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You are here: Home Community Minutes Conference Calls 2010 2010-02-23 Tuesday Meeting

2010-02-23 Tuesday Meeting

In Attendance: Brian, Josh, Ola, Will, Donald, JM, Jason, Chris, Scott, Andrew, Colin, Melissa


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)

    • Everyone: next Tuesday be ready to suggest new 'demo' things at next Tuesday's meeting.
  3. The Lab's Current Work: Jasons's presentation (45 mins)

  4. AOCB (<5 mins)

    • Everyone ok to start working on Agilo? Review on Thursday.
    • QA tracking


  • Accepting Minutes from Last Meeting:

    • Collecting example test code
      • Chris: We already have some examples
      • @Will & Andrew setup an overview after reviewing existing pages
    • What happened with everyone going and having a look at the bio-foramts stuff
      • Difficult
      • Chris can provide information.
    • @Scott will try to monitor everyone's usage of Agilo
      • likes / dislikes
      • Chris: a few of the reports no longer worked
      • Various bugs. Email Scott and/or Nitpick
      • @Chris will put up some slides for Thursday for best use of agilo
  • Matters arising

    • Demos
      • Colin gone end of this week for the FS demo.
        • We can still shoot for Tuesday next week for a brief talk on FS instead of a full demo
        • Discuss possible technologies: FuseFS, etc.
      • Carlos week after?
      • Chris & Melissa: perhaps wait until they're ready to merge in (beg. March)
  • Jason's Talk: OME Informatics & Quantitative Analysis for Biological Microscopy & HCAs

    • The bio side of things? or long-term OME work / vision...
    • cF. Jcb paper revision, 740 images online / one in paper
    • Perhaps we need another retreat for expressing what everyone is doing (cF. Michael & Matlab)
      • Users want more sophisticated functionality
      • Approaching scripting
    • We handle Images: time-lapse, HCS, phsyiology, EM, ...
      • But not really true
      • The systems are getting more powerful
      • Tiling! (Large images) we don't do it yet but need to!
      • People keep asking for it. What's the market requesting?
    • Interoperability (requirements for image informatics)
      • Something we're trying to build. (technically demonstrably)
      • Includes: Metadata, Interfaces, and what we will be talking about today, Analysis
      • We tend to focus on "backend-y" stuff, incl. data mgmt.
      • Need to put more sophisticated algorithms in.
    • We do the 'Boring' stuff?
      • data management made both front cover of Nature and NY Times
      • but in Nature article, work of many groups (incl. ours) was ignored
    • Being 'open' : Open Source and Open Community
      • Appreciation from the community for our process
      • But cF. above, we don't even know internally where the examples are
      • Some of the messages just aren't getting out there.
      • Quibbles with some of the stuff around the edges
      • "Product owner" (horrified; defined externally & unclear what it is)
      • Concerned about labels, but not clear how to work in our environment
        • Chris: if we aren't going to make our own process, we'll have to adapt to some process
      • cF. trying to test permissions, didn't know what to look at
    • Specifications
      • Need to push XML examples (Jason is working with Andrew on this, but we all need to work at it)
      • Standard image
    • Bio-formats
      • Melissa is getting hit pretty hard from us and the community
      • What's missing? Scoping. Still lots of formats out there.
      • ImageJ (largest consumer of bio-formats)
      • Responsibility to provide what people want.
      • There are non-biological folks using BF (geological stuff for example). What are we missing?
    • Architecture
      • Powerful, flexible.
      • Analysis
        • cF. measurement
        • Doing more. using backend.
      • Annotation
        • Time for us to go back to what this means
        • Number of people using tagging is very small (but yes PDI)
        • Still aren't getting much value.
        • Something else to go to Paris with
        • Using ontologies / structured descriptions for defining an image (machine readable)
      • What can it do
        • Warning: post-4.2
        • Examples. Needed! * There's a difference between having something doable and showing how to do it. * Going to have to put some time into these examples!
        • 3 different examples: FRAP, HCS, EM * Showing the commonality * How we support all. * Concept that's non-trivial
        • Simplified API * Calvinistic approach: it is complicated * Brings us back to the examples
        • Storing analytic results * Currently have two ways for storing this: Structured annotation & OMERO.tables * Experience suggests that one size does not fit all. Perhaps this approach is good. * We need to go out to the community and find out what their use cases are.
    • Image Library for 'The Cell' (an Application)
      • Janet Iwasa, great specs, mockups, etc.
      • coded by Carlos
      • work on the tools for real annotations
      • automatism for large scale import
    • OME & Glencoe
      • admitting the difficulties of split team
      • cool tech for customers
      • people are asking for more
      • amounts to testing
      • keeping the communication channels open
      • cost of breaking down isolation around the commercial projects, around the devs
        • but there are also benefits
      • what's the best way to deal with this?
      • Jean-Marie: hybrid-graffle for maintaining the commercial work?
        • Chris: already an issue: server, client, bioformats, ...
        • Andrew: commercially is it possible to have customer names, task items on the trac? * Jason: often ok, but there are people who would (needlessly) get upset
        • Chris: noting every customer has own trac, would rather have a login for Glencoe tracs to make it visible
        • Ola: bigger issue is what we're doing over several months
        • Jason: at a high-level, this will also happen with the application developers
        • Ola: something like "end of next month have to upgrade viewer, and it's 20% OMERO"
        • Jean-Marie: building bridges, having larger group discussing issues so we can reuse * e.g. the schema for ASCB and its relation to protocol editor * worried that each time it is a one-off * what have we / can we learn from each of the applications? * Chris: certainly true for the metadata
  • AOCB

    • Agilo: holding off for advanced functionality for Thursday
    • QA tracking: @Adding items to the agenda (and move them to tickets!)
  • Action Items:

    • Wlll/Andrew: set up a page where everyone can gather their examples (after reviewing existing pages).
    • Scott: try to monitor everyone's usage in Agilo.
    • Brian: confirm that the Agilo trac links in google still work.
    • Jason: need someone to go see Tom about his Gel's!
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