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2011-02-17 Thursday Meeting

In Attendance: Brian, Scott, Andrew, Will, Ola, Donald, Jason, Josh, Jean-Marie, Colin, Carlos, Melissa

Agenda

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)

    • Josh: Add minigroup notes to plone
    • Brian: Tickets for moving shoola -> ome
    • Brian: Ticket testing scenario changes needed
    • Will: Ticket the tests needing to be disabled
    • Jean-Marie: get Jos' presentation
    • Josh & Jean-Marie: discuss how to test stylesheets
    • JMB & Josh: breakdown milestones page with more details + tickets
    • Jason: send out calendar link
    • Everyone: disable tests and create bugs
    • Andrew will send some examples of how to structure data for HCS import

  3. Sprint Update (20 mins)

    • Will: investigation report (5 min)
    • Donald: investigation report (5 min)
    • Ola: investigation report (5 min)
    • Everyone else's status (broken link)

  4. Email and Forum Review - checked at 13:50 (5 mins)

    • Email -

      • Re: [ome-devel] Download original archived file with python

    • Forums - all answered or waiting user feedback

    • QA -
      link 

      3201    new     jason@lifesc...     Web 4.2.3-DEV-      2011 02 05      -   If I search on some text, get ...   -
3200    new     m.wasowicz@i...     Insight 4.2.2   2011 02 04  -   tagging images  java.lang.Exception: org....
3198    new     S.C.Moser@du...     Insight 4.2.1   2011 02 04  -   past settings   java.lang.Exception: org....
3180    new     N.Hegarat@su...     Insight 4.1.1   2011 01 29  -   I was doing a projection    java.lang.Exception: org....
3177    new     bhcho@cmu.ed...     Insight 4.2.1   2011 01 28  -   I was launching my Script. It ...   java.lang.Exception: java...

  5. Any other business (<5 mins)

    • College Research Symposium: Crieff Hydro Hotel 25th-27th March 2011

In Attendance

  • Brian, Scott, Andrew, Will, Ola, Donald, Jason, Josh, Jean-Marie, Colin, Carlos, Melissa

Notes

Notes

  1. Accepting minutes from last meeting

    • No comments.

  2. Matters Arising (<10 mins)

    • Josh: Add minigroup notes to plone - PENDING
    • Brian: Tickets for moving shoola -> ome - Story ticket added
    • Brian: Ticket testing scenario changes needed - Ticket added
    • Will: Ticket the tests needing to be disabled - DONE
    • Jean-Marie: get Jos' presentation - Email sent, waiting for reply
    • Josh & Jean-Marie: discuss how to test stylesheets - Ticket added
    • JMB & Josh: breakdown milestones page with more details + tickets - PENDING
    • Jason: send out calendar link - DONE
    • Everyone: disable tests and create bugs - DONE (except pytables)
      • Josh working on pytables fixes
    • Andrew will send some examples of how to structure data for HCS import
      • In progress
      • Creating some more detailed example files
      • Going to send him some guidelines on how we may go in the future

