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April 2006 Developers Meeting

Developers Meeting hosted by LOCI in Madison, Wisconsin.

2006 Developers Meeting


Meeting will be hosted by the LOCI group. Location is on campus of University of Wisconsin, Madison. The meeting sites are Room 274 Animal Sciences (at LOCI lab) at 1675 Observatory Drive (on April 21st) and the Penthouse of Bock Labs at 1525 Linden Drive (on April 22nd, 23rd, and 24th). To get to Bocklabs Penthouse, take elevators up to top floor (eighth) and then make a left and go up stairwell to penthouse. Maps of campus are here: [old-link] campus map, Google map


Dates are Friday April 21st through Monday April 24th. See Agenda for detailed schedule for these days.


Dundee, MIT, NIH, LOCI and other OME developers and users.

Travel Info

Most people are staying at Best Western InnTower which is at old University Ave. To get to campus just make a left onto old university ave and follow into campus. To get to the meeting locations it is recommended to cross at the people bridge from old university ave over university ave. This ends right at babcock and linded dirve. Animal Sciences is directly across with Bock labs down the street. Kevin will meet Best Western folks on Friday morning.

2006 Meeting Topics

Talk about an invitation for a flame war!!!! Ok, team, here's where we will nail down what we want to do, accomplish etc.

Ready, steady, Gooooooooooooo!

Key issues for the LOCI group

  • Status of OMERO and timetable
    • in particular status of OMERO's remote framework and support for regions of interest. It would be useful to also briefly verify that our intended use cases are going to be supported.

  • Current and future status of OME XML (and OME-TIFF)
    • This is a very important topic to us. We want to maintain compatibility while ensuring the format works well with OMERO. We may also want to present a list of metadata fields that do not currently fit into the specification.

  • Commercial adoption of OME-TIFF?
    • We have some concern that the status of OME-XML is not polished enough to push for this kind of thing. However there is significant demand from the community for a universal format and OME-XML/OME-TIFF has clear potential to fit this need.

  • Bio-Formats Package
    • Discuss and decide whether OME wants to utilize this package for OMERO.

  • OME Core Grant and key things we want in the grant such as XML gatekeeper

  • the OME Company and possible STTR

LOCI topics

VisBio presentation (Friday April 21, 11:45 - 12:15):
  • Current work is on performance issues (mostly memory with some CPU)
  • File format support from VisAD broken into separate Bio-Formats package
  • No recent work on OME integration (though [old-link ] OME plugin for ImageJ has been brought up-to-date with OME CVS)
  • Eventual goals:
    • Better OME data browser within VisBio
    • Iterative overlay (ROI5D) editing and storage in DB
    • Storage of spectral/lifetime data (both raw and processed) into DB

OME-TIFF & OME-XML (Saturday April 22, 2:45 - 3:30):
  • Verify the OME-TIFF specification is acceptable to all (final verification that TiffData tag suits all needs)
  • Inquire about [old-link ] LOCI OME-XML library (OME-XML parsing code, autogenerated from the package and OME SemanticType definitions):
    • Is it useful?
    • What should be added?
    • Should it be included with OME-JAVA?
    • What other OME-XML-related functionality would help encourage widespread adoption?
  • Discuss enhancements to OME-XML — see OME-XML Evolution page

Bio-Formats (Saturday April 22, 2:45 - 3:30):
  • Can provide a standard classification of metadata from proprietary formats into OME-XML
  • How can it be used for core OME 3.0 file format support?
  • Settle on standard format for pixels:
    • Abandon use of BufferedImages in API
    • byte[][] is nice for fast Java3D, but is more complicated for >8 bit depth
    • Handling RGB vs multi-channel "grayscale" image planes in the API
  • Any other issues holding us back from using it on the server side?

OME Developer Meeting Schedule

April 21-24, 2006; Univ of Wisconsin, Madison, WI, USA

Some Rules:

  • Sorry, but we will have to be a bit strict on mealtimes etc-- 2 hr lunches etc are out. We have alot to do, and alot of people with limited time. Also, we are trying to put reasonable amounts of discussion time into schedule. We are still working on this, but we will probably order food in.

