Dundee: Will, Helen, Mark, Petr, Dominik, Jean-Marie, Simon, June, Simone, Balaji, Jason, Kenny, Roger
Remote: Josh, Seb, Melissa, David, Andreas, Liza,
# Agenda - 2:00pm Start #
1. Accepting minutes from [last meeting](https://www.openmicroscopy.org/site/community/minutes/conference-calls/2017/2017-04-18-tuesday-team-meeting)
1. Project Timelines (2-3 minutes each)
1. [Files/Formats](https://trello.com/b/IBHfAIMP/bio-formats-5-x)/[OME Files](https://trello.com/b/WFYWCvoV/ome-files-0-4-0) (Sebastien)
- First review of tiling benchmark results from David on Wednesday
- Not public yet, but available internally gdoc
- BF started new minor release cycle - Large format changes, no API changes
- Olympus OIR format, from Glencoe. Public sample data.
- ndpis format - target to release next week & include in OMERO 5.3.2
1. [Metadata](https://trello.com/c/XQXwX6jj/6-metadata) (Josh)
1. Paper edits & new URL
- Resubmit soon.
- Drop -demo from url.
1. IDR 0.3.6/7 ‘production’ not demo
- Update urls everywhere
1. IDR 0.4.0
- Ola’s work. PRs rebased, everything green
- New server e.g. “idr next”
- Enable figure, iViewer etc?
1. [OMERO 5.3.2](https://trello.com/b/99FNECY9/omero-5-3-2)
1. 5.3.1 out last week
1. Only “key” cards for the 5.3.2 release - moving trello cards to new board
1. Focus on User meeting see point below
1. [OMERO 5.4.0-m1](https://trello.com/b/VkiONV40/omero-5-4-0-m1-new-role) (Petr/Mark)
- Mark: OmeroWeb integration test failures fixed, [thanks to Will](https://github.com/openmicroscopy/openmicroscopy/pull/5255)
- Mark: may have finally fixed rare group-related [flakiness in import](https://trello.com/c/DfulHH2y)
- Mark: working on improving performance
- finally got profiling working
- with the help of, `omero.jvmcfg.append -Xverify:none`
- identified bottlenecks
- proceeding with some adjustments to server code to check their effect
- Petr: live demo
1. Janelia report (Josh)
- Longer notes on card on outreach board
- first days “very biological”
- Lots of new imaging modalities
- New pieces of metadata
- ‘expansion microscopy’ - original pixel size -> x4
- nDim - multiple lasers in various dimensions etc
- Correlative microscopy common theme
- Often using matlab notebook to bring everything together
- Day 3, more computational
- Brain imaging etc
- Janelia DVID - ndim service for looking up blocks (binary data). Can we make use of this?
- czi - https://chanzuckerberg.com/ nice presentation
- hdf5 formats and other new formats.
- ITR ‘image tool resource’ project.
- e.g. http://sagebase.org/
- Available data & platform for algorithms to solve various challenges
1. Other releases/upgrades:
- Released 3.0.0
- Need to review 3.0.1 board priorities
1. Release last week
1. Reviewing UI - Will: prototyping in Photoshop
- Consistency between apps figure, webclient, iViewer
1. new website
- Working on Content for few remaining pages
- Explore OME in Action page to link to Demos etc.
- Developers getting started page needs content
1. Sysadmin (current board and recent PRs)
- 5.3.1 upgrade of nightshade
- GPFS -linked machine with VM for ansible
- Ports issue - limited ports for connecting to external machines/servers
- JM: mtools release for OMERO 5.3.x
1. Glencoe Update (Chris)
- webinar prep (tomorrow)
- oir etc.
- Emil & Melissa here for Users meeting
1. User meeting update
1. Analysis - Josh
- Analysis POTN board
- 2 or 3 workshops might include analysis work
- Biological tasks - few examples, more suggestions welcome
- Jason: analysis tools make for nice demos for other events / workshops & useful for testing etc.
- Josh: getting metadata into IDR so that it’s useful/accessible to other tools. Where to store metadata in what format. Jason: and generating it as automatically as possible.
- Jason: need to put names to workshops. Probably after standup later this week: https://www.openmicroscopy.org/site/community/minutes/meetings/12th-annual-users-meeting-2017/
1. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)
1. Josh: upcoming “proposals” (queues & tiles)
- Help users/satellites to solve hard problems
- OSARs scheduled for after users’ meeting, in June.
- New role demo, “administrators with restricted privileges”, or “Light Admins”
- super-users, acting for other users, e.g. “Analyst”, “Importer”,
- Not group-specific, but need to access data from many groups
- BUT, not ‘Full Admins’ of the server. Limited privileges.
- Balance to provide enough power, but not too much
- Webadmin UI:
- create/edit user form has link to “administrator privileges” docs
- Docs has table of permissions required for various use-cases
- e.g. “Manager” / facility manager includes Sudo, Chgrp, Chown, Create/Edit groups/users.
- In general aim to prevent accidental damage/delete etc
- Demo of workflow of “Manager” role
- Light-Admin cannot edit their own Privileges
- Create Groups & Users
- When Light-Admin creates users, should only be able to create regular users (not admins OR light-admins).
- Josh: client UI and server should allow same! (don’t make client more restrictive)
- bin/omero –sudo manager -u newbie -g othergroup login # Manager login as newbie
- Can then create Dataset as newbie, import as newbie etc.
- In webclient UI (not sudo) use chgrp permission to Move to new group.
- Bug: try to add comment in read-only group not disabled in webclient
- CLI chown to new user.
- Bug: thumbnail creation for non-owner in new group in webclient UI?
- Bug: CLI insists that user must be in target group to chgrp (webclient doesn’t)
- Insight ‘import as’ doesn’t show all groups
- Jason: important to remember (remind users) who you are logged in as.
- Josh: e.g. sudo in webclient - show prominent indicator. Jason ‘red and bold!’
- Jason: nice demo, thanks!