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
-
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 - 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
-
Should others look at it?
-
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
-
2010/06 to Feb 2008 version: Current transform ditches most data, needs better transform (complete conversion)
-
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
-
Chris: Noticed no objective on the list of 'needed improvements'?
-
Lots of things not appropriate for some detector types, needs to be split up into types
-
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
-
Chris: For this, more of a documentation issue then modelling. Telling folks how to save out their data
-
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.
-
Josh: Gonna need to have other files added in (not just binary blob) ex pdfs, hdf5. Need original file holder for this
-
Ticket for model orginal file in model. Not sure what this is for.
-
Big images:
-
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)
-
On hold for detector object changes
-
FLIM/SPIM:
-
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
-
Have a plan, not implemented
-
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
-
One suggestion is to have units on everything (with additional atribs)
-
N-Dim:
-
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
-
List of changes from Cailin's work (see long list from presentation)
-
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
-
Jason: Maybe ROI? Chris: Could make changes here
-
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
-
alignment issues, discrepancies. primarily requires code changes across the code-base
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