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You are here: Home Community Minutes Conference Calls 2006 2006-01-12 Boston, Baltimore, Dundee, Canada? ... oh my

2006-01-12 Boston, Baltimore, Dundee, Canada? ... oh my

Attending: Chris, Brian, Donald, Harry, Jason, Jean-Marie, Josh, Sheldon, Tony


  • Review of last week's notes/issues
  • Week-in-review
    • Dundee
      • OMERO Status update
      • milestones vs reality
      • Resurrect (data transform component) introduction/status (CA)
      • Rendering Engine (<Import) : Thumbnails, Stats, Zooming/Projections
      • Model : Containers (Classification,SPW,...), Rois, Image/Pixels,
      • Model : Deciding what to do with Experimenter, Group and Contact Details
      • Omero2 : Groups, Non-MutualExclusion, Counting
      • Preferences : Local/Server
      • Writing API
    • MIT Questions
      • What is going on with image collections in shoola?
      • How does one classify images in shoola?
        • as in... the way Jeff was classifying images doesn't exist anymore
        • we want to be able to classify a(n) image(s) into a category group
        • we want to use whatever way will be supported in the future
    • Baltimore
  • Meetings
    • dundee
    • SF
    • April Meeting/Madison
  • Week-to-come
  • And as always, WhoNeedsWhatFromWhomByWhen


  • Omero2 Extensions that are upcoming
    • Counting
    • Experimenter and Group

  • Omero3
    • Dundee?
      • Render Engine (Which is looking really good)
      • Import Engine (on hold - doing a data transfer from Omero2 for now) - CA
        • Chris is currently working on "Resurrect", the Datamodel translation tool for OMERO2 to OMERO3
        • Most likely dead-ended after import is finished. Just to get data in for now.
        • Note: perl not needed for this.
      • Writing API (sending graphs over the wire) - JAM
      • Changes to the Data Model (adding LSIDs, SPW & ROI collections )
      • "Roaming Profiles" discussion: What preferences does a client want to be able to access? Use Cases? needed! (Once finalized, these setting will be stored in the database). Suggestion is that the preferences be stored as name=value pairs.
    • MIT?
      • Working sets: where are we at? (Jean-Marie and Barry will be discussing this next week). Can a working set span multiple datasets? (Yes - we are also hoping to save these properly in the DB as a 'working set' We are also trying to write out the Use Cases for work flow).
      • What are MIT's time lines in terms of what you need from who, by when. When are you closing up your project? (They need to be finished coding by End of March).
        • Terminology: Image Collections (Working Sets in Shoola)
        • Lots of talking next week with Barry
        • Starting point is multiple datasets.
        • Save working sets (currently as new Datasets) (Future: new data types!)
        • Harry: dynamic "tag" model. (flikr model)
        • Chris: and categories is the idea of tags. VirtualFolders for queries,lists of items
        • Jason: still drafting (how would users use it)
    • Baltimore?
      • Connections to other ontologies (go, mged, etc) - DMcD, HSH
        • problem with data model is the "model" (difficult)
        • annotations (links) — prevents marriage
        • Harry's group has been setting up their own STs (defined in XML) that they are using for a lot of their work. Their work can be found in CVS and the code can requested from Harry (he will email anyone who needs).
        • Goal: public OME linked to from the mouse database and linked back.
        • Lsids are stll mythical
        • extracting things out is difficult; let's not re-invent
        • abstracting it out is going to be difficult

Action Items

  • Chris suggests we have a more detailed discussion about the ontology integration for around March 1
  • Need a user friendly tool for converting from OMERO2 to OMERO3
  • Jason: Does the tiki page need a 'what's changed from O2 to O3' page? (I know we had it at the conference - should it be more prominent on Tiki?)
  • Get Barry working on Use Cases so these are in MIT's hands by End of the January (So they can finish their work by the end of March).
  • Jason will put something up on the Tiki about the upcoming April meeting and then send out an email
  • Josh will write up the (un-written-up) data model items on wiki
  • Harry will write an email on the mouse annotations
  • Sheldon will write something up for next week on what they are doing.


  • Previous/Upcoming Meeting Comments
    • Upcoming meeting suggested for 'around' April 21-24 with everyone.
    • Previous SanFran meeting: official intro of OMETIFF by Kevin.
    • Main thrust of Dundee and SF was lowering the user/support person learning curve.

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