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You are here: Home Community Minutes Conference Calls 2008 2008-10-24 Omero Review Meeting

2008-10-24 Omero Review Meeting

Attending: Jason, Brian, Chris, Jean-Marie, Donald, Ola, Colin, Melissa, Will, Andrew


  • OMERO iterations
    • Metadata
    • Blitz (also: sessions #1114)
    • Upcoming...
  • Editor strategy for beta 4 (standalone or integrated)


  • Meetings
    • Every Friday at 2 o'clock Dundee time
  • Iteration
    • Metadata
      • We've got it. More in there than can be parsed out
      • String "...100x/1.3 uplan apo ix70"
      • Mag / aperature / correction / model number
      • Should be in all DV log files
      • plan apo is a standard
      • uplan apo is a derivative (Olypmus lense)
      • field: "other"?
    • Data transfer
      • Re-architecting for performance
      • Previous problem: standard 4 colors --> fixed
      • Current problem: gray scale showing up with three colors
        • Leica software interprets that somehow to come up with grayscale
        • Data acquired is stored as "color", even if grayscale.
        • If channel was "green", stored as green. (For use in Photoshop)
        • Bioformats sees "RGB", i.e. multicolor
        • Should be one color, and that color should be set to "green"
        • Problem is the channel filler? ... should only be getting one channel if its an "indexed color tiff"
        • Could be that we're getting wrong indexes?
      • Original files
        • Were swamping the file. Really large ones are crashing server
        • It's the number of objects which are swamping things.
        • There aren't many options while running under JBoss
        • Moving forward it will be solved
        • Arrange a time to talk to Imperial (using file format which is a pain)
        • Tar'ing the files together?
        • Note: The issue will rearise with OMERO.fs
      • Creation dates
        • Not storing creation dates with images
        • Strategy was that we were storing them with the original file
        • but with the tar we will only have a single timestamp: first, last, average?
        • Ola: Creation date in events? No. But server-side service. * Concept of a fileset / logical file
      • Summary: Do both for Beta3.1
        • Zip/tar tons of files in importer
        • Discuss the creation date (database upgrade)
        • How critical is this?
    • Remaining in metadata iterations
      • Currently not reading from database
      • Need to get model loosened up to get things dumped in (next big step)
        • objects, detectors, illumination ... mid next week
      • Remaining performance issues
        • Interleaving in the bioformats setters
        • Everything has to be stored on the client before moving forward
        • But to ultimately get the performance, will it always just come down to ftp'ing files?
      • Annotations et al
        • Been changing how users interact with the annotations to make it more natural
        • Also looking into more natural data entry * TextAnnotation --> Url, Xml, * Moving away from UrlAnnotation * Initial intent was to embed URL. Working. * Making links, i.e. parsing wiki texts (re: editor) *, Java parser. * Service to translate links into HTTP:// * Need to define the language
        • Moving annotations into the server
        • Making tag non-annotation
        • Need to standardize the little language early on (for editor & web)
    • Other
      • Graz : wiki linked with OMERO
        • Looking into which terms are equal, synonymous
        • How to we work toward interoperability?
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