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You are here: Home Community Minutes Conference Calls 2009 2009-04-03 Project-wide Conf call

2009-04-03 Project-wide Conf call

Agenda

  • Beta4.0
    • Cleaning up all tickets & closing milestone
    • On schedule for 4.0.1? (Windows/DV)
    • Moving tickets to 4.0.2?
  • Beta4.1
    • OMERO SPW extensions and Bio-Formats integration
    • Progress made on the user stories?
    • Moving tickets & description to 4.2?
    • Everything committed on both branches?
    • Breaking up the 8+pt stories?
  • Nitpick e-mail from Curtis "ROIs in the XML schema"

Attending

  • Carlos, Colin, Curtis, Dundee (Jason, Chris, Jean-Marie, Donald, Andrew, Brian), Josh, Melissa, Ola, Will

Notes

  • Beta4.0

    • Melissa, Jean-Marie, Chris have a few remaining tickets
    • Windows seems to be on schedule.
    • Colin will test and give feedback on Windows deploy
    • DV threshold: will work for demo but need to think about other stratgies
    • Tuesday for packaging.
    • Doing it on Windows image with EXE4J
      • Try Insight
      • Extra build for editor? (Otherwise by hand)
    • OMX Data & Negative pixel intensities
      • issue only applies to 32bit float issues
      • shrinks positive from 64k to 32k to -32k. possibly issues. @Jason checks data.
      • possibly needs other adjustments somewhere: slider?
      • wait for 3.1? (wait for 32bit switch)
      • if just a two line change and it works, give it a try
      • important in other domains (dicom, EM-tomography) to accept non-positive values
      • @Chris gives Melissa DV file with altered header for testing
      • @Brian tests the broken dicoms
    • Few importer format issues (Leica, xcde, ND2 white images).
      • Would be good for Tuesday
    • No 4.0.2 - Push to 4.1
    • Feedback
      • Naming of leica files? (Paulo)
        • Creating an image folder?
        • Originally a request to keep the original file names
        • Now users who don't change their file names have many image with the same name
        • Perhaps use image full path on import?
        • Was: [Full path]
        • Possibly don't give user a choice of dataset, just project?
        • @Brian writes to list and discuss (possibly with GUI mockups)
        • Curtis: should bioformats create a dataset in the format? * Giving users data management choice. * If there's a concrete choice, it'd be fine. * Vendors will probably start doing this more often. (file as DB) * So should it be bioformats role to say "there's a field 'X', ..." * Traditionally PDI was user driven. Possibly use > * Need construct to differentiate between from user or file. * Using image-image links? * Series name is often the same as the experiment. Or file as patient study <li>
        • Regex/etc. in DB for how you name things based on field 'Y'
      • Import in general
        • Regex in file filter ?
        • Users want things to be as fast as possible
        • No choice if multiple images chosen?
        • Button: "Ask me again?"
        • @ Leads to preferences issue! 4.2 Discuss in Paris. * New table with user_id, format_type, colA, colB, colC, ...
  • Beta4.1

    • SPW
      • Need extra metadata coming from bio-formats, without modifying the model
      • Adding 4 methods to be filled out in the InCELL reader (origin, sequence, naming scheme)
    • Other big user stories
      • ROI
        • lots of mapping into each languages
        • hibernate-spatial requires PostGIS
      • OpenGL
        • can no longer just write on top of the viewer (its a window onto the hardware)
        • working on it while J-M is gone?
      • Movies
        • Chris spent some time on exporting movies
        • Doesn't need client to start
      • Gateway, ImageJ, & FS over samba via IM
      • @ The big stories need to get broken up soon to make them manageable
    • All not in 4.1 into Future
      • Coming up to Paris we point people at Future
      • @ Discuss in Paris
  • ROI in XML Schema

    • Why is the naming scheme the way it is? (capitalization)
      • Matching SVG is good. Exporting to illustrator, etc.
      • If we are breaking anyway, then don't have to worry about it but have a XSLT.
      • Trying to get something other than measurement tool for use cases
      • @ Discuss in Paris
      • If you have to change, change early.
    • Supported as is with custom methods to start parsing values from files (OIF)
    • Doing ROIs server-side in 4.1, then the tables will be created
    • Slowness of some parsing. Java DOM issue? Possibly rework XSD-FU (also solves ordering issue)
    • Q: Anything that isn't representable?
      • Arrows, SCALE BARS, color bars, text overlays (w/ rendering details)
      • origin of text as one of the overlay attributes
      • have seen: bounding box + font + color (undisplayed rectangle with text?)
      • trying to break SVG as little as possible. (cF. bitmask)
      • angled rectangles? (cF. affine transform attribute)
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