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You are here: Home Community Minutes Conference Calls 2006 2006-11-30 Project-wide 3:30 GMT

2006-11-30 Project-wide 3:30 GMT

Attending: Brian, Cat, Chris, Curtis, Donald, Harry, Iggie, Jason, JMarie, Josh

Agenda

  • Review of last project-wide meeting notes/issues
  • OMERO/Shoola Roadmap-- see Roadmap
  • Integration of Usable Image-- see UsableImage)
  • Web site update for releases
  • OME-XML evolution-- see OME-XML Evolution?
    • filter updates
    • Pixels updates
    • Updates to OME-XML
    • Add Levels?
  • OMERO/Shoola-M3 tag-- see M3 page
  • Shoola trac??

  • Week-in-review
  • Other


Notes


  • Ilya has email for release. Sent to nitpick. We're good.
    • Short discussion of how to do the release.
    • Need announcements, and webpage massaging. (Ilya will do. Possibly even today)
    • Curtis: should add it what's coming in 2.6.1
      • Soon
      • Possible LDAP support.
      • Bioformats interfaced with server side. (Jar packaged)
        • Runtime.exec() & HTTP
        • Use default with Bioformats as a fall back
        • Problems with lots of files in import directory, etc.

  • Ilya asked about Omero at Janelia Farm
    • Good to have some sort of statement about the relationship between the two projects.
    • Jason: make home page less text driven, and more of a portal.
      • Clear what software, what they do, don't do. File formats stuff.
      • Changing first couple of layers; so it's clear what's available (how to get to bioformats, omero, 2.6.0, 2.6.1 and what they are.)
      • with public statement of what omero is in a non-developer-centric way
    • Ilya: would be good to have something about the vision of what it will become.
      • What it is is straight-forward.
      • Questions are: Where is it going?
    • Jason: short statements of short-term & long-term goals.
      • Distilling the roadmap(s) into html
    • Ilya: But people are asking about the relationship between the two projects.
      • Jason: Two systems which are built on the same underlying data model.
      • Curtis: Sure on all sides, but a 'public' statement would be nice.
        • Had been said that at M3 we'd do it.
        • Who's going to be at cellbio, to hammer out a statement.
    • Ilya: Is one a replacement? Do they work together? What do users use?
      • Jason: we use both. They do different things. We're providing tools for different needs.
        • Specification and resources for image-formatics in a remote system
        • Storage, mgmt, analysis
      • Ilya: But users can't move back and forth between the two. Where do dev resources get allocated?
      • Brian: Won't a better web presence help us to make this clearer to people? What can/can't be done today, and what we're trying to do.
    • Ilya: What about dual-system access to the same data?
      • Jason: Looking at if it's possible.
    • Jason: Our goal is to have that on the website within 2 weeks.
      • Jason: I'll send our working copy; open to comments.
      • Jason: I'd like to see the same from all of us.

  • Jason: I'd love to see something from you guys on the agenda. Our meetings are public, our notes are public. At least we're trying. (Sorry for being grumpy.)
    • Curtis: Don't want to consume your time with bioformats bugs.
    • Jason: But bioformats is strategically important for all of us.
    • Chris: Singapore was asking about bioformats, for example.
    • Curtis: There is a mailing list with announcements, but no, no specific versions.
      • Roadmap is on the agenda.
      • Dedicated student for redoing website with CRM (~80%)
    • Chris: And a bug tracker for bioformats?
      • Curtis: Currently mostly ImageJ users.
        • Ilya: Just saying what's planned for the next release would be good.
    • Chris: We're going to start doing more with formats in the new year. Would be good to know where you guys are and where you're going. We're dependent.
      • Curtis: Can install bug tracker or use one installed centrally (a la Chris)
    • Ilya: Important to know that all the various importers produce equivalent things.
      • Chris: Discussion with Brian to start setting up test suite, so we know which formats are working, and that the results are always consistent.
      • Jason: Especially with the new discussion of making OME-Tiff a standard file format.
        • Need updated spec & tools
        • Lots of people are watching (and waiting)
      • Ilya: Perhaps Killer.app

  • Usable Image
    • Curtis: Is this internal only? Seems cryptic.
      • Cat: Ethnographer will just being coming online next week.
        • Then there should be information of general use there.
    • Ilya: Web user interface?
      • Not currently.
      • Jason: Cat, reviewing web interface?
      • Cat: Once ethnography gets online, we'd like to look at the whole environment.
        • Wiki for some remote work.
      • Ilya: Would be really useful to look at web interface. Good to have some feedback.
    • Harry: Ideas from working in Ilya's group, about concentrating on importan tasks.
      • Cat: Bit of a plan. Let's talk and then get in touch with Ilya.
        • Will be looking at installations in Jason's lab.
      • Curtis: Loci did some work on improving interface.
        • Cat: Great. Will be looked into.
      • Curtis: Contact me for svn repository link.
        • Some of that was done with Josiah and may have been merged back in.
        • And also search box on main page.
    • Jason: Grant has money for anything that talks to OME.

  • OME-XML
    • Jason: OME-XML Evolution? is what has been agreed on as update to specification
      • Only two questions (to my knowledge)
        • Specification/Compliance Levels
          • Most basic (Level0/Bronze/...)=ImageDimensions,DataType,PhysicalDimensions(?),etc.
          • All of the flexibility ( LevelOmega/Gold/...)=the whole enchilada
          • Ilya: Most people are interested in Level0, do that, and leave the rest of it up in the air.
            • Curtis: Can't allowed PhyiscalDimensions pixel size in Level0.
            • Level0 is what's needed to read and display the image.
      • But we need to have our software updated to use the specification.
    • Ilya: Features->Regions? Fairly simple...
    • JMarie: Did you (Ilya) get any feedback on screening model?
      • Ilya: Bernd seemed to be fine with the latest version of things.
        • But there are already parts in the spec.
        • Backwards compatibility?
    • Jason: Possible Andrew can help some of this get done.
      • Fix up OME-XML Evolution?, make it into a TODO, and get to it.
      • Screening model, etc.
      • Ilya: Style sheets need work. Question of man hours.

  • Other
    • Tagging
      • Yes. And binaries going up.
    • Jason to Curtis: Time to offer Omero to developer's list, or wait on webpage.
      • Curtis: Shouldn't hurt to dev list. They've heard about it anywhere. Might as well announce things. More information is better than less. Statement of what it is and where it's going.
      • Chris: But it's Beta1 crunch time. Deluge of "How do I install?" emails.
      • Curtis: Say "No support" / "Fiddle at your own risk"
      • Josh: Until Dec. 15th.
    • ShoolaTrac support.
    • Multi-channel tiffs (SoftWorks/3rdParty)
      • Chris: Effects everything.
      • Curtis: Send us data and we'll look at it. (As time allows)
      • Jason: Want to link the multi-channel tiffs to the original data.
        • Import with BioFormts or only store it as binary?

Action


  • Discuss bioformats bug tracking (Chris/Curtis)
  • Need importer test suite for consistency guarantee (Chris/Brian)
  • Features->Region: Ilya puts up suggestion to get feedback
  • Everyone look at OME-XML Evolution?
  • Get trac/omero's specificalizations for trac/shoola (Josh/Chris)
  • Melissa looks into multi-channel tiffs, when Chris gets stuff to Curtis.

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