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You are here: Home Community Minutes Conference Calls 2007 2007-06-14 Project-wide 3:45 BST

2007-06-14 Project-wide 3:45 BST

Attending: Alexa, Andrew, Brian, Cat, Chris, Curtis, Jason, David

Agenda

Review of last project-wide ConferenceCall 2007-05-31 if necessary
    • News and Updates
    • Review of who is doing what
    • Other
      • Bob Freeman's issues (Josh)


Notes


  • bio-formats
    • maint. and bugfixes. release notes cover it.
    • issues with email.
    • added logging
    • melissa half-time on ome-notes
    • jrs: formats? cr: ?
      • jrs: ? reformatting the webpage?
      • cr: working on it as a whole reworking
        • main thing we talked about was a level-of-supported with thermoeter graphic. work along with ome-xml.org. bioformats could definitely go on ome-xml.org. not visbio, etc.

    • chris: issue 1
      • problems merging things into loci.* Mostly solved
      • reading tiffs. All ifd into memory. For Leica, large table consumes memory
      • question: how do we handle this since everything depends on ifd's being read out.
      • curtis: exclude list? so that they aren't parse. only if you don't need that info.
      • brian: basically the color table.
      • curtis: used?
      • chris: don't know. brian: don't think we do.
      • brian: and can we get it back after being excluded?
      • curtis: do we need it?
      • curtis: reason for long initialization is to make each plane short. (visualization use-case)
      • brian: excludes are happy medium with lazy loading
      • chris: threshold on the ifd's in memory with cache.
      • curtis: worried about the complexity of caching (at several layers)
      • chris: objectizing ifd?
      • curtis: good idea. plus yes-or-no lazy. leave LRU to the application code.
      • chris: if object hierarchy small, and have ifd factory then each app-dev can set things up as desired.
      • curtis: makes sense. you taking a stab at it?
      • chris: need to see how complicated. if too bad, just add exclude list (or based on size) @
      • curtis: complicated
      • brian: we really need it. should also help visbio.

    • brian: problems with totally white channels
      • curtis: try with command line and via imagej to see if it produces the same results
      • brian: possibly due to omero's conversions

    • brian: stk files. being supported?
      • curtis: ask melissa

    • jason: nd file support status
      • brian: may be working. let me check @

  • importer
    • some optimizations re: TiffTools (openByte) couple of quirks
    • all of the series stuff is working. tested with leica. Full leica support.
    • stks working.
    • not ome-xml working. need changes to our system. not as easy as expected.
    • jason: priority xml or tiff?
      • curtis: should be the same
      • brian: correct
    • beta2: leica, metamorphs, pics, lsms, dvs, full-tiffs (w/o raw file)

  • server
    • chris: whole bunch of IO optimizations. thumbnail retrieval and PGI calculations
      • issue: if channel mapped to compound color. last kicker before beta2 to the world. @
      • monday: successfully deployed omero in homburg (AIX 8cpus/16gigs ram)
      • jason: problems with importing very large files (multi-gig)?
      • brian: fixed a while ago. need to upgrade to beta2. there was no upgrade. will check with user.
      • chris: upgrade should be relatively straightforward. just upgrade, but old clients should work (just don't download files). need new importers.

  • clients
    • package java clients together
    • moving to web admin
    • chris: for beta3 need shoola/insight more deployment friendly. (use built-in user directories. eases importer/insight deployment. dmgs and exe)
    • then should be able to ship as dmg?
    • jean-marie's summary
    • donald's not here
    • jason: cat, user comments for beta2 minor?
      • cat: yes. roi's mostly.
      • on schedule.

  • release
    • beta2 testing next week (Monday). on issues, wait on brian for thursday.
    • beta2.1 in 2 weeks.

  • misc
    • need list of formats from lars. @

  • ome-xml
    • some feedback from chris and curtis. on the tiki
    • next week is putting together website
    • next week after that is putting together a validator (min. specs)
    • curtis: validator in python? andrew: for integration...
    • chris: goal is to get a command line script to validate xml and produce a report. then xslt to transform xml report into html. integrate into a turbogears application. bundle download: A) CLI validator or B) small turbogears that you can start up and visualize the report.
    • curtis: sweet.
    • feedback period is coming to an end.
    • ome-xml.org a trac? Still plan? (python script can also be plugged into script)
      • curtis: bioformats content to ome-xml.org?
      • chris: then you lose a lot of the power of trac
      • chris: use interwiki links.


"Every day is OME day" (T-shirt @)

  • Alexa
    • ldap: things working automatically without rewrites.
    • adding trac page on server development doc deficienies
    • Brian: 2.0 has WebAdmin release? documentation?

  • David & CruiseControl
    • two builds currently running
    • slight difficulties due to svn:externals
    • test reports are published
    • email sent to a distribution list: josh, david, chris, alexa, brian?, jason?

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