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You are here: Home Community Minutes Conference Calls 2007 2007-10-18 Project-wide 3:45 BST

2007-10-18 Project-wide 3:45 BST

Attending: Alexa, Andrew, Brian, Curtis, Donald, Iggie, Jason, Josh, Kevin, Will

Agenda

  • ASCB
  • OME-XML Data Model: latest changes, updates and versions
  • http://openmicroscopy.org Updates ?
  • Bio-Formats: status update
  • OME-TIFF: status update
  • OME 2.6.1: Status update
  • OMERO Beta-2.2: status update
    • server
    • importer
    • insight
    • webadmin
  • Review of who is doing what
  • Other
    • Deletes - what all should go (statsinfo, lightsettings, etc.)
    • bio-formats build
    • Should we add a "formats" component on trac?
    • Failing tests
      • Various.
      • RenderingEngineTest - removed
      • RenderingSettingsTest - hard coded values
      • LdapTest - no ldap. set to manual
      • PixBufCreationUnitTest - compile error. fixed.
      • PlaneReadUnitTest - "
      • PlaneWriteUnitTest - "


Notes


  • ASCB
    • Getting things together
    • booth diagrams, square/round/etc...

  • bio-formats
    • should try to push OMERO-verification for formats to melissa
      • brian: process includes
        • gather as many images as possible
        • import to omero
        • look at viewer
        • third party app. to look at it (re: dicom)
        • certified files are md5'd and checked from the command-line
      • what happened was got some last minute tests
      • we should try to get everything into the repository
    • negative pixels value
      • bio-formats should tell us that (int8 v. uint8)
      • does omero support the signed types? yes
      • display of the dicom images displays incorrectly in loci tools
      • @bug
    • there will always be corner cases
      • usually only hear about it when things go wrong
      • would be best to get the extreme cases in while defining the format
    • tiff/xml
      • Curtis mocked up 2007 Java classes, Chris updated generator
      • can start using those in bioformats
      • would like to start using "ome.xml.r2007_06.*" package (with subpackages)
    • hdf (Eric working on it)
      • for spectral
      • xml->tree structure
      • can split binary into tree in various ways
      • eric writes up how things are stored
      • TIFF can do tiling
      • but multiresolutions? not really.
      • cF. seadragon: http://www.ted.com/index.php/talks/view/id/129
        • No changes in rendering settings, etc.
        • that's our bread and butter
        • beautiful, but ...
        • but it is a backend for providing scaled data at a high rate
    • heads-up for 2.6.1 and formats which aren't working
      • bio-formats could be prioritized but is failing some edge cases
      • @add tickets please
      • htd for example isn't working (one example, with companion file)
      • incell difficulties
      • certainly stop using perl TIFF importer
        • bio-formats: support compression and packed bits
    • curtis: brian, you can use the commandline, or even save files with README in data
    • @move TestImages from webpage to bio-formats master repository
      • all our lsm files are probably the same

  • b2.2
    • just import issues
    • videos cover a lot of it
    • out by next week, or perhaps monday after

  • python
    • ilya's getting nibbles
    • colin coming soon

  • delete
    • lightsource hardware
    • josh will err on the side of deleting too little

  • build
    • get rid of svn:externals?
    • bioformats-omero would keep them, brian uploads a new jar to skyking
    • what should the jar be?
    • @brian will commit jars to svn
      • add jar to lib/repository
      • delete old jars
      • update omero.properties version number
      • possibly use loci_tools.jar <-- needed for the formats (mdb, etc.)
      • might need "ant tools-light"
      • for 2.2 brian PINGS josh when it's time to try again

  • "formats" component
    • use importer instead

  • tests
    • setup public ldap server??
    • try to setup test data
    • omero.properties ldap property is false, then don't run test

  • anyone test 2.6.1 ldap impl. in Dundee
    • ask Chris.

  • protocoleditor
    • not sure of the scenario of wanting to edit the custom attributes
    • experimental protocol/description: free-form<-->miaca
    • custom attributes, or something else?
    • ilya: having directory structure with files which get all sweeped together
      • data types aren't in core model, but there is information
      • keeps tracks of genes (external databases, manipulations, probes)
      • ... display tool, relies on custom attributes to work
      • movie or howto? movie lets us see what the person who built it is working
    • validator should ignore the custom attributes
      • checked against semantic type definitions?
      • STDs could come from different document
      • andrew thought you could specify a schema for a separate block. will check.
      • ilya: shouldn't be anything you want, just can't define the schema properly
        • can use the stylesheets to see the core types as CAs.


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