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You are here: Home Community Minutes Conference Calls 2009 2009-05-08 OME Group Conference Call

2009-05-08 OME Group Conference Call

Attending:

Agenda

  • OMERO 4.1.0

  • Paris Meeting

    • Final list of points to ask users (all submitted listed below)
      • Day 1 Presentations: General topics we want to introduce to all. This could include...
        • Publication
        • Sharing
      • Day 2 Session 1: OMERO.fs - what is important. This could include...
        • File duplication
        • Automation - importing, processing.
        • Workflow.
        • Distributed - Digs, incl. automatic backups.
        • Archiving.
      • Day 2 Session 2: Scripting - what are the core requirements to create and use scripts. This could include...
        • Core functionality - FLIM, projections, deconvolution.
        • Sharing - Script repository, citation index.
        • Deployment, infrastructure
          • IceGrid.
          • Cluster, MPI.
          • Scripting syntax, processing, and writing, including Exception handling.
        • Provenance.
      • Day 2 Session 3: Metadata/Datamodel - moving to cover new domains. This could include...
        • Other types of imaging, EM.
        • Acquisition Metadata.
      • Day 2 Session 4: Data In/ Data Out - Being more than a black hole. This could include...
        • OME-TIFF.
        • OME-XML.
        • OME-HDF.
        • Thirdparty tools.
        • Towards more complete bio-formats integration.
        • Other types of data, not image data, excel.
        • Interfaces to Bio-Formats.
        • Sharing images and metadata - how, how much, changes and edits.
  • Website

    • Plone re-installed and updated, in process of adding theme and dropdown navigation.

Notes

Extra Information

Full list of points submitted (duplicates removed)

  • What other formats should OMERO.fs target?
  • What network topologies need supported?
  • OMERO.fs as a desktop client for local watch folder?
  • What is next for OMERO.fs after Drop Box?
  • What is the wider use of distributed file system? What new areas to explore?
  • What are the initial ROI types/operations needed for analysis?
  • What are the initial scripts (algorithms) needed for analysis?
  • What are the initial analysis storage requirements?
  • What are the initial provenance (input/output) requirements for analysis?
  • Is support for clustering important for analysis?
  • What kinds of native code do developers want to interface with Bio-Formats?
  • What obstacles do developers still face in supporting OME-TIFF?
  • Feedback from anyone who's used the Beta-4 OMERO.editor
  • Discussions on future directions/features for Editor.
  • Aside from HCS, what imaging domains should we work toward supporting?
  • Is there anything preventing people from using Bio-Formats (either as a user or as a developer)?
  • Acquisition Metadata: Next phase. We need to define priority.
  • FLIM (hopefully soon): What is next?
  • Interaction with third party.
  • Are we in a position to define OME-HDF? Is it needed yet? What are key features?
  • Where should the data model & schema be moving?
  • What formats should come next in OMERO.importer? Prioritised list.
  • How do we best handle container file formats when importing?
  • Most pressing OME XML field needs for analysis metadata
  • Data Export: MPG, JPG, XLS, OME-TIFF?
  • Ideas for archiving solutions
  • How would you like to look at someone's images or dataset?
  • How much data associated with an Image would you like to share?
  • Would you like to make changes to a share, can an image in a share be edited?

Proposed FAQ questions

General

  • Which server?
  • Do you have 64 Bit support?
  • What license do you use?
  • How do I capture other information about my experiment?

File Formats

  • Can I save/convert into microscope proprietary format XXX?
  • What application can open an OME-TIFF file?

OME Server

  • Updating Bio-Formats version in OME Server?
  • What is Shoola?
  • How do I use MATLAB from the OME Server?
  • Why does the OME web interface check my browser to see if it has the adobe SVG plugin?
  • Why have you stopped development of OME Server?
  • How do I use ImageJ with OME?

OMERO

  • Why have you changed to ICE and what happened to JBOSS?
  • Do I need a server? / Why?
  • How do I use MATLAB from OMERO?
  • Manual Install versus Quick Install?
  • What metadata does OMERO read from imported files?
  • How do I install OMERO?
  • What languages are there API bindings for?
  • Why is format XXX in Bio-Formats but not in OMERO?
  • What browsers does OMERO.web support?
  • Why can I connect locally to OMERO but not remotely?
  • How do I use ImageJ with OMERO?
  • We do not use PostgresSQL - are you going to support my database?
  • How/Where is my data stored by OMERO?
  • How do I backup the OMERO server?
  • What ports are used by OMERO? (dev system and production system)
  • Can I retrieve my original file from the server? / How do I get an image back from the server?
  • My file failed to import. What do I do?
  • How do I delete XXX?
  • What are the requirements for OMERO server?
  • What log files does OMERO create? (turn logging up/down/off)
  • What client version do I need for a version X.X.X server?
  • What is the upgrade procedure if I miss a version?
  • How can I do bulk imports? (command line interface)
  • What support is provided for high content screening?
  • How do I encrypt OMERO communications?
  • I cannot login. Why?
  • How do permissions work in OMERO?
  • Does OMERO store data in OME-TIFF/OME-XML format?

