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You are here: Home Community Minutes Conference Calls 2010 2010-05-04 Tuesday Meeting

2010-05-04 Tuesday Meeting

Attending: Brian, Scott, Colin, Andrew, Chris, Donald, Will, Jean-Marie, Jason, Josh, Melissa, Carlos


Remember: Agenda must be complete (with estimated times) on the day before the meeting. Any additions after that must go at the bottom (AOCB)

  1. Accepting minutes from last meeting

  2. Matters Arising (<10 mins)

    • Put in action points from last Thursday's meeting.
    • Brian: Find out if Michael is available for next Tuesday ASAP
    • Brian: Rough testing script for next week
    • Brian reply to QA aperio tickets (#2412)
    • Chris reply to QA (#2403)
  3. QA and User Testing: Brian's presentation (20 mins)

  4. FLIM: Donald's presentation (10 mins)

  5. Model Changes (10 mins)

    • Eveyrone: Make a decision next Tuesday about interative model changes
  6. AOCB (<5 mins)


  • Minutes accepted

  • Matters arising

    • QAs replied to
    • QA 2403 outstanding. retrieving Leica file
  • Paris

    • meeting done
    • Johannes and Pavel attending
    • Andrew working on final program
    • to-be-confirmed for one title
    • @Make page live
  • Visit from Christoph and Ingvar next week

    • They should discuss with Angie about accomodations
    • Discussing Java volume viewer integration (Insight & Web)
    • Status update:
  • Possibly attending OSSWatch meeting

    • Scott will provide details quickly
  • Testing presentation / Brian

    • State of where we are
    • Very little repeatability of our tests
    • two pairs of eyes: at least at the client level
    • matching external developers as testers with internals devs
    • technical lead for maintaining the design of what we've decided
      • best practices maintained by that person
    • continuous integration for knowing what breaks
      • but don't have that at the testing level
    • "TEST" tag for tickets?
    • using videos as the test suite
    • Q/A
      • Scott: disagree with the separation
      • Jean-Marie: User story is roughly this definition
      • Brian: less repeatable test but tests attached to the user story?
        • Scott: Yeah.
      • Jean-Marie: need concrete tests (reality is we have no testers)
      • Next point: formalize the set of things we test
      • Will: that's why the movie is a good starting point
      • Chris: watch a movie and reproduce, or spend 30 minutes to write it down
      • Will: what actual problem are we trying to fix?
        • bugs (4.1 release wasn't too bad)
        • duplicating testing?
        • Brian: user perception - we don't do a lot testing
      • Jason: have own memorized
        • Why don't we just write down the scripts?
        • Jean-Marie: I think that's what needs to be done.
        • Jason: wasn't able to keep up with the development
        • Didn't know what was accomplished
  • FLIM presentation / Donald

    • very complicated workflow currently
      • generates an Excel spreadsheet for each ROI which end up being compined
      • Jason: no guarantee that each cell is the same
        • Differences in lifetime measurements may be real and shouldn't be averaged out
        • Donald: want to add statistical analysis to test fit
    • New workflow:
      • uses omero ROIs and keyword
      • runs a script against the dataset to get 5 spreadsheet results (k1, k2, a1, a2, chi)
      • proposed next additions:
        • combined results
        • generate histrograms
        • generate heatmaps
    • Basic workflow done, but a few problems
      • Polygons not a mask (Andrew would like to scream) [Blocker]
        • Josh: perhaps we could use vertex arrays?
        • Donald: can still store polygons (have to be fixed) * Doesn't work properly in measurement tool (bez. issues)
      • Extended workflow, allowing user ability to add steps
        • Andrew: just use coloring/labelling of cells?
        • Donald/Chris: want something more formal (set keywords)
        • Jean-Marie: like ticket fields in agilo
      • Big issue: NDIM
        • need time and channel information
        • examine it in Paris
    • Future
      • / for defining the namespaces, etc.
        • i.e. allowing scripts to put scaffolding in place for UI
      • cluster deploy
      • reusing for FRAP
      • better quantification (stats, LDA, fisher score, etc)
    • Q/A
      • Jason
        • name "roi script", to stay away from the cluttered names
        • slide 3 (black v. red): David's response? * He liked it. Will he use it? Can he use it? * Can't use it without polygons. * We've got SPCImage but in OMERO without polygons * To be better: needs to have the stuff in red
        • If it's more or less the same amount of work,... * what's reasonable for us to expect red stuff for David to use? * Time scale? 2 weeks to get something in front of him * Donald: have done the hard work already * polygons & the math are a wee bit tricky (couple days of work) * Showing it in Paris? Definitely. * Chris: how hard to get it merged? A day of work. * Will: release as 4.2? Hopefully all of it. * Jason: syncing earlier rather than later is usually a good idea * @Donald: commit by the end of the week. Hopes David can use by then * Chris: releasing this as a preview with a flag
        • @Chris: David needs a box to run this (by week's end?)
        • Pieta also wants to do her divisional talk on the scripts
      • FLIM issue (mathematical)
        • Discussion with Kevin/Curtis re: Paul Barber at Kings
        • Rewriting math around flim analysis
  • Model changes

    • Currently: 2 big releases of the model per year
    • Example: SPW timepoint(int->timestamp)
    • Chris: stripped 2 properties out of mask (width/heigth)
    • Itermediate release or do we make changes for 4.2?
    • Andrew: changes would require a major release
      • but it's only been out there 1-2 weeks
      • Chris: another version at Paris?
      • Jason: @but do have to write community now.


  • Andrew publishes the page
  • Jason writes to the speakers for info
  • Jason writes to Angie, and CC's EBI
  • Scott sends details on OSS meeting
  • Brian: Start the ui testing scripts for most tasks
  • All: send new name suggestions for "workflow" Donald
  • Donald commits FLIM code for the end of the week
  • Chris: David needs a box to run this (by week's end?)

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