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You are here: Home Community Minutes Conference Calls 2010 2010-09-14 Tuesday Meeting

2010-09-14 Tuesday Meeting

Attending: Brian, Chris, Andrew, Colin, Will, Ola, Josh, Brain Jones, Scott


Remember: Agenda must be complete (with estimated times) on the day before the meeting. Any additions after that must go at the bottom (AOCB)

  1. Accepting minutes from last meeting

  2. Matters Arising (<10 mins)

    • Add story: Need to refactor XML Mocks so Andrew can use as samples.
    • Everyone: Try to get things green again!
    • Chris: Send email for server upgrade reminder
    • Josh: Will send out changes to poster to nitpick list
  3. OMERO.fs Discussion lead by Colin (45 mins)

    • Where we are now
    • Repository management
      • Admin view
      • User view
    • Binary data
      • Thumbnails
      • Pixels
    • Where we want to be
      • Minimum for ASCB demo?
      • Further ahead
  4. SPIM format proposal (5 mins)

    • Converted files to Guenter for apporval
    • Once approved, sample file on
    • Need to incorporate n-dim proposal-- plan for doing this and supporting it?
    • email to SPIM community
    • anything else?
  5. Monitoring Forums

    • emails not working, and some events being missed
    • ideas? Manual check 2x / week?
  6. AOCB (<5 mins)

    • Hotels for ASCB


  1. Matters arising

    • Holding off on XML mocks
    • Hudson green
      • Remove "OMERO" job? Probably. Chris will look into it.
      • Disabling the two failing python tests? May point to bugs though.
      • Will will take a look at one of them to see what's up.
    • Nightshade upgrade, one big problem:
      • any changes to groups takes the server down!
        • basically a database upgrade every time
        • currently disabled this feature for admins (Jason)
        • Chris will have to manually make any requested changes for now
        • May want to note this problem in the 4.2.1 docs and web admin page
        • One other issue: import causes raw pixel store to disappear sometimes (ice not exist exception)
  2. FS/Repo Talk (by Colin):

    • Current status

      • Multi-image filesets being imported, etc. with sensible names
      • Two-stage process: registration (creates OrigFile or Pixels), then metadata-only import
      • May become a single-stage process in Insight (from user perspective);
        • depends on speed and value of just being "registered"
        • Not currently using the "partial" flag on image
      • Currently only using the test repos originally set up by Josh
      • Thumbnails: Using BF thumbnails, cashing thumbnail and displaying
        • No resizing, changing planes, etc.
        • Do we want to change/improve thumbnailing?
    • Repository management

      • System admin decides where files are stored?
      • Users' home directories, or using some subfolder. Or will they be using a shared folder?
        • Josh: These sorts of details will need thinking!
        • Similar to how we needed to re-think the permissions system, the FS-level access is also quite tricky.
      • What type of file-system permission models do we want to support?
        • Chris: Need to plan for this in advance to avoid problems
        • Josh: Have some code that starts to do this. (Sanity check on building a repo)
      • Registration is a way of signalling that something can be accessed
        • Currently in-place to some degree in Insight
        • Not ideal in a scenario where one person acquires and one visualizes.
      • Similar to group permissions, there's a single flag ("group-based", etc.)
        • That influences the repository implementation
        • This is going to be like group permissions: won't know what everyone needs to start
        • Colin: Per User Private seems like a reasonable starting point
      • For a private repository, there must at least be a private group (possibly a special private group)
      • Initially no sub-repositories
      • Josh: Will probably need a repository server
        • Chris: Can't just use proxies?
        • This may be the time to work on the general launch functionality (cF. icegridnode)
      • Need to be ready for Windows
    • Binary data

      • Filling in the stubs is probably a good start
      • Josh: The major barrier should be performance, already technically possible.
      • Chris: the work on "minimal metadata" should be a good start
      • CRITICAL: memory management and cleaning up BF Readers.
      • Will: will need to early on create thumbnails pre- and post- registration
        • Need to measure the cost of just registering all the images.
        • Managing users' expectations.
        • WebAdmin will need a lot of work
          • If we move to another launcher framework,...
          • Move things to bin/omero config
          • Allow creating repositories
          • etc.
    • For ASCB?

      • What's the minimum?
      • A single-repository type and render the image (may not perform the best)
  3. SPIM

    • Proposal this week? May need to hold off till Josh is back next week
    • Chris: Lots of folks away for awhile as well over the next few weeks
    • Andrew will email folks via nitpick for ideas
    • Will: After examing Guenter's xml, there's a lot there which should be OME
    • Andrew is hoping to get more sources of data
  4. Monitoring Forums

    • Forum emails fall apart if you don't read them all the time
      • Must keep on top of logging in, no other solution?
      • Chris: Maybe we need a daily python script to email nitpick with new unread posts
      • Chris: Need to investigate the php to see if its fixable
      • For now we all must login daily
      • Chris: May want to look at
  5. AOCB (<5 mins)

    • Hotels for ASCB
      • Enough double rooms for everyone is now reserved
      • We can change up to December if needed
      • Anything else people need done? Should get things bought soon
      • No talk this year, just a poster
        • T-shirts? XKDE comic?
    • Chris is looking at upgrading Agilo
      • Better whiteboard, burndown fixed
    • Chris is using a new java library for scaling images on trunk
      • About the same speed, multi-threaded, should look better with low grade images
      • Needs feedback from team/end users
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