Developer

  • Where can I get the source?
  • Where can I track issued and daily builds?
  • How do I build OMERO from Eclipse?
  • How do I add my own agent to OMERO.insight?
  • How do I add Structured Annotations to an object(image/project/dataset...)?

OME-XML and OME-TIFF

  • Is my OME-XML/OME-TIFF file valid?
  • What file extension should I use?
  • What other applications can read/write OME-XML/OME-TIFF?
  • You are missing a piece of metadata. How do I get it added to the
    schema?
  • Which version of the OME-XML schema is used by XXX?
  • Why is my LSID not being accepted?

Bio-Formats

  • How do I use ImageJ with Bio-Formats?
  • How do I use MATLAB with Bio-Formats?
  • Do you support XXX?
  • We have a lot of data from a home built system. Can you read it?

Questions to save for later

General

  • How do I collaborate with you?
  • How do I get support for your software?
  • Help!?

OME Server

  • Installing OME on OS X?
  • Import error in OME?
  • How do I install OME Server?
  • How do Analysis Chains work?
  • What browsers does OME Server support?
  • What is the file size limit in 32-bit OME? (2GB)
  • How do I add new users?
  • How does find spots work?
  • How do I share images between groups?
  • Can I import into the OME server using the web interface?
  • How do I use OME through Apache?

OMERO

  • The default OMERO.web is in a test configurations: How do I deploy a production version?
  • Can OMERO use our existing user accounts?
  • It crashed - help?
  • It failed to start - help?
  • Where are the bottlenecks in the system?
  • Why has setup-db failed?
  • How is an upgrade different from a clean install?
  • What permissions does OMERO need?
  • What memory does the server require?
  • How do server quotas work?
  • How do I add annotations to an object(image/project/dataset...)?
  • Why is my image so small. (Have you imported the thumbnail from the file?)
  • How can OMERO support distributed computing?
  • How do I use OMERO through Apache?
  • I have a crash/exception that occurs, how do I send a bug report?
  • Do you support heatmaps?
  • What is the maxium size supported by OMERO.importer?
  • Can you use 3D-JPEG2000 compression in OMERO?
  • Can I combine multiple files into channels?
  • How do I store my image analysis results in the server?
  • Can I edit metadata in OMERO?

Developer

  • What is Ivy?
  • How do I login to OMERO?
  • How do I run OMERO.importer from Eclipse?
  • Sample code?
  • Is there a database diagram?
  • How do I use RawPixelStore?

OME-XML and OME-TIFF

  • Support for BigTiff?
  • Support for HDF?
  • Where can I get sample date?
  • How often are new schema versions released?

Question to not include

General

OME Server

OMERO

Developer

OME-XML and OME-TIFF

Bio-Formats


Friday May 8, 2009 Meet

In Attendance: Brian, Colin, Jason, Chris, Jean-Marie, Scott, Donald, Keven, Curtis, Andrew

  • We need to do a server release to fix save/copy/paste and release after testing. We will put 4.0.3 up on nightshade for testing this weekend and plan for a next week release.
  • The Paris grant submissions are all on the sorts of topics we expect to be seeing and we don't seem to be missing any major topic.
  • Sessions:
  • does everyone think we are covering everything needed?
  • Seems OK. The list in the meeting minutes, just that, a list. Expect serious scheduling to come.
  • Some concern about having enough time for all of this
  • Andrews point is that we should use this as an opportunity to collect use cases
  • We need extra time for installs. Perhaps we should do the discussions in a round table split into sessions in the morning and afternoon.
  • Suggested schedule: Half hour for project status, 2 hours of sessions, lunch, the 2 to 4:30 for more discussions, then have further discussions at the poster session.
  • Andrew suggests using post it notes and a discussion board to collect topics for discussions.
  • Kevin suggested something similar. Break the room into one hour focus groups to work out what to discuss on day two - then on day two the discussion would include a lead biologist as well as the developers in leading the discussions. Everyone seems to like that idea.
  • What is the communities expectations for releases. How do they feel about our release cycles?
  • Jason suggests we put the FAQ up in a wall at Paris and let people add to it
  • Scott is going to collect use cases, that they do, priorities, and publication references using OMERO. More of a one on one questions meeting. Introduce him in the morning so folks know the score and can also seek him out.
  • Meet again next Friday to go over this one last time.
  • Paris schedule will be finalized on Monday so everyone can see it.
  • Plone redeployed with new themes and forums are up. All on schedule and mailing list is being worked on. Should have community pages working for Paris.
  • Will have SPW and Movies demos ready for Paris
  • Update the list with 4.0.3 release coming.
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