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You are here: Home Community Minutes Conference Calls 2010 2010-06-17 Thursday Meeting

2010-06-17 Thursday Meeting



  1. Accepting minutes from last meeting (no Tuesday meeting this week)

  2. Matters Arising (<10 mins)

    • Andrew: Add SPIM to experiment type!
      • Should this go in AcquisitionMode on Channel or Type on Experiment?
    • Chris: Donald can't see Squig. Please fix!
  3. Review of Paris User's Meeting

  4. Email and Forum Review - checked at (5 mins)

    • Email - : m.woodbridge@... [ome-users] Deleting images

    • Forums -

      • link Re: saving the Global Metadata by bhcho » Thu Jun 10, 2010 3:11 pm
      • link Re: Instalation problems - omero 4.1.1 (Blitz errors) by sreyaxy » Wed Jun 16, 2010 11:46 am - How do I get my computer to hibernate again in vista?
    • QA -

link to last 7 days open tickets

ID  Status  User/email  Type    Created Selected file   Comment Error
2486    new filipevb@gma... Insight 4.1.1   2010 06 16  -   -   java.lang.Exception: Abno...
2485    new a.j.d.melvin... Insight 4.1.1   2010 06 16  -   -   java.lang.Exception: Abno...
2484    new N.Hegarat@su... Insight 4.1.1   2010 06 13  -   I was deleting a folder java.lang.Exception: org....
2478    new unknown Insight 4.1.1   2010 06 09  -   reproducible now. tried to log...   java.lang.Exception: Abno...
2477    new unknown Insight 4.1.1   2010 06 09  -   had just entered username and ...   java.lang.Exception: Abno...
2476    new unknown Insight 4.1.1   2010 06 09  -   trying to connect to a remote ...   java.lang.Exception: Abno...
  1. AOCB (<5 mins)


