2016-02-16 Tuesday Team Meeting
Dundee: Petr, Kenny, Mark C, Gus, Dominik, Simon, Jean-Marie, June, Ola, Roger, Simone, Jason Remote: Sebastien B, Josh M, Luca L, Ian, Chris A, Helen, Andreas, Harald, David, Melissa, Wilma, Eleanor, Balaji, Emil
Agenda - 2:30pm Start
Accepting minutes from last meeting
- accepted
Project Timelines (2-3 minutes each)
Spaces - 14:31 UK
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Mainline (J-m)
- card updated re. Ola updating documentation re. download
- posted on ZeroC forum re. Ice
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PR freeze this Friday
- maybe units/scalebar PR coming from Will
- not as much infrastructure / generation progress made as hoped but will seem the same from outside
- Josh: general ticket cleanup going on, especially moving into milestones that correspond to boards/topics
- Balaji did 5.1.8 release of Bio-Formats
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Model (Sebastien)
- Mark: has been making small Shape model changes and collecting comments on others for discussion
- open PR freeze for m1, Bio-Formats should be done this week
- on OMERO side still design decisions / mockups to finalize scope of m1 for next week’s demo
- ongoing discussions to decide backend content of m2, will also need to choose end-user use cases
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Metadata (Josh)
- working on generating WND-CHARM features
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scaling issues again rearing their head
- may need to look at Django session backend
- Eleanor: working on another dataset, small study represented as HCS but without screening (more “analysis” of plates)
- Simon: has installed gpfs
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Mainline (J-m)
Other releases/upgrades: - 14:39 UK
- Figure
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FLIMfit/OPT (Ian)
- about to release from new CI setup (based in Australia)
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ImageJ
- Josh: discussed with Ian and Curtis; Alison Walker has been working on table stuff, so need to manage work with respect to other current table work
- Learning
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Sysadmin
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Josh: now have a production docker, looking ahead to migrating data from beluga to minke, then Jenkins can run jobs on beluga
- should start up a testing server now, some bugs may appear after longer uptimes
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Jason: useful to know soon if more hardware resources would help
- Josh: alas not all six of IDR servers yet up; maybe extending something?
- Simon: good to work back from what we actually want to use the hardware for
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Josh: now have a production docker, looking ahead to migrating data from beluga to minke, then Jenkins can run jobs on beluga
Glencoe Update (Chris) - 14:46 UK
- helping Ola with deployment with new workers
- opened some small PRs (marshalling, viewer configuration, etc.), probably the last for 5.2.2
- now shipping 5.1 patches for physical size bugs so speak up if there are any issues with the proposed fix
AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled) - 14:49 UK
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Jean-Marie: at Montpellier got their off-line import to work with our clients
- https://github.com/c0c0n3/ome-smuggler
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Jason: attended advanced imaging methods meeting in Berkeley
- OMERO well appreciated
- Damir described usage at OHSU
- also visited UCSF, OMERO may solve some issues there
- Jason: Wellcome Trust grant due at the end of the month, grateful for ideas for getting letters of support
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Jason: thanks to those who updated the upgrade / statistics databases
- in 2015 worldwide around 100,000 starts of Bio-Formats per day
- C++ upgrade check statistics would be useful
- still many BF 4.x users
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Jean-Marie: at Montpellier got their off-line import to work with our clients
Presentation on Openseadragon and OMERO by Luca Lianas of CRS4 - 14:53 UK
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Jason: so, hybridized image server?
- Luca: yes; currently uses only one rendering engine or the other at once, but working on increasing flexibility
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Jean-Marie: students can save their drawn ROIs to the server?
- Luca: yes, then later teacher in Moodle can review answers
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Jean-Marie: what kinds of shape?
- Luca: circles by students, ellipses, rectangles, etc. by teachers, but also working on that
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Jean-Marie: are the ROIs annotated, by text, etc.?
- Luca: teachers can add text but not currently using OMERO annotations
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Jean-Marie: some ROIs visible or not, where is that visibility stored?
- Luca: in Moodle, it is part of the data that defines the question
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Jason: any OME work we should prioritize to help you?
- Luca: not high priority
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Chris: issues when tile sizes are not powers of two or not square or images with odd-numbered dimensions, like with part-tiles at edges, are those still issues?
- Luca: tile size is a problem, but with SVS OMERO and openslide can give a portion of a tile
- Luca: many aspects do seem now to work fine on various formats but more testing to be done
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Jason: when does it go into production?
- Luca: since end of last December, since bug-fixing, etc., yet to test scaling with large student class
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Jean-Marie: how difficult was integration with Moodle, etc.
- Luca: quite easy, arranged as a few plug-ins
- Harald: has seen other examples of systems giving the zoom level, tile, etc. that is wanted, adapting stored image accordingly; is very nice
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Jason: so, hybridized image server?
Done 15:30 UK