2017-04-25

25th April

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. Spaces

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

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:

1. Figure

- Released 3.0.0

- Need to review 3.0.1 board priorities

1. Release last week

1. iviewer

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.

Petr:

- New role demo, “administrators with restricted privileges”, or “Light Admins”

- Rationale:

- 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!