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2010-03-09 Tuesday Meeting

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

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 - No actions for today

  3. File System: Jean-Marie & Colin's presentation (45 mins)

  4. AOCB (<5 mins)

    • Microscopy Image Analysis for Biomedical Applications - One Day BMVA technical meeting in London, UK, on 21st April 2010

Notes

  • Accepting minutes: nothing for today (all for Thurs.)

  • Matters arising

    • Permissions testing phase II
      • Will sent feedback
      • @Jean-Marie and Ola need to synchronize some insight/web issues
      • also need to gather various things which are disallowed (usability)
      • and then integrate that into security system
    • thumbnail overhaul
      • Chris: important to try wacky things
      • "go to someone else's image"
      • goal: make sure you don't get someone else's views
      • @everyone will need to import data into mage
      • @look out for issues in BOTH web and insight
      • Which importer build to use? (Jason)
        • No changes made. You will always get your default group.
        • Or you can import from Insight. DON'T
        • But not from OS X .... BUG!
      • @Brian makes a QA build
    • Warlock / HCS_PREVIEW
      • Preview build is crashing
      • Downloaded from download page
      • Linked version seems to be broken.
      • @Fix Hcs preview page
    • ticket:1855 (4.1) - session timeouts
      • @send an email to ome-devel
      • Josh will commit to trunk for testing.
    • FAQ
      • @Should be done by Thursday

  • Demo server statistics (Ola)

    • no real feedback from any of the demo users
    • ~300 images. mostly OIF and tiff. also jpeg, lsm, ...
    • mostly PD, some few screens
    • opinion: mostly looks like people are testing import
      • some examples of import failing
      • @How many bugs came from demo accounts?
    • Jean-Marie: would be interesting to ask what people are importing
    • Chris: maybe they aren't sending feedback?
    • @Could we get the list of terms? (possibly pre-defined values)
      • Ola: mostly "test", "test1", ...
    • 36 accounts. 12 imported something. (excl. our & KIT accounts)
    • Chris: can we find why 2/3 didn't import? cF. logging in.
      • Jason: do we then offer to get some data in for them
      • Ola: shouldn't be so hard to send an email

  • NB: be sure to update the agenda if you want to talk so external folks know

  • OMERO.fs status

    • user acceptance: users are familiar with their file system; makes life simpler for them
    • fs returns which images are import candidates
    • local filesystem? no, it's the server file system
    • an image gets registered with the server as soon as you try to say something (happens automatically)
    • thumbnails generated on the fly for the files which are relevant to you (even when unregistered)
      • No settings interaction with the generated thumbnails
      • The thumbnails get generated for use later
    • Josh: @we'll need to decide how to handle the same hierarchy for multiple users / groups
    • Jean-Marie: needs to be as smooth as possible
    • Colin: repository is a public API
      • can only view into the repository
      • currently registering importable files as "Image" and other as OriginalFile.
      • How much information needs to go into the OriginalFile to be useful for the user?
    • Very crude thumbnail holding system
      • cached on local filesystem
      • Nothing pre-emptive; directory with 1000 files could take a file
    • format
      • need is to do OS-based "Open with ..." functionality
      • currently using mimetype (everything octet-stream)
    • next phase
      • address issue of files with multiple parts (LIF)
      • deregistering objects
    • @adjustment to importer to pass the original file id for linking
    • @adjustment to server for better identifying files which have been registered as file and/or image
    • How much should we associate with the image without a full import?
      • Chris: perhaps we can start with metadata only imports (performance?)
    • future API
      • methods exist for getting existing services. should we use them?
      • file services necessary -- copy/rename files, etc?
      • where does monitoring come into play? (watching for moves/deletes/etc.)
    • biggest problem is non-UNIQUE for original file
      • Josh: plan is along the lines of UNIQUE (path, repo_url, group_id)
    • Jean-Marie: would like to get to the point of importing data for Paris
      • But likely don't want to do this work for May release
      • Need to handle security issues
      • Still a long way to go, but we can go to Paris with a good list of questions
    • User wants it all (Jason)
      • easy, movable, see what I want
      • Balancing act: when is an image in OMERO and when isn't it
      • Overriding issue: we've worked through server-fs visible, but data duplication isn't solved
      • Chris: data duplication is easy to solve
        • once this interaction (exchange of files, registration, display etc.) is settled
        • the rest is done (bioformats can already read from the fs)
        • Jean-Marie: adjustments that you get data at a reasonable speed
        • Jason: suspect the thing to do is go after the data dupe solution * i.e. focus on the partial (metadata-only) import * while keeping caveats in mind * Chris: warning for sysadmins (ldap, fs, etc.) * Chris: will soon start reviewing bioformats for getting access to binary data with metadata
    • Thumbnail location
      • local v. remote
      • using extended attributes for recognizing files

  • BMVA (21.Apr)

    • OME has been invited to present
    • we've missed several other invitations
    • @Jason will respond, confirm, and say contact Donald (abstract end of this week)

  • Tickets

    • Update the workplan pages. Bring deviations to everyone's attention
    • Some work to do for FLIM ("Flim integration"). Assigned to iteration. Positive feedback.
      • Curve fitting time may go up to 20 minutes. @Discuss with David
      • @Donald moves Flim work to requirement, and links in Stories and Tasks
    • NDim workplan page is linked off the roadmap page
    • NoSQL meeting
      • interacting with compsci community
      • keeping an eye open for what's going
      • what else would be interesting? (DB, OpenGL, Java, ...)

Action Items

 * Jean-Marie & Ola: synchronize some of the permission insight/web issues
 * Everyone: import data into mage, then look for issues in BOTH web and insight
 * Brian: make a QA build of the importer for everyone to use
 * Someone: Fix the HCS preview page (Josh? Andrew? Chris?)
 * Josh: Send an email to ome-devel re: ticket #1855 (session timeouts)
 * Everyone: ALL FAQ QAs should be done by Thursday
 * Ola: follow up with demo users about what they were doing (why were they creating lots of empty containers). Find out how many bugs were generated from demo users.
 * Ola: Check the sessions table to see how many of the demo users actually logged in.
 * Chris/Brian: adjust the importer to pass original file id for linking
 * Josh: organizes a discussion on ofiles [UNIQUENESS(https://trac.openmicroscopy.org.uk/omero/ticket/1753)
 * Josh: we'll need to decide how to handle the same hierarchy for multiple users / groups
 * Jason: respond/confirm presentation for Donald @ BMVA 
 * Everyone: Update your workplan pages for anything new and let folks know
 * Donald: move FLIM work to requirements and link in stories and taks
 * Everyone: Any suggestions for NDim workplan please let Donald know
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