  • We have a large amount to get through, so we will need to keep discussion focussed. Note we have time to discuss most issues throughout the 3 days. But long diatribes, and discussing plans for future when we are doing current status (for instance) must be supressed.

  • On the schedule, we are trying to include major bullet points that have to be discussed/resolved etc for each topic. Please feel free to add; we are hoping these guide the discussion.

  • Can we please minimize use of laptops during presentations? I know this is painful, but we have many presentations to get through. Checking email, pages, etc, can wait. Some big no-nos: audience members conversing about ongoing presentation via IM, and doing personal emails and coding work during presentations and discussions. I know this is pretty drastic, and am happy to hear other feelings. Indeed, it is useful to be able to look up things, check things, etc. But this has to be minimized, in favor of what the group is doing, and discussing points openly. Sorry to be img alt="twisted" src="img/smiles/icon_twisted.gif".

  • Notes: PDFs etc of presentations, notes from talks will be taken by one person (changes each session ???), placed on Tiki.

  • Presentations MUST be kept to time, so will require planning, practice etc. Where PPT's are used, plan less than half the alotted time for presentation, rest for discussion.

  • Where possible, having general visions of priorities for each group (what each group will do, and what that will depend on) would be great to have ahead of meeting-- on Tiki.

Meeting Participants

(as of April 14, 2006)

DundeeCatriona Macaulay, Jason Swedlow, Jean-Marie Burel, Chris Allan, Brian Loranger, Donald McDonald
NIH-NIAIlya Goldberg, Harry Hochheiser, Josiah Johnston
MITTony Scelfo,Sheldon Chan
MadisonKevin Eliceiri, Curtis Rueden, Melissa Linkert, Mike Hlavenka
ColumbiaBernd Jagla
UCSBKris Kvilekval
VanderbiltMichael McCaughey
MITSheldon Chan, Jeremy Muhlich, Tony Scelfo

Draft Programme (please make comments etc as necessary)

April 21: OME Project Status & Updates Meet in Room 274 Animal Sciences (conference room right next door to LOCI lab). 1675 Observatory Drive

These presentations will be short, 20 min overviews, with the expectation that participants are familiar with the basics and general status. Include Current Status, Release Plans, 2006 Roadmap. Leave 10 mins for discussion.

Morning: Servers and UIs

Time TopicSpeakerCommentsMilestones
9:00 - 9:30 Arrival and Setup
9:30 - 9:45Welcome and AdminKevin Eliceiri
9:45 - 10:15OME ServerIlya Goldberg GUI Installers,External interfaces,DAE
10:15 - 10:45 OME Web UI Josiah Johnston/Harry Hochheiser Overview slide Generic framework, CG/C toolkit, Custom apps
10:45 - 11:15 OMERO ServerChris Allan talk (pdf)
11:15 - 11:45Shoola UIJean-Marie Burel talk (pdf)
11:45 - 12:15 VisBioCurtis Rueden talk (ppt) MISSING see Discussion topics page for details
12:30 - 1:30Lunch

Afternoon: OME Analysis

Again, 20 min + 10 min
TimeTopic SpeakerComments Milestones
1:30 - 2:00Image Signatures Josiah Johnston See slides attached in the line below Sig chain, ROIs+Pixels, Internal/External use of sigs
2:00 - 2:30 MATLABJosiah Johnston Slides, Timing Results interface (pixels,meta-data,modules), performance
2:30 - 3:00External Analysis & VisualizationSheldon Chan & Tony Scelfo Slides
3:00 - 6:00DiscussionSummary and RoadmapTo Do's:

In Attendance

  • Jason, Brian, Chris, Donald, Jean-Marie, Catriona – University of Dundee
  • Ilya, Harry, Josiah – NIH-NIA
  • Jeremy, Sheldon, Tony – MIT
  • Mike M – Vanderbilt
  • Bernd – Columbia University
  • Kevin, Mike H, Curtis, Melissa – Madison
  • Kris – UCSB

