Agenda

• Status Report
  • OMERO.server
  • OMERO.insight
    • Status: interaction with new server
    • Directions and evolutions i.e. integrate new Annotation (not only textual working)
    • Search
  • OMERO.importer
    • New file formats?
  • OMERO.webadmin
  • Protocol Editor
    • New name??
    • Screenshots and info from NCBO
  • Scripting Engine
    • Feedback from BioImage Informatics mtg
      • Updating the data model to support "my data"
      • Integrating ITK, VDK; problem with BSD license?
    • Current design and progress
  • OMERO-FS
  • ome xml
    • TiffData - assigning a FilePath attribute
      • If you have files image1.tiff, image2.tiff image3.tiff
      • In the ome-xml in image1.tiff you can refare to ./image2.tiff and ./image3.tiff
      • Is it also ok to refer to itself as image1.tiff rather than not specify a FilePath?
    • Location of ImageRef -> move from spw to ome (anyone using this yet)
  • Website changes
    • JRS and AJP Jamboree next week
    • Links to Biosig, UCSB, and others?
  • Bio-Formats

• Beta 2.3 Notes of Interest
  • Downloads--

• The future of scientific data repositories

Notes

• server
  • search is coming along well. defining the interface
    • need short-term wish list soon
    • otherwise can make longer list for b4
  • sessions
    • coming along; tedious but should be benefitial
  • nightshade
    • some minor issues but hopefully system related
    • otherwise b2.3 trucking along
  • upgrades
    • all automated bug reports are using older version (b2.1, b2.2)
    • @automatic upgrade or @better communication of milestones
    • @email registration when they download
      • disconnect between ome-users and downloaders
    • @dialog to the user that a new version is available
    • @have server send email on upgrade
    • how
      • client connects to dundee
      • if new, dialog with need new client (and possibly server)
      • then talk to current server and see if compatible.
    • jean-marie adds a ticket
    • josh moves UpgradeCheck to OMERO

• insight
  • many changes made
  • don't have any images; need new importer
  • begin with tagging middle of next week
  • first version of UI to get it in front of the user
  • are we getting rid of category/group?
  • will need to migrate data
    • beta3?
    • issue with having two DB rows which are the same semantical concept for users
    • cat: it would be good to make the jump from a building-the-user-base PoV
    • jrs: huge number of categories (legacy data is the big problem)
    • cat sets up meetings to get feedback
    • UI for search over different types is already in place
    • will look into having "saved options" of what types one wants to search for
    • searching on pre-defined terms comes later
  • structured annotations seems to be resonating

• measurement tool
  • probably won't see anything until beta3
  • small changes from user perspective
  • should be more configurable/customizable
  • a partial rewrite; but something that can be used further
  • or may need to get tabled for beta3 w.r.t. scripting engine
  • what's preventing people from adopting omero is attachment to external tools

• importer
  • file formats. 6 of 7 tests for beta 2.4. haven't tested with latest version of code base
    • incell. difficulty of SPW
  • haven't updated omero metadata store.
  • possible to use the previous release?
  • bug fixes to all the formats since the big change
  • brian back on saturday
  • tenatively more testing with 2.4 and out by end of the month
  • otherwise, fixing bugs & efficiency

• webadmin / web-?
  • possibility of resetting enums original values
  • need to look into the algorithm, so there's no data loss
  • written some preliminary code
  • waiting on looking at carlos' code
  • needs to get started
  • getting new license to carlos to commit the file
  • carlos will contact ola when everything committed
  • use case: define a set (projects, datasets, ...) in insight (, importer, ...)
    • ask server for URL which gets sent to collaborator
    • collaborator connects with URL and is shown that set
    • josh: use omero sessions for flickr-like links
    • possibly something that doesn't exist in our current permissions model
      • request coming from tech-agnostic users. just want it.
      • need to define what we can do now, and what later
  • see blitzconnector.py

1. beta 3 is looking around first of may after user testing, etc.

• protocol editor
  • no response on email re: new name
  • feedback from michael
  • integrated with phenote
  • need a new movie
  • will add links to screenshots

• scripting engine
  • bioimage informatics mtg
    • good mtg.
    • model to support "my data"
      • flexibility again
      • what can we support?
      • what can we make easy?
    • structured annotations for analysis was welcomed
    • "matlab!"
    • ITK/VTK~ bsd license. will discuss later
  • donald
    • 2 things
      • scripting engine
        • integrated into the server
      • matlab
        • allowing people to connect to server from matlab
    • first blast of the projection script
    • writing matlab blitz interface & gateway
    • to test: need an updated importer
    • getting something to these developers, a way in.
    • hard parts
      • guis
      • matlab as server

• colin
  • needs to get an idea about interfaces
  • what should the omero.fs server expect and pump out
  • currently is kicked off my server saying (directory, include, exclude)
  • will then send back events saying: ok, X files done done
  • colin: will send emails to work things out

• jrs: what does everyone need to make this easier?
  • documentation on the python side?
  • sufficient to have carlos' work visible?
  • colin: need something more

• OME-XML
  • completing tickets
  • some things need to discuss with people
    • "recursive link": image1.tiff refers to itself as ./image1.tiff
      • makes logic more generic
    • SPW
      • moving ImageRef definition between files
      • easy to do as long as no one is using it
      • jason: don't know, but apparently cellomics says OME-compliant
        • have to act assuming someone is using and go through the proper revision process
  • renaming release to february
  • @andrew sends a logical view of SPW to josh

• website
  • any feedback?
  • none. good!
  • carlos can help with plone
  • jason and andrew reviewing all of web documentation
  • migrating tiki->trac: Add "THIS PAGE HAS MOVED" links
  • ...and we should start cross-linking our image-informatics efforts

• downloads
  • 60 downloads this month

• storing on google

• paris
  • tentative: april 29/30th ?
  • room better for communicator
  • starting to use omero in mid-february with a rollout to super users

• moving day?
  • not yet

• mtg. in two weeks
  • jason giving talk on 8th.
  • let's have a ticket day
  • or later on the 22nd?

Action

• upgrade check for clients
• setup user sessions re: tags/category groups