2017-01-24

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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)

1. [Metadata](https://trello.com/c/XQXwX6jj/6-metadata) (Josh)

1. Upcoming MULTIMOT meeting (Thurs. travel)

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

1. [Outreach](https://trello.com/b/Da6OAWam/outreach)

* Possible date for summer training in Cambridge 29-30/06/2017

1. Other releases/upgrades

1. Figure

1. Iviewer

1. Learning

1. Sysadmin

1. Website redevelopment/redesign (Liza)

- no update until mid-February

1. Smuggler (Montpellier)

1. Glencoe Update (Chris)

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

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.

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