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You are here: Home Community Minutes Conference Calls 2007 2007-11-1 Project-wide 3:45 GMT - NOTE: UK IS ON GMT; ONLY 4 HOURS AHEAD OF EDT

2007-11-1 Project-wide 3:45 GMT - NOTE: UK IS ON GMT; ONLY 4 HOURS AHEAD OF EDT

Attending: Alexa, Brian, Cat, Chris, Curtis, Donald, Jean-Marie, Josh, Kevin, Lars, Will, Andrew on the road

Agenda

  • ASCB
    • Furniture
    • Servers and laptops
    • Artwork
  • OME-XML Data Model:
    • CA and Flexible Annotations
  • 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
    • Hudson
      • http://warlock.openmicroscopy.org.uk:5555 for folks within dundee.ac.uk
      • Dead link to Hudson Gallery on old tiki removed
      • Links to trac, polls svn, slices, dices, etc. (findbugs, checkstyle, coverage reports)


Notes


  • ascb
    • how many servers needed?
    • need another computer?
    • chat offline on that. (no andrew or jason)
    • otherwise, all set.
    • andrew
      • everything as one reimbursement to kevin
      • artwork: david's suggestion not for mixed audience
      • have to look fashionable and not cheap
      • kevin handling getting posters there

  • data model
    • curtis: curious what this is referring to.
    • chris: trying to get some of will's stuff into CAs
    • undeclared rules
    • what happens to ome-server, or bioformats if there's another top-level block
      • curtis: don't know. can't test.
      • or try imagej bioformats importer
      • Will: can produce files using the top-level file.
      • - http://users.openmicroscopy.org.uk/~will/ should contain files soon.
      • trivial test: on sample.ome with garbage, barfs in bioformats
      • seems to work in ome-server
      • Would a non-ome block first barf?
      • What happens with two ome blocks?
    • andrew
      • what schema's do we provide?
      • would like to have a DAG with no backlinks (SPW-->OME-->SPW, same with analysis module)
      • documentation is technically correct, but not very clear
        • after next release, start to get doc moved over and rewritten
      • possibly a schema along for internal references
      • two ways to add data
        • write valid CA and STD file
        • write outside of block
      • curtis: like strengthening the CA block contract (docs)
      • ome-validator: what's the complexity of that? (curtis)
        • largely, mostly technical issues. and getting the error reporting good
        • also does some high-level checks. number of planes in tiff/binary data
        • bioformats can do some of this.
        • similarly to recently written validator?
        • http://support.svi.nl/wiki/OmeValidator
        • @try to get source code

  • openmicroscopy.org
    • all files moved out of TestImages
    • stripped files from www.openmicroscopy.org (previously for anyone)
    • some problems with making everything public
    • starting campaign to get one of every file
    • perhaps a simple script which defines what's public and gets copied
    • feedback: for ome-xml implementors, etc., it's pretty buried
      • no screenshots, more examples, pretty deep
    • perhaps a video from Loci on XML.
    • training site
    • similar to what paula is working on
    • need to separate user/dev focuses
    • dev are users, too.
    • data is spread about a bit: loci, ome-xml.org, openmicroscopy.org
    • andrew should let curtis know if he wants help with ome-xml

  • bio-formats / ome-tiff
    • revamping interfaces to handle 2007 stuff
    • problem is building old stuff and new stuff in parallel
    • haphazard method adding to MetadataStore
    • trying to autogenerate that code, too.
    • issue of methods which take 20/30 methods
    • possibility of using builders
      • e.g. someLongMethod(a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p) becomes
      • shortMethod(new SimpleBuilder().setABC(a,b,c).setMNOP(m,n,o,p)); // rest null
    • do we deprecate interfaces?
      • one complaint about stability of bio-formats

  • volocity
    • ome-tiff support. someone is trying to convert, and emails are comming with errors.
    • how do we determine if something is "OME-approved"?
      • links on our webpage
      • need to be cautious about what we can help to support
      • another star ranking system?
      • don't say "partial" but "yes, but doesn't support a,b,c"
    • what is "OME-XML" or "OME-TIFF" support?
    • curtis looking into issue, what's causing it.
    • trying to work it out

  • multiple tiff files
    • scanning images in a directory
    • images/pixels ids
    • if lsid, no problem. internal, causes an issue.
    • can't match across tiff files.
    • rule: "must use an lsid if you are spreading among files"
      • for some form of file mangaling
      • "strongly encouraged"

  • 2.6.1
    • couple small things that curtis wants to look into

  • omero
    • waiting on float4 widening (OMERO35-->OMERO37)
    • remoting errors. seems to not be happening with the jar. (4.2.1 has 2.2.1)
    • background thread seems to make valewalker happy
    • formats
    • ome-xml will be in 3beta3
      • want to also support split schemas in bioformats and then in importer
    • insight has been ready since middle of the weak
      • needs to upgrade user guide with formats
    • webadmin: no changes everything fine
    • pack this week; integration testing next week


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