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February 2007 Dundee Team Meeting

Items for Discussion and Resolution

Introduction-- why are we doing this

This meeting is to define activities for the OMERO and Usable Image teams over 2007. With the release of OMERO3-Beta1, we want to leverage the foundation we have built to provide a commonly used image data platform. Meeting will be all day Feb 7, in WTBM Meeting Room.

At this meeting, we will:

  • define major functionality and management goals for 2007
  • define how Usable Image will continue to drive forward functionality provision
  • develop a draft set of milestones and stories
  • re-initiate the Cycle-based development process

There are two sections below-- what we listed as critical in november that we (as far as I can tell) didn't do, and some ideas for 2007. There is certainly alot here Please add/update/comment etc.

OMERO functionality (from Beta1 list)

Items that were on the list that, as far as I can tell, were tabled, not done etc. need to be tix for beta2, RC1, or whatever, or just agreed to be de-listed.

Developer list

  • displaying the remaining free disk space (Jean-Marie)
  • sanity check the server from the admin tool (Donald)
  • Test server/client build with Derby/HSQLdB and VM bundle for turnkey solution (Chris)
    • If we offer this, how do we handle database migration

Other functionality

  • release strategy statement. Who its being released too, etc. (Jason)
  • community page / forums for feedback
  • Customer support: Buy server. PHPBB, etc.
  • icons, branding, etc. Naming, release numbering, etc.

Usable Image

These are in fact large stories, and not really broken into individual tix/tasks.
  • Help System (PF/DS/BL)
  • Paper Prototyping Workshop (DS/PF)
  • Video output and upload (General populate UI website) (Catriona)
  • Use Case writing (and gather and reformat OMERO UCs: NB consider where to store this stuff) (David)
  • Scenario writing & workflow mapping (Catriona)
  • Persona writing (Paula)

Major functionality for OMERO 2007

OME Data Model Updates

  • Transfer OME-XML Evolution to XML, database models (uml)
  • OME-XML, OME-TIFF validators
  • OMERO Data Model updates to support analytic types in OME Server
  • SVN control


  • Identify 5 formats from Bio-formats that are easiest and most important to support and get them in
  • PDI Updates
  • Resolution of importer/insight separation
  • Server-side import, including upload from client.

Data Export

  • Original Files
  • OME-TIFF (implies OME-XML)
  • Download of binary objects from DB (to support structured annotations, so still very crudely defined)

Data Migration

  • Backing up and restoring a database
  • Moving from one DB (e.g. hsqldb) to another (psql)
  • Moving from one vesion (Beta1) to another (RC1) !!
    • Vital to be able to change the DB (Add ProjectAnnotations, e.g.)


  • allow input window out of range for images with same pixel type.
  • Compression for reduced bandwidth requirements
  • Projection (to be stored as new Pixels?)
  • .mov, .avi, .jpg, .png-- store in DB, deliver to client
  • support for defined ROIs of Pixel data (to support client measurements?)


  • ICE, for better client support
  • Easier mapping of data model updates (as UML) to Hibernate, pojos, etc. See EmfAsDsl
  • Lucene, Compass for indexing
  • Save, delete objects linked to PDI, CG/C/I
  • Model Validation (Currently a significant percentage (20-30%) of the model UML is NOT implemented in the server. These are constraints that don't take place at the SQL level and need code. This could possibly go hand-in-hand with Josiah's idea of various spec-levels. (Josh) )
  • Batch operations: supporting HiViewer multi-selection, to include annotations, cascading deletes, processing, etc Might have to reverse this concept, making a separate service that is batch manager, client of server. This needs some study.


  • Server-side related: Permissions strategy
  • Components-- move to new environment?
  • Given the functionality we want to add in 2007, is Java the right environment? (Obviously, this is the wrong question-- maybe the right question is, how do we support a plethora of clients tools under a single umbrella?)
  • Viewer
    • 3D viewing
    • Annotation of 5DROIs
  • HiViewer-- multi-selection and Actions/"Do Its" so that a selection and be sent for batch operations
  • HiViewer/DataManager-- rationalization of functions for finding, querying-- what is the portal for metadata query?
  • Major expansion of metadata viewing, editing, querying; must define how to show all, but layer so most important is easy to get to.
  • Analysis Functions
    • Distance measurements
    • Intensity measurements in defined UIs
    • Save as object (probably CSV file) linked to Pixels
    • CellProfiler Plug-in


  • OME Registry-- log for all "up" OMERO (and OME?) servers
  • Bug reporting for OMERO

Usable Image

  • Update of website and vision
  • Definition of metadata usage (CRITICAL!).
  • Output from PP workshop
  • ????

