- some Jupyter-based computational resource coming within next few days
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OMERO 5.3.0 (Jean-Marie)
- 5.2.6 now released
- new screenshots out, more coming (new viewer, etc.)
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Outreach (Jean-Marie)
- Balaji still producing videos, useful for coming training, next in November
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Files/Formats/OME Files (Sebastien)
Other releases/upgrades - 14:32 UK
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Figure
- Jean-Marie: announcing renaming of repository
- Ola: try with web-error first so as to work through checklist and see what breaks in renaming
- ImageJ
- Learning
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Sysadmin (Josh)
- cowfish still a problem, doubtful about octopus
- web-prod timeouts, already tried resetting plone
- notifications about embassy
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Website redevelopment/redesign (Liza)
- working on Bio-Formats content
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Smuggler (Montpellier) (Andrea)
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quick presentation on proposed project for students
- funded six-month masters student
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idea: machine health report via analysis of acquired images
- want certain scripts available only to facility managers
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idea: integration of analysis scripts, extending Balaji's work
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including sandbox for analysis applications, directly accessing managed repository while respecting OMERO permissions
- Josh: tricky
- Jason: Douglas (Harvard) showed OMERO.forms which somehow respects OMERO permissions and is for annotating images
- analysis is a big selling point for OMERO
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including sandbox for analysis applications, directly accessing managed repository while respecting OMERO permissions
- Josh: idea: single sign-on, bit tricky though
- Josh: idea: generalize Smuggler as compute resource, cf. our celery work
- can now batch multiple imports into single submission
- may get to introduce Toulouse to OMERO / Smuggler
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quick presentation on proposed project for students
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Figure
Glencoe Update (Chris) - 14:56 UK
- finishing JPEG-XR work
- sorting out Windows build stuff
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working on PerkinElmer formats
- image naming, plate naming, etc.
- Jean-Marie: also issue of well naming now annotations being exposed in GUI
- work on Python BF stack as shim in CellProfiler
- PathViewer 1.1 coming soon
AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled) - 15:01 UK
- Jason: HMS visit next week: stitching 27-channel images, may be relevant to tiling API
- Jason: seek Orbit demo from Basel
- Jason: make sure all have done security survey
- Jason: HDF5-based file format emerging in EM tomography
Done 15:07 UK