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You are here: Home Community Minutes Conference Calls 2007 2007-02-01 Project-wide 3:30 GMT

2007-02-01 Project-wide 3:30 GMT

Attending: Josh, Chris, Brian, Cat, Curtis, Ilya, Jason, Andrew, Brian


  • Review of last project-wide meeting? notes/issues
  • OMERO Roadmap-- meeting on Feb 7
  • OMERO Release Issues-- how often for updates?

  • Week-in-review
  • Other

From Curtis:
  • Status of Bio-Formats with OMERO.importer
    • Is current API sufficient? I.e., openBytes method; what about Plane2D?
  • OMERO version confusion
    • 3.0-M3-Beta1 vs 3.0-Beta1 — downloads page still says Dec '06
  • Will try out OMERO next week
  • Web site says: "Details on this work [a single integrated data management system that leverages the advantages of both systems] will be available towards the end of Q1/2007" — is someone working out these details?
  • Any questions/thoughts about OME Notebook vision or status?
  • Possible OME-TIFF spec improvements:
    • Change file extension to .ome.tiff [CTR: in favor]
    • Store duplicate OME-XML block under custom tag [CTR: in favor]
    • Create schema variant for OME-TIFF to eliminate redundancy of certain Pixels attributes (SizeX, SizeY, etc.) — ideally using XML constructs (substitution groups?) that limit duplication between OME-XML and OME-TIFF schema versions [CTR: tentatively against]
    • Embed a copy of the OME-XML block encoded within the first image plane; also potentially store an additional "cover page" before the encoded image plane with rendered text offering an explanation and links regarding OME-TIFF. [CTR: strongly against]
    • Expand OME-TIFF definition to allow BigTIFF — allows single files larger than 4 GB [CTR: in favor]


  • Last week; nothing (release)

  • Feb 7th is planning. Notes will be up then.
    • Dicussion in two weeks

  • Website
    • Issues? (jrs)
      • CR: 3.0-M3-Beta1 v. 3.0-Beta1 (fixing other minor website stuff)
      • IG: Kudos on the website.

  • Versioning
    • Beta1.1, etc. ? On a weekly basis as things come in.

  • BioFormats Integration
    • Plane2D and Channel separator
    • Need release schedule and tags
    • CR: Planned anyway. Can also do self.
    • CA: Better if bio-formats team does it.
    • IG: Tagging along with API changes?
    • CA: Possibly tags/current and get the jars or tags/head for source
    • CA: Let's start with tag

  • "a single integrated data management system ... (Q1/2007)" ?
    • CR: Really?
    • JS: Planning on Feb/7

  • OME Notebook
    • CR: Excited about UsableImage+Notebook
    • CM: Try to get to Madison

  • OME Tiff changes
    • CR: duplicate tags for photoshop
    • IG: hash of image rather than duplicate tag
    • CA: Editing the file in anyway may invalidates the XML.
    • IG: but that's a different image. You have to get it back together.
    • CA: tools to compare the XML in the Tiff with the image (timepoint removed, etc.)
    • CR: MD5 for each plane?
    • CR: Or XML warning "DO NOT EDIT"?
    • IG: Not feasible to manage the changes.
    • IG/CA/CR: Notebook as the tool to "re-metadate" images.
    • CR: Purpose of OME-Tiff is to make it a standalone image (just don't screw it up)
    • IG: We only provide the rope.
    • CR: BigTiff
      • 64bit pointers for +4Gb images
      • Minimal differences
      • CR: Just allow OME-Tiff to be BigTiff

    • Removing duplication?
    • IG: If you are just trying to detect change, use checksums.
    • CR: Digets of XML block to detect changes?
    • CA: Custom tag with the digest of XML block
    • CA: Is this a real concern?
    • CR: If there's nothing against the digest, then will be proposed


  • Curtis will try to try it out.
  • Chris send doc on bio-formats changes to curtis
  • Curtis is going to propose OME-Tiff digest and other ideas to list
  • Jason and Ilya talk next week.
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