  • Matters arising
    • CellProfiler: Licensing & distribution of bio-formats
    • SPIM: Goes in AcquisitionMode
    • Squig is fixed.
  • Review of Paris Users' Meeting
    • Public notes should go up on website
    • Any confidential notes should be put on the internal page
    • Anything that's small might go in 4.2, all other tickets are unscheduled
    • General feeling
      • Model actions/timescale:
        • Andrew: seemed to be mixed messages; "too unstable...but we want X"
        • Chris: Too much responsibility on the implementors.
          • Need better help (reference implementation?)
          • Andrew: using codegen for other languages
        • Jean-Marie: we are quiet for too long
        • Jason: the world needs to know our priorities, but the output of a release is more than the model,
          • includes software, validators, libraries, examples, ...
        • Jean-Marie: why did some companies go to another university for implementation?
        • Chris: did the university not contact them?
        • Jason: is a summary, "more updates on what we're intending to do and more information for implementators"?
        • Andrew: licensing for reading/writing our file format cheap? Chris: BSD? Tabled.
        • Jason: But work we should do? Chris: yes. Like stylesheets.
        • Currently, very few sites will use bf to write
        • Andrew: had misunderstood the conversation about dc:creator
        • Jean-Marie: that's another issue - still need to have a methodology for release
        • Josh: 2 things we've discussed before...
          • Having StructuredAnnotations registered as a namespace so that we can upgrade them
          • intermediate, unstable releases that implementors don't upgrade to
            • A stable once per year, unstable each month
            • Andrew: issue of not being able to open files created with the intermediate releases
            • Jean-Marie: need to find a middle ground
            • Andrew: bioformats would need to read the unstable versions
            • Andrew: we will have to provide an upgrade (Josh: and/or downgrade) path for any intermediate releases
            • Jean-Marie: is that too ambitious with our personnel?
            • Jason: a month sounds too frequent. 2 months sounds realistic.
            • Jason: We could make a plan, the 6 2-month releases between stale releases
            • Jean-Marie/Jason: we need the data in the system. have real use so we can test.
            • Chris: need to have - codegen, objects, db tables, ...
            • Chris: do we target the tiff library?
            • Donald: what objects are we targeting? if the library changes, then it would break implementors
            • Tabling for next releases. Roughly: Stable release for end of 2010, with new methodologies, fixes/cleanups, etc.
            • Will wants to know if the community wants us to spend time on that effort.
            • Chris: the commercial community certainly does
            • Jason: cF. the "Metadata Matters" paper. We want them writing compliant TIFF. Want to avoid invalid TIFF.
            • What's to prevent somone just using bf? Model support, speed/Java, and licensing.
            • Chris: might not be in the next release
            • Andrew: sooner rather than later
            • Could discuss with micromanager for re-use (further decouple on the Java side)
      • HDF
      • Jean-Marie: is that something we want to pursue? Jason: ok, why?
      • Donald: NDIM
      • Josh: things to keep in mind...
        • need to balance this against efforts on FS since they are orthogonal
        • will need to use JNI library to do things in our stack
        • if we have the JNI library in our stack, we need to do installers
      • Chris: benefits include whole plate in a file, ...
      • Donald: for something like FLIM, you don't want all channels (seek problem)
      • Open questions: do we store XML? (Josh: No.) Would we then move from XSD? Etc.
      • Jean-Marie: putting it on the table just to be ahead of the pack
      • Chris: concretely investigate how much effort its going to be
      • If there's a ref. impl. (I/O provided), then perhaps no one cares about the format
      • Andrew: conversation with Robert (PE), previously worked on VLDB (features/characterizations)
      • Chris: what did they tell us about FS and result storage?
      • Will: need more examples of what we have
      • Jean-Marie: we may need to get pytables hooked up and break it before we re-implement
      • Will: perhaps get a heatmap working
      • Jason: eye-candy stuff to exercise it - add heatmap to browser in insight/web
      • Donald:
      • Paul Barber & FLIM were a highlight. But a script repository is a requirement.
      • He also wouldn't be doing rlong.getValue() in matlab. API issues.
      • pytables could be excercised by CellProfiler
      • Jason
      • Credit to everyone for having work recognized by the community
      • Nice to have people like Bob Murphy saying this is what we want
      • Concerned that we've worked so hard on 4.2, have so much to do but we tend to be focused on big infrastructure
        • Martin (PE): "You need some simple stuff that looks great" (e.g. heatmaps)
      • Europe/US: "I want my group to be subsumed by what you've done but it's complex"
        • We could constantly go on road trips
        • Our tendency would be to work like dogs until ASCB, but do we need to pick our heads up
        • Adamant about having big images solved in some form by the end of the summer (e.g. SVS works in bf, chokes in importer, etc.)
        • Planning for road trips around September
        • Validation of our work is Gianluigi "it's not about images" (hadoop, xen, model generation, etc.)
        • Chris/Josh/Jean-Marie: clean up dead bodies, do some easy/flashy stuff, and then work on penetration
        • Jean-Marie: maybe we don't decline too many invitations.
        • Jason: something like 2-3 weeks at a couple of places. Chris: probably a good time.
        • Jean-Marie: Internally, going through future tickets for easy/flashy bits.
        • Jason: an iteration on low hanging fruit, then several on the big stuff, maybe some on the road
        • Things to think about
          • Invitation to Bob Murphy's lab, in combination with bio-imaging bioinformatics (Janelia, this year in Pittsburgh)
          • also to M. on Atlantic French coast for another meeting.
      • Josh
      • PSLID/modelling
      • Knime/flashy/analysis
      • Work for other clients/fiji. Andrew: Should there be a webpage with 3rd party extensions? Could be combined with success stories.
      • Planning: when/how? Jason: Make list. Jean-Marie: But how do we have a healthy, open discussion for priorities?
      • FS
      • Two camps: people who want to use OMERO as backup and those who want full flexibility with their own data store
      • There are still even folks who want to just dump TIFFs to disk
        • Jason: If people want to use native TIFF to use other applications, why don't those talk to OMERO??
        • Chris: people who say, "unless if you read my files, I won't use it"
        • Doing the simple case. No automated reconciliation.
        • Need the manual reconnection functionality, but it's not platform specific, etc.
        • Jason: As a user, if I can see the data in the repo, then I should be able to do everything.
        • Chris: the only thing you can't do is view it.
        • MAJOR issue: permissions/security/user-mapping
        • For now, won't be running as root
        • And files may get hidden you depending on who imports it
  • 4.2 Release
    • Open
      • 2010-06 schema added. Need stylesheets. Then test_images_good run through.
      • Export. Shouldn't be very complicated.
      • Bug from Demo servers
      • Config seems solid. Need
      • Josh puts in quick fixes for mage.
      • Callbacks: Ice bug which prevents Usermode processor and all other callbacks. Might not be too important.
      • Database ugprade: on the order of a week. 2 weeks on nightshade after done
      • Script workflow: performance of scripts
      • deletePlate OOM; 12-13 seconds regardless of size of images. 120 hours to delete plate. Some iterations that won't fit into 4.2.0
      • Hibernate performance. (Another point release)
      • Chris: need almost a month
      • Jean-Marie: people coming in and out. If it takes longer, than it'll be September
      • Donald: still delivering new stuff (matlab/cellprofiler/flim)
        • Don't have matlab version for the latest CellProfiler 1.x version
        • Michael evaluates Matlab bindings. QA build tomorrow for him.
      • Two reports about Windows not installing on 4.1.x. Josh needs to track down the leads.
      • RC end of next week (June 24). and upgrade nightshade for


  • Andrew starts a TODO list/schedule (jul1-dec15) of methodologies (plone) and pass off to Jason
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