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You are here: Home Community Minutes Conference Calls 2011 2011-10-13 Thursday Meeting

2011-10-13 Thursday Meeting

Attending: Simon, Andrew, Chris, Scott, Jean-Marie, Jason, Elwood, Ola, Will, 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)

    • Scott: create scripting testing story N/A
    • Melissa: merge and send email to nitpick about exposure of changes on Wednesday. DONE
    • Elwood: test ldap changes. In PROGRESS
    • Chris: handle Upload/Download OME-Tiff
  3. 4.3.2 Milestone

    • OME Model - plan for next 12 months (ajp) #6487

      • Model changes to mention

        • Pyramids
        • New 3D ROI model
        • Rework Detector
        • EM Additions (Probably needs detector changes)
        • Rework Lightsource
        • Rework Instrument
      • Other Model Related

        • Code generated samples
        • Build validates all samples
        • XML Mock work
      • Do we mention N-dim in next 12 months?

    • Closing sprint after meeting.

  4. 4.3.3 Release plan

    • Thursday 13/10:
      • Commit freeze lunch time.
      • Check with Melissa B-F status. Should be ready to go. If so merge to develop
      • Documentation Snapshot (ajp)
      • JM: update contributors page. DONE
    • Friday 14/10:
      • Make insight and importer build with latest B-F.
      • Tests B-F changes see tickets #6992, #6991, #6990, #6989.
      • Merge remaining pull-request i.e. #6, #2+#7
    • Monday 17/10:
      • Version number upgrade.
      • Review all commits again i.e. go through the list of tickets, click again.
    • Tuesday 18/10:
      • Package: test build on windows, mac, linux
      • Update website with new links.
      • Announce release on devel and users
      • Deploy and announce internally.
    • Add few more days to sprint, one extra week?
  5. 4.4 and OME-5

    • OME-5 buffer milestone.
    • new sprint (2011-27-10 (1)) created to add first "cleaning" tickets.
  6. Email and Forum Review - checked at (5 mins)

    • Email -

      • Johannes Schindelin Re: [ome-devel] bio-formats slow under WIndows
      • Harri Jäälinoja Re: [ome-devel] Update on OMERO and HCS - Have we got suitable sample data?
    • Forums -

    • QA -
      link

      -- -- Add list indented 12 spaces
      ID  Status  User/email  Type    Created Selected file   Comment Error
      4008    new john.lim@imb... Insight 4.3.1   2011 10 06  ...S2 LVX-PTuner-DsRed-LaA_002.nd   Unable to import a MetaMorph 7...   loci.formats.FormatExcept...
      3996    new Michael.Kres... Web 4.3.2-8fc9  2011 09 30  -   Dear Omero Team, thank you...   -
      3992    new jason@lifesc... Web 4.3.1-6d4b  2011 09 29  -   test    -
      3991    new leejb@missou... Web 4.3.2-8fc9  2011 09 28  -   Just tried to create a discuss...   Traceback (most recent ca...
      3986    new boguslaw    QA  2011 09 26  -   -   -
      3985    new ahmed@linuxi... Web 4.2.2-r871  2011 09 23  -   -   Traceback (most recent ca...
      3981    new b.n.melgert@... Importer 4.3.2-8fc9 2011 09 21  ...Cd1 - 2011-07-28 10.54.29.ndpi   Importing a big ndpi filr (50M...   omero.ResourceError s...
      3978    new lem@stowers.... Insight 4.3.0   2011 09 13  7th YY1 and 8th Ies2.l2d    This file was generated by LiC...   java.io.FileNotFoundExcep...
      
  7. Any other business (<5 mins)

    • Light Sheet Microscopy event (14/10) Modulo Proposal to contact?
    • Mark Hiner e-mail SCIFIO white paper

Notes

  1. Minutes accepted.

  2. Matters Arising (<10 mins)

    • Melissa: merge and send email to nitpick about exposure of changes on Wednesday. DONE
      • J-M:Scott created 4 ticket for your list.
    • Elwood: test LDAP changes. In PROGRESS
      • still testing
    • Chris: handle Upload/Download OME-Tiff
      • pending
  3. 4.3.2 Milestone

    • Last movie remaining. Andrew is going to make it after the meeting.

