2009-05-08 OME Group Conference Call
Attending:
Agenda
OMERO 4.1.0
Paris Meeting
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Final list of points to ask users (all submitted listed below)
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Day 1 Presentations: General topics we want to introduce to all. This could include...
- Publication
- Sharing
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Day 2 Session 1: OMERO.fs - what is important. This could include...
- File duplication
- Automation - importing, processing.
- Workflow.
- Distributed - Digs, incl. automatic backups.
- Archiving.
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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.
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Deployment, infrastructure
- IceGrid.
- Cluster, MPI.
- Scripting syntax, processing, and writing, including Exception handling.
- Provenance.
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Day 2 Session 3: Metadata/Datamodel - moving to cover new domains. This could include...
- Other types of imaging, EM.
- Acquisition Metadata.
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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.
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Day 1 Presentations: General topics we want to introduce to all. This could include...
-
Final list of points to ask users (all submitted listed below)
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?
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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.