24th January 2017
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 #
1. Accepting minutes from [last meeting](https://www.openmicroscopy.org/site/community/minutes/conference-calls/2017/2017-01-17-tuesday-team-meeting)
1. Project Timelines (2-3 minutes each)
1. Spaces - 14:00 UK
1. [Files/Formats](https://trello.com/b/O3d1aegk/bio-formats-5-3-0)/[OME Files](https://trello.com/b/wA1T35Ld/ome-files-0-3-0) (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
1. [Metadata](https://trello.com/c/XQXwX6jj/6-metadata) (Josh)
1. Upcoming MULTIMOT meeting (Thurs. travel)
Simone, Seb, Josh - back on Sunday
‘Selling OME files’. Also OMERO.
MIACME? Minimum recording exp
1. Demo32 released on Wednesday (i.e. IPs swapped) - openstack
1. Demo33 in-progress with a focus on ‘tricky’ re-annotation
1. [OMERO 5.3.0](https://trello.com/b/FoyfXCaf/omero-5-3-0) (J-M)
1. [Possible DB change](https://trello.com/c/V7KF838s/127-db-change-source-to-annotation)
- No DB changes required. To consider in next major release
- ARGB update testing (Mark’s script)
1. [Web API](https://github.com/openmicroscopy/design/issues/65)
1. FYI:[Java 1.9](https://trello.com/c/Eh7p5387/18-to-watch-java-1-9)
1. failure with javadoc (code OK)
1. Test CentOS7 in devspace.
1. [New Roles](https://trello.com/c/t0nT7KYa/133-new-role) (Mark)
* 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
* Possible date for summer training in Cambridge 29-30/06/2017
NEUBIAS - Feb. Graham, Anatole, Josh
March - aiming for IDR meeting in Dundee
1. Other releases/upgrades
Open small images without tiling.
1. Website redevelopment/redesign (Liza)
- no update until mid-February
1. Smuggler (Montpellier)
1. Glencoe Update (Chris)
Web api & omero-marshal progress
OME-TIFF writing setups working: 64bit tiffs
Design issues for read-only & scalability
1. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)
* comment on [formal design proposals](https://trello.com/c/pMZs69R4/538-formal-design-proposals) by next Tuesday
Some updates to proposed template… Any more?
OME meeting: 31st May - 1st June (+ 2nd June)
1. Ian’s presentation
Single molecule microscopy on cluster
SMLM processing, localisation using cluster, ThunderSTORM
Use low concentration of fluorophores - active a subset - acquire image
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.