Personal tools
  • We're Hiring!

You are here: Home Community Minutes Conference Calls 2008 2008-07-10 Project-wide 3:45 BST

2008-07-10 Project-wide 3:45 BST

Attending: Andrew, Brian, Catriona, Jean-Marie, Alexa, Donald, Jean-Marie, Melissa, Curtis

Agenda


  • Sharing (Josh)
    • Status
    • Best way to share sharing.

  • SPW
    • Status


Notes


  • website
    • "awesome"
    • any issues?
      • not that Andrew's aware of
      • blog got mapped in a bit late
      • movies in AVI format: sound doesn't work on some people's machines
        • worked for Andrew under parallels / flip4mac
        • complete range: no sound ... cracking/hissing ... speeded up ... no video but sound
        • codecs! (compressed with Windows Media 7, standard settings)
        • VLC ok. Quicktime under Flip4mac. Media player under Win.
        • Everyone who had problem please send configuration. There shouldn't be a problem.
          • Ola will try to find out why.
          • Brian/Will: ok.
        • Not a parallels problem
        • Did anyone check under a real Windows install?
          • Yes.

  • formats
    • 3 new formats in the last week: MINC-MRI, Olympus APL, TillVision
    • release 1.5 weeks ago; now fixing bugs
    • [http://twitter.com/bioformats]]
    • memory leak in matlab (Gaudenz)
      • replied to his email
      • contact at mathworks
      • tested locally. no problems. (r14sp2)

  • sharing
    • Josh will write up on trac, and send a link
    • fairly limited "smarts" — have to add all items (Image->Pixels->Channel->...)

  • hcs
    • wellsample in workable state
    • one or two little kinks; importer looks ok, look into insight
    • Jean-Marie: wellsample is now connected to correct well?
      • Doesn't seem to be working. Sent screenshot.
    • other than wellsample issue, insight can now display the entire plate
      • lots of wells have nothing (only black with "no-image" message)
      • can link screens to plates, etc. can annotate plates/screens/...
    • discussion with andrew
      • adding parameter to column/row how they are named
      • perhaps just a display setting
      • "D7" or "4/7"
      • would possibly help acceptance of the tool
      • Jason: fall under rubrik "need more information"?
      • Andrew: will we be getting offsets? A plate which starts at 43X47 (extension of other plate).
      • Jean-Marie: Not a decision to make right now.
      • Jason: Very local expectations?
      • Cat: Can look into it.
      • Jason: dedicated ourselves to tackling metadata problem.
        • places have defined models that they are using (existing workflow)
        • largely fixed, no interest in changing them
        • adapting to them is a big challenge
        • will try to raise question at an upcoming mtg.
        • important to handle correctly
        • balance between acceptance and how much we can do
        • reference sites?
          • doing that for 5 years with varied results
          • new efforts on the hcs front

  • client mtg
    • list of priorities over 4-5 weeks. metadata issue
    • creative with conversations because of vacations, etc.
    • open call for metadata questions the devs want answered

  • will
    • making fairly significant changes
    • moving more toward insight model

  • curtis
    • switching to components folder like in omero
    • need integration with hudson
    • loci-tools: bioformats & ome/omero
    • plan for beginning of august
    • hudson as our ivy repository

  • roi
    • andrew looking at making ROI structures. initial draft
    • setup in file will not work in the database
    • in two places in file
      • shapes under <image><roi/></image>
      • rendering/display settings: in structured annotations bit with link back to shape
      • 1000 ROIs --> 1000 links to structured annotations table
      • postgis? Still seems reasonable.
        • timescale? don't know. but 9 month is reasonable. Before Beta4 for scripting.
        • Andrew: doing ROI first because it provides nice example of structured annotations
        • Jason: let's do 4-6 weeks and then start thinking seriously about this?
        • Donald: Sept/Oct/Nov
        • Andrew: Should be in Aug/Sep release

  • beta3
    • someone didn't understand having to go and get something and build


Document Actions