2011-03-29 Tuesday Meeting

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

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)

Accepting minutes from last meeting
Matters Arising (<10 mins)
- Andrew: Book another meeting with Jerome Thursday next week - mail sent
- Andrew: Add new page for job posting - waiting on HR job page to go live
- Jason: job postings to various mailing lists - waiting on HR job page to go live
- Brian: Get some sample data to Jerome (esp. HCS) (PENDING)
  - Jason: Can put it up on users.
  - JMB: Need to send him some smaller ones
  - Jason: ACTION Point out useful data for Brian to send
- Will: Send Jerome docs on Editor + create ticket (DONE #4802)
- Scott: get screenshots from Mike's app DONE (J-M has screenshots and code)
- Scott: Code sample snipets from michael's code added to an 'examples' page for Jerome DONE (J-M has screenshots and code)
- Scott: Send Brian updates for testing scenarios (In Progress Ticket created #4811 )
- Chris: emdb.ome.org needs to be set up! (WORKS EXTENNALLY). Set up for internal page for this
- Team: Find tickets without owner to assign (4373)
  - 4373 "New Gateway" wiki page (DONE)
- Team: Tickets that have been around for awhile (3838, 3976, 3989, 4289)
  - 3838 openmicroscopy.org should say "GPL or commercial license available" - DONE
  - 3976 Extensions to "user data" landing page
  - 3989 Rendering definition lookup methods
  - 4289 ThumbnailService: Storing Thumbnails for bigImages
- Team: Fix timing on tickets (Carlos, Will, Andrew, Brian)
  - Carlos
  - Will - DONE
  - Andrew - DONE
  - Brian - DONE
- Team: Tickets without owner/time (4579, 4578, 4304)
  - 4579 Hudson jobs link - DONE
  - 4578 Link to svn code - DONE
  - 4304 SCM: Investigate adding gitweb links to all commits
- Team: Testing for this next sprint
  - Scott/Will: Insight import (In progress)
  - Will: Viewing ROIs on the web can be tested now (add test process to testing page - DONE)
  - Scott: Right hand panel in web client should be ready for testing (DONE ticket created #4780 )
  - Will: Some scripts for testing
- Colin: Does Re: [ome-users] OMERO with iRODS? need reply? DONE
- Chris: Pick up forum messages from Josh (see meeting notes)
- JMB: Create tickets for QA (see above) DONE
- Brian: Close web QAs and ticket them DONE
- Scott: Ticket created for Crieff Notes/outcomes (#4814) OME team will be CC in.
OME Data Model - What next? : Andrew's presentation (30 mins)
Any other business (<5 mins)