  3. Sprint Update (20 mins)

    • Will: investigation report (5 min)
      • Tested 3 different libraries, code available in web figure django app
      • Currently drawing ROIs, seems to handle scaling, zooming, clicking nicely
      • Not sufficient for full scale editing of shapes on the web (its read-only)
      • Alternative "SVG-Edit" library does allow drawing and is the way to go
      • Still have to do more testing with SVG-Edit
      • JMB: Where is the code for this?
        • Django app linked from ticket via commits
      • JMB: Need a discussion about legacy code and how to do update script
        • Monday/Tuesday meeting for this (2:00?)
    • Donald: investigation report (5 min)
      • Got head around bio-formats
      • Has wrapper that will import and render
      • Can then save data a jpgs
      • Should be done with this testing today
      • Next is to look at visual inspection + speed of (de-)compression review
      • Some quantification of results would be good
      • JMB: Where is the code? Donald will commit this to a branch
      • Last step would be convert test code to use in insight
      • Jason: any of this useful to Melissa? Melissa: possibly in the future
      • Colin: Also look at JPG2000 pixel buffer, lots of overlap with Dmacs work
        • Need to think about how to tie these together
        • Should be able to meet on this issue next week
    • Ola: investigation report (5 min)
      • Testing tiling web plugins
      • Caswari tiles are stiched on the fly
      • PanelJS is a set of images under DOM object
      • Problem with Caswari loading regions into the canvas
      • PanelJS was able to integrate into the viewer with test website now
      • Ola will commit both for folks to see
      • Need to discuss how tiles are generated in bio-formats (with Melissa)
        • After meeting will discuss
      • Josh: On Caswari tickets did you record the problems?
        • Ola will detail the issues she had
    • Strategy for where to place results of investigation
      • JMB: Strategy we will adopt for committing these research projects?
        • Josh: These sub-projects should get their own directory
        • Josh: Can then be merged if needed in the future
        • Ola: Perhaps for simple tests just commit to 'OmeroWeb/web-test' as long as it doesn't break anything?
          • Seems reasonable
          • Ok to put broken investigations there as well
          • Will: This directory is nice and simple to use, make sure we don't complicate it
          • Josh: Could also just branch off this directory in git to keep things comprentalized
          • Conclusion: Web-related goes into web-test, Dmacs will branch to commit his codes
    • Everyone else's status
      • Josh: several tickets are not getting moved
      • Brian: wasn't sure what to do with things 'pending review by someone else'
        • Jean-Marie: don't close; move it back to left column or given it to another person
        • Josh: worst thing is to close a ticket too early
        • Jason: can we have one meeting without talking about how to use git and/or trac?? ;)

  4. Email and Forum Review - checked at 13:50 (5 mins)

    • Email -

      • Re: [ome-devel] Download original archived file with python
        • Will: User has question about big deployments
        • Read from original file needs 'trim'. (Will can create ticket for bug)
      • Will (Re: HCS formats) There was a message about this on the forums, did we respond to this one?
        • Jason: Yes, emailed Michael Held about our future plans. Josh is going to talk to him in person

    • Forums - all answered or waiting user feedback

    • QA -
      link 

      3201    new     jason@lifesc...     Web 4.2.3-DEV-      2011 02 05      -   If I search on some text, get ...   - PENDING
    * Jason: On devel servers & nightshade, searching results and then viewing web seems to slow down the site
    * Ola: will follow up on this
3200    new     m.wasowicz@i...     Insight 4.2.2   2011 02 04  -   tagging images  java.lang.Exception: org.... - CLOSED
3198    new     S.C.Moser@du...     Insight 4.2.1   2011 02 04  -   past settings   java.lang.Exception: org.... - CLOSED
3180    new     N.Hegarat@su...     Insight 4.1.1   2011 01 29  -   I was doing a projection    java.lang.Exception: org…. - CLOSED
3177    new     bhcho@cmu.ed...     Insight 4.2.1   2011 01 28  -   I was launching my Script. It ...   java.lang.Exception: java... - CLOSED

  5. Any other business (<5 mins)

    • College Research Symposium: Crieff Hydro Hotel 25th-27th March 2011
      • Jason: Are we going?
        • Andrew: Need to respond soon
    • Admin
      • OME Grant Review: One of the things that came up was how we are reporting OME useage
        • Going to redo those query results
        • Andrew: Had something like that recently - will give Jason those results
        • Need: starts in the last month, starting/stopping dates
        • Have 1 week to do this!
        • Interview for review is April 12th
      • Jay HMS will now be using ISA-TAB
        • Will: Looked at this tool, has trac page about mapping between this and OMERO.editor (PP presentation)
        • JMB: Have to see about possible integration
        • Will: Probably best to represent this data in tables
    • Glencoe Review
    • FLIM
      • David interested to continue; using VPN to connect. JMB is in contact and will follow up
    • Accelrys
      • Apparently have a prototype working with Bio-Formats and OMERO

  6. Actions

    • Josh: Add minigroup notes to plone
    • JMB & Josh: breakdown milestones page with more details + tickets
    • Donald: commit jpeg2000 code to a branch, commit processing code to a branch
    • Donald: possibly committing alternative storage investigations
    • Ola: commit paneljs code to a branch (or a mainline)
    • Will: commit to webfigure, but still turned off.
    • Ola: Look at QA 3201
    • Will: create ticket about rawFromOriginalFile
    • JMB & Scott: Start documentation for QA and what client they are using
    • Jason: Update 'omero in production' page
    • Andrew: submit poster to CRS
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