2017-01-24 Tuesday Team Meeting
Dundee: Will, Jean-Marie, June, Mark, Balaji, Kenny, Dom, Simone, Simon, Ola, Remote: Sebastien, Josh, Eleanor, Ian, Andreas, David, Melissa, Wilma, (later) Chris, Jason
Agenda - 2:00pm Start
Accepting minutes from last meeting
Project Timelines (2-3 minutes each)
Spaces - 14:00 UK
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Files/Formats/OME Files (Sebastien)
- Stable line 0-2-x performance tests on Windows. Linux next.
- Roger back soon. Need to finish by end of next week
- Python bindings for OME files (Simone) nearly done
- BF 5.3 more bug fixes.
- Writing OME-tiff with BigTiff fixed (David) being used by Emil
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Metadata (Josh)
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Upcoming MULTIMOT meeting (Thurs. travel)
- Simone, Seb, Josh - back on Sunday
- ‘Selling OME files’. Also OMERO.
- MIACA? Minimum recording exp
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Demo32 released on Wednesday (i.e. IPs swapped) - openstack
- Tweet mentioned openstack. Present in openstack summit in Boston in summer?
- Demo33 in-progress with a focus on ‘tricky’ re-annotation
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Upcoming MULTIMOT meeting (Thurs. travel)
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OMERO 5.3.0 (J-M)
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Possible DB change
- No DB changes required. To consider in next major release
- ARGB update testing (Mark’s script)
- Web API
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FYI:Java 1.9
- failure with javadoc (code OK)
- Test CentOS7 in devspace.
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New Roles (Mark)
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last week's work was:
- split WriteFile privilege out separately for WriteOfficialScript, also Write privileges out from Delete privileges
- map OriginalFile.repo into OMERO object model but prohibit changing it
- this week's work is: focus on on user management privileges: create group, add to group, etc.
- added to 5.3.0 work: prefix light administrator privilege names in Experimenter configuration so as to clearly separate them from other configuration settings
- Will expose some of this in webadmin UI. Need to decide on subset.
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last week's work was:
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Possible DB change
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Outreach
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Possible date for summer training in Cambridge 29-30/06/2017
- NEUBIAS - Feb. Graham, Anatole, Josh
- March - aiming for IDR meeting in Dundee
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Possible date for summer training in Cambridge 29-30/06/2017
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Files/Formats/OME Files (Sebastien)
Other releases/upgrades
- Figure Balaji’s PR re-opened
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Iviewer
- OpenLayer update.
- Open small images without tiling.
- ARGB fix/handling
- Learning
- Sysadmin
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Website redevelopment/redesign (Liza)
- no update until mid-February
- Smuggler (Montpellier)
Glencoe Update (Chris)
- Web api & omero-marshal progress
- OME-TIFF writing setups working: 64bit tiffs
- Design issues for read-only & scalability
AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)
- comment on formal design proposals by next Tuesday
- Some updates to proposed template… Any more?
- OME meeting: 31st May - 1st June (+ 2nd June)
Ian's presentation
- Single molecule microscopy on cluster
- SMLM processing, localisation using cluster, ThunderSTORM
- Use low concentration of fluorophores - active a subset - acquire image - repeat…
- ThunderSTORM - IJ plugin to process raw images ‘blinking movie’ -> image
- 30 - 60 mins on Desktop for 2D. 10 x Longer for 3D
- Can’t see result until experiment is finished (can’t fix errors etc)
- Need ‘real time’ results
- Run on cluster.
- ThunderSTORM is preferred app for users.
- But, ThunderSTORM won’t run headless
- Each user has their own preferred version of ThunderSTORM
- Last release 4 years ago.
- Use ‘vanilla’ ThunderSTORM
- VNC to provide ‘virtual’ graphics for each node.
- Parallel is easy - work on subset of frames each.
- Need to load frames separately.
- Later frames quicker to process (fewer points - bleached)
- Upload, Localisation, Merging .csv, Visualisation - 6 mins total (2D data)
- Post-processing by user interactive using VNC on login node (don’t have to move data).
- Skilled manual process.
- Some automatic tasks possible - E.g. drift correction.
- Future work: Parallelising “Visualisation” step.