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You are here: Home Community Minutes Conference Calls 2008 2008-05-16 Omero Review Meeting

2008-05-16 Omero Review Meeting

Attending: Andrew, Briwn, Chris, Colin, Jason, Jean-Marie, Josh, Melissa, Ola

Agenda


The background to this meeting: we are feature-frozen, have initiated user testing, and well into testing.


  • Status Report
    • Bio-Formats
    • OMERO.server
    • OMERO.insight
    • OMERO.importer
    • OMERO.editor
    • OMERO-fs
    • OMERO.web (nee OMERO.collaborate)
    • OME-XML
      • ome-xml 2008-2 update;
    • Website

  • General
    • movie making- problems?
    • Deployment and installation


Notes


  • Jean-Marie/Annotations
    • working with tag hierarchies
    • need to make a servicevi
    • no build for Michael because of working on tag-of-tags
      • possibly later today
      • @Chris might try on weekend to reproduce freeze on mage.
      • Any changes to how accessing thumbnail? Still one at a time.

  • Bioformats/melissa
    • hcs. Coming. More data?
      • Just SO big. (+10Gig, one plate) Generate a smaller one?
      • Paul Andrews needs a solution, possible source of data.
      • @Chris sends an email.
      • @Brian gets more than one plate (3 plates?) from Michael and uploads it.
        • Not on users.o.o.uk.
      • Notice: some of the datasets have 100K+ files, each one huge.
        • Lots of issues
        • Tricky testing on real data
    • other format requests
    • more time fielding emails
    • Q: Happy with the tranformations/xsd-fu? A: a few minor changes; will commit

  • server
    • josh
      • freeze hopefully gone
      • tightening up loose ends; need to get script jobs into database. @Discuss with Donald
    • chris
      • fixed issues with bulk uploads
      • documentation things in the install (trac: repository, upgrade information)
      • time to try some mac os x upgrades
    • Q(j-m): Looking into the search issue reported? A: Hopefully next week.
    • tickets
      • #903 got to get upgrade script tested
        • @Chris sends test database
        • @Josh writes
        • @Chris tests
      • Josh working on #940s
      • #11 (projects) in a Beta3.1? #6 save movies from the projectsion StructuredAnnotation
        • Want to download something for Powerpoint
        • Is scripting the solution?
        • Yes and No. Still has to be stored somewhere for the user to download.
        • "backgroundy"
          • technical: server should generate something for me to take
          • an example of "you gave me this; then it's easy to give me that"
            • compression --> movies --> ...
            • people getting frustrated
            • provide tools in ways to utilize our tech; keep as focused as possible
        • need support for blitz in clients
        • perhaps provide way to access matlab script inside server
        • 4-6 months to put the rest of the components in piece
      • push distro packaging

  • importer
    • changes to OME-TIFF have gone in; can get working on that
    • OME-TIFF-->HCS (a la gantt)
    • command-line stuff. easier now with all the svn restructuring.
    • @dealing with huge dataset issues on mac!
    • deleting bioformats-omero? Not yet. Switching day or whatever.
      • No changes made except for DO_SHA1 commented out

  • insight
    • worked out several bugs from Michael/Josh
    • refresh synchronization and tag-of-tag is coming
    • version for Monday
    • localhost regex; probably not too important
    • most of them should be fixable or are already addressed.
      • lots at one time; but largely duplicates
    • donald should be able to close several of the tickets already

  • editor
    • chris: discussion in heidelberg, lots of people are interested in attaching protocols, etc.
      • trying out for biological protocol, less on microscope.
    • jean-marie: @95% in protocols are also in tables
      • need to target that to make it more flexible
    • have to work out the rows&cols issue
    • some want to build a template of what they want to search
      • based on the type of microscopy that you are doing and build UI accordingly
    • new movie from will of editor

  • OMERO.fs
    • tickets are appearing!
    • not too much
    • @meeting with: chris, josh, colin, melissa
      • Tuesday: 2:00BST
    • extends bioformats RandomAccessStream to pull data directly out of OmeroFs
      • setup in a particular way. Could be more flexible.
    • looking at weblitz some
      • use latest version of server
      • will try to get built

  • OmeroWeb
    • Go, go, gadget, go
    • cleaning of backend in weblitz
    • customization planning
      • Q: how much customization should be allowed? A: adding a new template?
      • That's done. Django provides everything.
      • For Dummies or for Programmers?
      • For Programmers!
      • Integrating for CSS at a particular site. Embedding in their environment?
        • Effort on our side, to make it look more like their work?
      • Portlets?
        • Who's going to use it and how?
        • Probably not. Focusing on solving problems of biologists.
      • Was looking at scripting engine
        • You define the whole script and recieve the HTML from the script.
        • embeddable output.
    • How to read from webclient, get a link to an image
      • SOAP server?
      • Don't think so. Let's talk.

  • Andrew & all things XML
    • OME-XML
      • changes to schema going live, probably Monday
      • X-Ray tomography
        • description of what they are trying to collect
        • possibly using our data model with custom attributes
        • generating sample files to see how to fit data at different scopes
        • down to the plane level
      • images currently stored in proprietary database. People only taking away tiff files.
        • allow remote access with OMERO
      • need any help?
        • access to OMERO server, since they don't have anything to import
        • @dedicated demo server after release
          • security? management?
          • performance? In this case, that'd be a plus.
        • vmware image as a compromise?
        • movies as a compromise?
    • www-dev
      • hasn't changed largely
      • lots of small annoyances
      • kevin had issues with not being able to find things
      • what's front and center? everything can't be top-level
      • http://.../news?categories=partnership - Collection based on search term.
        • content based on live search
      • tabs:
        • video+screenshots -> gallery
        • file formats -> documentation
        • another way (not tab) to get between OME-XML, OME, TRAC)
        • file formats linking to www.ome-xml.org ?
        • news & events to second position; about as last tab
      • @screenshots are out-of-date; done post release
        • also for mac and windows
        • OMERO.insights --> OMERO.insight
        • getting OME-Perl server, web client
      • feedback fast please


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