Notes

In Attendance

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

Notes

Accepting minutes from last meeting
- Accepted
Matters Arising (<10 mins)
- Andrew: Book another meeting with Jerome Thursday next week - mail sent
- Andrew: Add new page for job posting - waiting on HR job page to go live
- Jason: job postings to various mailing lists - waiting on HR job page to go live
- Brian: Get some sample data to Jerome (esp. HCS) (PENDING)
  - Jason: Can put it up on users.
  - JMB: Need to send him some smaller ones
  - Jason: ACTION Point out useful data for Brian to send
  - Brian: Michael is looking into his data for something.
  - Chris: Paul's data is probably not usable
  - Will: Can point Jerome's users to Gretzki
  - Jean-Marie: Make some screen shots (Will will do this)
- Will: Send Jerome docs on Editor + create ticket (DONE #4802)
- Scott: get screenshots from Mike's app DONE (J-M has screenshots and code)
- Scott: Code sample snipets from michael's code added to an 'examples' page for Jerome DONE (J-M has screenshots and code)
- Scott: Send Brian updates for testing scenarios (In Progress Ticket created #4811 )
- Chris: emdb.ome.org needs to be set up! (WORKS EXTENNALLY). Set up for internal page for this
- Team: Find tickets without owner to assign (4373)
  - 4373 "New Gateway" wiki page (DONE)
    - Chris: Know how to change this now but not going to hack it - just have to remember to change
- Team: Tickets that have been around for awhile (3838, 3976, 3989, 4289)
  - 3838 openmicroscopy.org should say "GPL or commercial license available" - DONE
  - 3976 Extensions to "user data" landing page
  - 3989 Rendering definition lookup methods
  - 4289 ThumbnailService: Storing Thumbnails for bigImages
- Team: Fix timing on tickets (Carlos, Will, Andrew, Brian)
  - Carlos - DONE
  - Will - DONE
  - Andrew - DONE
  - Brian - DONE
- Team: Tickets without owner/time (4579, 4578, 4304)
  - 4579 Hudson jobs link - DONE (NEEDS TO BE CLOSED WAS OPEN)
  - 4578 Link to svn code - REOPENED
    - Any links to revision numbers need to be found: rXYZ, [XYZ], source:trunk/components/..., ...
    - Goal: list all wiki pages with WikiLinks to svn
  - 4304 SCM: Investigate adding gitweb links to all commits PUSHED
    - see http://git.openmicroscopy.org
    - Shows all tags, branches, etc faster than trac.
    - But we should put links to this from o.org/ documentation
- Team: Testing for this next sprint
  - Scott/Will: Insight import (In progress)
  - Will: Viewing ROIs on the web can be tested now (add test process to testing page - DONE)
    - Should others look at it?
      - Will: Short scenario has been added
  - Scott: Right hand panel in web client should be ready for testing (DONE ticket created #4780 )
    - Scott: Discussion with Brian/Will about web testing scenarios
    - Some aren't available in the web. Mark them, then it's clear where they diverge.
  - Will: Some scripts for testing
    - Will: A bit early in the process - leaving this for now
- Colin: Does Re: [ome-users] OMERO with iRODS? need reply? DONE
- Chris: Pick up forum messages from Josh (see meeting notes) PENDING
- JMB: Create tickets for QA (see above) DONE
- Brian: Close web QAs and ticket them DONE
- Scott: Ticket created for Crieff Notes/outcomes (#4814) OME team will be CC in.
  - Scott: Working on this
  - JMB: Put up the material asap please
  - Scott: One user really liked the videos!
OME Data Model - What's next? : Andrew's presentation (30 mins)
- alignment issues, discrepancies. primarily requires code changes across the code-base
  - bio-formats: primarily licensing
  - creator: our code will have to start filling it out.
    - Josh: Do we have a ticket/samples? Andrew: Not yet
    - Josh: Should get that before going through all these changes
  - Andrew: Bit of a problem with names being optional(not optional?) in SPW. Needs alignment to model
- Improvements
  - Lots of things not appropriate for some detector types, needs to be split up into types
    - Jason: Good reason to do this for representing new semi-conductor materials, pmts, diversity is growing
    - Will: Should we wait then to do this? Jason: Always going to need updating, ongoing issue
    - Chris: Strategy, on all-singing-dancing object, or special objects?
      - Andrew: Its harder with one one objects to specify contraints
  - Light Source:
    - big issue is multiple light sources need supporting
    - Not all have same illumination path - this is a pain
    - Chris: Decision was to avoid path order, just list things
  - ROI:
    - Tweaking how fonts are changed, some other minor tweaks
    - Linkage of ROI (related to linking images as well)
    - Shape points are defined different between model and db. *Needs reworking to use vertex array (might get rolled into one ticket for this)
      - Did propose to community, no reply so will have to decide
  - Images:
    - Linkages. Done once, can use this above for ROIs
  - Instrument:
    - Field rotation (e.g. zebrafish orientation) and pinhole spacing needed
    - Pinhole: not one value - complicated object
      - Will: Like Arry Disk? Andrew: yes, meaningless without specific setup
  - Legacy:
    - 2010/06 to Feb 2008 version: Current transform ditches most data, needs better transform (complete conversion)
      - Chris: Do we have stylesheet already? Andrew: Yes but basic (strips most data)
      - Also have tickets for command-line tools
      - Also chaining transforms now to go from one to another in some cases currently
  - Objective:
    - Chris: Noticed no objective on the list of 'needed improvements'?
      - Andrew: Either on the spim ticket or we don't have a ticket for this - will check
- Simple Additions
  - Big images:
    - Chris: For this, more of a documentation issue then modelling. Telling folks how to save out their data
      - Not a bit point to backporting this to XML (not being done much now)
      - Andrew: We do have a suggested tile image layout, maybe use similar for big images
  - Original File:
    - Ticket for model orginal file in model. Not sure what this is for.
      - Josh: Gonna need to have other files added in (not just binary blob) ex pdfs, hdf5. Need original file holder for this
        
        Chris: Should be called something like attachment in schema for this
        
        Andrew: File annotation or binary file object already for this?
        