    • OME Model - plan for next 12 months (ajp) #6487

      • Model changes to mention
        • Pyramids:
          • A:simple change, just structure of annotation
          • Chris: last discussion was about how do we store data, not how to model it in OME-XML. Lets just leave this alone and get the examples in place that have compression, tiling, etc. in them.
          • Chris: this is more about documentation.
        • New 3D ROI model:
          • Andrew: are we going to support n-dem ROIs. at the moment Donald’s impl uses vertex array to handle n-dim object.
          • J-M: we do not support 2-dim correctly now.
        • Rework Detector:
          • Andrew:do we bother to do Lightsource?
          • Will: (missed part)
          • Jason: there are now commercial microscops from commercial vendors using ome-tiff with CCD camera and PMT detector. Those products exist.
          • Will: this should be 2 detectors which has two chanells
          • Chris: this is more linking change.
          • Will: not exactly, we link them together now.
      • Do we mention N-dim in next 12 months?
        • Chris:sub resolution are not needed as a model construct.
        • Pyramid is more related to other changes rather then Model.
        • J-M: I will put it on hold once we revisit that list next week. We currently ofer 2 formats we need to store about 6.
        • Jason: who is doing analyses on more then 3D? who has that analysis concept depends on that data structure
        • Will: Jerome.
        • Jason: The number of people doing this is fairly small
        • Chris: You have someone, who done segmentation, and have 3d volume to store.
        • J-M: Lets put it on hold. We do not send any email. We close the ticket, at in 4.4 we will make a decision.
        • Andrew: from the list stuff I had before we haven’t really looked on EM data.
        • Jason: we also needs to have good dataset and good expertise.
    • Closing sprint after meeting.

      • YES
  4. 4.3.3 Release plan

    • commit freeze is today.
    • Chris: we are just finalizing IE issues.
    • Andrew: just additional documentation issues.
    • Melissa: I do not have any pending changes to include. Everything was cherrypicked.
    • J-M: ok we need to update bioformat jar and start testing tomorrow.
    • Scott: Check with Andrew if he is available tomorrow.
    • Will: where are testing scenarios?
    • J-M: remaining to merge are LDAP PR2 and WEb PR7. once is done all is in place.
    • Tomorrow we will have RC1. Then you suppose to go through the tickets, looking for the description about how to test. TESTING ON MONDAY.
    • Chris is going to send an email when Gretzky is ready to test with appropriate links.
    • Jason: missed revision of 4.3.3 milestone page.
    • J-M: I will update it.
    • Documentation:
      • Andrew: I would like to take a snapshot then people can change live pages. The other way we can let people edit the snapshot. That is the way we did last time, but I need to change every single aliases (less convenient).
    • Andrew: I will go for easy way, Hurra!
    • J-M: Last thing to do it Download page.
    • J-M: contributors page, I just put there some of the names.
    • 4.3.3 will be extended till Tuesday afternoon.
    • There are no merge conflicts.
  5. 4.4 and OME-5

    • J-M: We need to decide what should go to milestone 5.0. We have 200 tickets already.

    • Chris: 70-80 are Melissa’s what has to be prioritize.

    • SCIFIO: white paper describing the goals to re-work Bio-Formats:

      • Jason: Marc prepared completed document and he has got very tight timescale. I sent him email that we need some time to understand. This is very good starting point
      • Melissa: Are we consider this as a fork?
      • Chris: depends on Curtis,Kevin plan and ideas. That is very nice they want to complete is quickly, but to demonstrate is possible and have all pieces is fine goal. But if we have to drop all we are doing is unrealistic. DO you know what is they plan?
      • Melissa: Mark is graduating in May, that is the timescale.
      • Jason: is there any guidance how do we/they take it forward.
      • Melissa: The project is not Mark’s idea. lets ask them for presentation, then we can consider for discussion.
      • J-M: We need at least a week to go through the document. Discussion has to go on the list, feedback on nit-pick. Suggesting 25th October for the presentation.
    • From the page 5.0 we need to move some tickets to 4.4.

    • Chris: we need to collectively decide. currently is difficult to integrate with our software because of the way we change the core. In order to have stable core , we should have general cleanup in 4.4. Then we can build on that for next 12 months and give community stable tool.

    • Andrew: there will be 4.4.x but we those will cover only bug fixes.

    • Chris: If anyone wants large/infrastructure changes it must be done 4.4.0 and this has to last for longer period of time. Changing stable core after couple of moths is pointless

    • Andrew: once this is finalize, then will be quite clear to define timescales and what we are doing and send it to the list.

  6. Email -

    • Harri Jäälinoja Re: [ome-devel] Update on OMERO and HCS - Have we got suitable sample data?
    • Andrew: Do we have any suitable data ? J-M got some Leica matrix sample.
  7. Forums -

  8. Any other business (<5 mins)

    • Light Sheet Microscopy event (14/10) Modulo Proposal to contact?
      • Jason: I think I did write Stefan and Pawel directly. It is tomorrow.
    • Mark Hiner e-mail SCIFIO white paper
      • Jason: Sent him an email.
      • J-M: As we discussed before. We need at least a week to go through the document. Discussion has to go on the list, feedback on nit-pick. Suggesting 25th October for the presentation.
    • HIC:
      • Simon: We need to discuss how do we want to plan it and potentially engage more people from the group to accomplish the tasks within the next few months.
  9. Action points:

    J-M: Suggesting 25th October for SCIFIO presentation.
    Chris: sending an email with RC1 and appropriate links when Gretzky is ready to test.
    J-M: 4.3.3 milestone page.
    Andrew: Taking a snapshot of documentation allowing people changing live pages.
    J-M: put on squige some Leica Matrix sample.
    
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