Draft Programme (please make comments etc as necessary)

09:00Coffee, setup, gossip
09:30Summary of StatusJason, Catriona
09:45Major OMERO goalsChris, Josh(via skype)ICE, Data Model, Data migration, Docs (admin guide,...)
11:00Major Client GoalsCatriona, Jean-MarieHow do we use the UI/OMERO process to drive this functionality??
15:30Tickets on trac, Notes on Tiki, Docs on UsableImage
17:30Wrap up

February 7th, 2007 OMERO Roadmapping Meeting

  • In Attendance:

    • Jason, Brian, Josh, David, Chris, Jean-Marie, Donald, Paula, Catriona, Andrew, Xinyi

Meeting Notes

  • Could this be our new tagline?
    • "Easy, Quick, and what you never imagined."

  • Opening discussion about UI functionality for the client
    • Need to redesign the hierarchy structure to either expose it better or remove some of the rigidness of the system (especially the many-to-many model)
    • Decide on what the core elements of the application suite is and expose those elements better
    • Decrease complexity of the UI
    • Decide how to integrate other activities (like lab book)
    • Generating new ideas about what the scientists can do
    • Improve the ability to Collaborate
    • Need to make the underlying work practice more transparent and less rigid.
    • Window Mgmt.
    • Batching
    • What's the core client? View, annotate, modify...
    • Underlying work practice. Doesn't suit. More transparent, less rigid.
      • Hierarchical approach.
      • Don't expose the flexibility of the data model
      • Especially the many-to-many model.
        • Posit: Structure is going to support this. It's about the clients.
        • Because: "What does this thing do?"

  • Had a discussion about the flexibility of the current data model
    • How easy it is for "some other guy" to add and change the data model to fix his needs.
    • Talked about the model levels concept (level 0, level 1, level 2) specifications. This needs to be addressed soon.
    • Need to adjust the server to manage model validation and build a "business model" for the system.
    • Need to start compartmentalizing the components used in the server and clients more so they can be shared by various applications as well as internally (such as 3 rendering services running under one roof)
    • automated process.
    • Not just some spec.
    • Providing support for DataModel changes.
    • Support for legacy. Versioning.
    • Minimal Set of Information

  • Server
    • Currently don't deal well with thumbnails. (multiple num/size)
    • Setting window settings on multiple images.
    • Performance and overhead. Compressing can be a bad idea.
      • Client needs to be more intelligent about its connection type.
    • IO Services : are very conservative. (re: garbage collection)
    • ICE : collaborative working environment (one-way communication)
    • Temporary objects (scratch space)
    • Data Model :
    • Interoperability. (Ilya)
    • Need to get over 4yr. hump of non-delete.
    • Component model. (Will ICE need a new one; doesn't work well with JavaEE)

  • Analysi results
    • ROI5D : is it the proper model?
    • Attaching binary files (pdf,xls) to db objects
    • Possibly local only
    • Questions
      • How does Donald get the regions from the db?
      • What do users /want/ to attach?

  • Import
    • Is server-side & gui. What's shared? What's in OMERO.insight?
    • Multi-Tiffs almost fixed.
    • New field on Pixels, etc. to know what's supported.
    • GUI for saying what metadata gets stored (like OME Notebook)
    • Test cases in BioFormats
    • Unify the repositories of test images.

  • Insight
    • Need to decide on how permissions works. Admin functionality
    • Need to fix how groups work in the admin tool
    • We need to improve the way we interact with the permissions data model - too complexed right now
    • Moving forward with Java.
      • We need to canvas our user base and get a better feel for our requirements.
      • Look at moving to Java 1.6 functionality - we need to start experimenting with it now!
      • Should we start prototyping and exploring Java 1.6 functionality now?
      • 1.5 is currently adopted as our 'official' lowest common denominator.
    • Need to look UI design / programming tools.
    • Need to decide on the "top 5 items" to search and add functionality to support that.
    • How do we handle users preferences?

  • Looking at our Resources
    • Web Presence
      • Internal Documentation
      • External Documentation
        • All of our guides, etc, should be on the "main website", and presented in a format that is clean and user friendly.
        • Change the menu to not make it so "OME server" centric
        • Integrate OME stuff from Usable Image into the OME site with ample links to the "UI site"
      • Data Model
        • Model on the website is out of date needs to be updated
        • Model on the website needs to be updated to reflect general OME-XML and not OME server specific
        • Add an OME Data model section to the main website NOTE: Tell folks what is the difference between beta / release candidate / and final release - put this explanation on the website
      • Releases, Roadmaps
      • The Website
    • UI/OMERO
      • Cat recommends a quarterly release meeting
      • Really need to do a demo site / scripting "15 minute" web-demo, etc
      • PI's: Funding
    • What are our rough milestones? What goes in:
      • Beta 2?
      • RC Series?
      • Final Release?
      • Office Space?!?!?!

  • The Image Workflow
    • This represents the minimum set of functionality we need to support in the client for final release:
      • Microscope
      • Storage
      • Deconvolve
      • Maximum Intensity Project
      • Export TIFF
      • SUM the intensity inside some ROI
      • Measure the distance between two points
      • include: data management, organization, visualization tools
      • Now we should prototype this process with the Usable Image group!!

  • Meetings:
    • Trac: 12:30 Every seconds Friday
    • OMERO: 3:45 Every other Thursday

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