        Josh: Close to this, binary file is off in its own little world though
        
        Josh: Binary file has to 'almost' become a top level object to do this
        
        Andrew: In that case would like to use something else thens
        
        Chris: Is there two versions of binary file? Not sure
        
        Josh: one example of the goal is:
        
        import image
        
        attach PDF to it
        
        export the image in a zip, and it points to the PDF (relatively?)
        
        when that gets imported, the PDF is attached to the image appropriately.
- New Pastures
  - FLIM/SPIM:
    - Andrew: Hacked solution for FLIM/SPIM. Really need n-dim
    - Not much more can be done till n-dim ready
    - Chris: What's the current status, Jason? * Jason: Not sure on this, probably should follow up * Jason: Zeiss is doing a SPIM microscope, would be good to know what they are doing * Jason: Annual SPIM meeting is Sept/France. Interesting to see * Jason: Getting something from Gunter and implementing a SPIM-compitent file from ImageJ would be good * Chris: All encompassing changes to make this work * Jason: SPIM will cause FS issues. Should solve FS problem before n-dim problem
  - X-Ray/EM:
    - On hold for detector object changes
      - Jason: Worth looking at x-ray detectors and adding them (and 'light' source)
      - Chris: "IlluminationSource" a better term?
    - Will: Trying to follow the model in light microscopy, a lot of this is in the instrument
    - JMB: Some adjsutment to display needed here (over model)
- Big Changes
  - N-Dim:
    - Have a plan, not implemented
      - Create schema, generate tests, read by viewer to check data
      - Chris: Fall at the earliest for this
      - Will: Replaces or lays on top of current dimentions?
        
        Chris/Andrew: Keeping XYZ in wrapper functions, underlying is done differently
    - Jason: Would be good to have some concrete test samples for this
      - Andrew: we've looked at FLIM & SPIM, this is a generic solution
      - Jason: Still need some concrete examples to test this - needs planning
  - Units:
    - One suggestion is to have units on everything (with additional atribs)
      - Andrew: Massive change to DB
      - JMB: Satisify a lot of users with this
      - Will: only really a small set of places where we want to configure this? Will: Can we make everything else a parsible value in the schema? Josh: Have to be careful that we don't run out of bits for way out values then * Andrew: We did recently go through and check all the ranges recently * Andrew: don't want people editing these values in the XML and breaking 'fixed' values though * Jason: Needs some thought, lets work this out over the next few weeks
- Repository (previously Library)
  - List of changes from Cailin's work (see long list from presentation)
    - Andrew: previously these were listed as "Future"
    - Chris: some of this has arisen with respect to ASCB celllibrary
      - e.g. creationDate of film from 25 years ago
    - Andrew: Experimental conditions and remove experimenter was one suggestion we got
    - Chris: for publishers, creation date is publication date
    - Josh: Have or more of these are standardized somewhere (cF. Dublin Core)
      - may be possible to have a block of XML that is pre-defined from someone else's schema
      - Andrew: some of this has no specifications, will have to make up
- Top Things to Look at Next
  - JMB: Small things, Detector, Illumination Source
  - JMB: At the ROI level, minor things addressed
  - Chris: Realistically for 4.3 can we do anything here but small beasts?
    - Jason: Maybe ROI? Chris: Could make changes here
      - Andrew: Three things for this
      - JMB: Some of it done already, first need to align what we have in client to model
      - Chris: If we don't make changes to DB now, won't have time before 4.3.
        
        JMB: Listed in ticket already but need to be done
        
        Jason: Need review and concrete proposal for changes, impact
        
        Jason: Look at things like splitting detector to change structure in prep for later detector types
        
        Can this be done without a massive amount of work? Would be nice to lay groundwork if we can
  - Chris: Will have to go through small fries and assess each one to determine what must be done for 4.3
    - Andrew: Filer change is purely schema and can probably go in
Any other business (<5 mins)
- No other business

Action Items

* Will: Screenshots of HCS data to Jerome
* Team: ("Tickets that have been around for awhile", ...)
    * Chris: 3976 Extensions to "user data" landing page
    * Chris: 3989 Rendering definition lookup methods
    * 4289 ThumbnailService: Storing Thumbnails for bigImages
    * 4578 Links to svn code
* Chris: forum messages
* Scott: Working on Crieff Notes/Outsomes. Could be someone to follow up with
* Andrew: by end of week, list of 4.3 model suggestions
* Andrew: schedule a longer term discussion
* Andrew: Check spim ticket for objective (or add new ticket)
* Andrew: follow up on the SPIM status
* Andrew: make tickets for proposals (Creator, OriginalFile, etc.)
* Andrew: tickets for getting more NDIM examples, data, sites
* Andrew: Need ROI review, concrete proposal, and impact assessment