Meeting Minutes

  • Ilya’s Presentation (9:30)
  • Josiah’s Presentation (10:00)
    • The Category Group/Category Type model seems to fit with the users needs in Dundee (as opposed to the use of Symantec types).
  • Harry’s Presentation
    • During Harry’s discussion there was some talk about sharing OME data with others. Several methodologies seem to be in development, from making images searchable within the lab environment to making parts of OME publicly available on the web. Clearly, this issue seems to an important one that needs further refinement.
  • Chris’ Presentation (11:00)
    • The need for interoperability between OME and OMERO was brought up. This is something that needs in-depth discussion. For example: having the java-based client images link to OME web-based services (which allow custom annotations).
  • Jean-Marie’s Presentation (12:00)
    • Some discussion about using lazy loading features needed in Shoola.
  • Curtis’ Presentation (1:00
  • Josiah’s Presentations (1:30)
  • Tony’s Presentation (2:30)

Action Items

  • Ilya invites existing Power PC Mac users to install and test the OME Installer application and provide feedback. The OME Installer can be found at [old-link] here.

April 22 Meet in Penthouse of Bock Labs (1525 Linden Drive)

Morning: Interacting with OME

9:00 - 9:30 Arrival and Setup
9:30 - 10:15???Mike McCaughey (Vanderbilt) Slides
10:15 - 11:00???Kris Kvilekval (UCSB)Slides
11:00 - 11:45HCS with OME, InCell3000, Partek Bernd Jagla Slides
11:45 - 12:30???Catriona Macaulay (Dundee)PDF (397.39 Kb)12:30 - 1:30Lunch

Afternoon: Models, Formats, and Specs

2:00 - 2:45OME-TIFF and BioFormatsKevin Eliceiri see Discussion topics page for details
2:45 - 3:00Project Management and EvangelismIlya Goldberg NotesMaint.+support (help!), Videos + Hello Worlds, automated testing, Website
3:00 - 3:15Provenance, PDIF->STs, AssociationsJosiah JohnstoneMeta-model notes, AE oddities SPW, table/class, Provenance, PDIF->STs, Associations
3:15 - 3:30Scheduling BreakoutsJason Swedlow XML Spec, ROIs, Import and Formats, Overlays, Release, WebPage
3:30 - 6:00Discussion, breakouts Inerop/Merge b/w OMERO and OME datamodels + meta-model


  • Mike M’s Presentation (9:30)
    • The presentation prompted a discussion about the positioning of OME within the workflow process. Where does analysis occur (before or after images are put into OME)? How and where does file deletion occur? Where do you store images before they are deleted?

  • Kris’s Presentation (10:15)
    • UCSB’s Digital Notebook application can be found at [old-link ]
    • Bisque can be found at [old-link ] Connect using the username: guest/bioimage

  • Bernd’s Presentation (11:00)

  • Catriona’s Presentation (12:00)

Open Discussion

  • Bio-formats Import Discussion
    • Bio-formats / VisBio and OMERO import must be inline with each other.
    • Java OME/XML in memory representation of the data would be nice.
    • Making the Java model available in a separate jar would be nice.
    • Decided on XML DOM tree that Java developers will transform for their work.
    • API should iterate over ZCT (or whatever) one at a time.
    • Needs a command line tool.
    • The next step for this process is to go back and look at what our work flow is going to be.
    • See Bio-Formats Import Discussion page for more details.

Action Items

  • Everyone please modify your OME websites to provide your existing use cases and user numbers. Help get OMEs name out there!
  • Need a continuous build repository. Two separate builds seem to be required. An end user build brought out to fix bugs (perhaps on a monthly basis), and a daily developers unit tested build. Hibernate has a release checklist we might want to adopt (see [old-link ] ). Also look at [old-link ]. As well as NUnit and JUnit.
  • We need a demo for the OME website. We need to identify what features to highlight and assign folks to document those features.
  • We need a set of simple “Hello World” OME examples to cover various simple tasks that OME can handle.
  • Ilya asks that everyone check the OME mailing list and help out with the “customer support” side of the project. If you see someone ask a question on the mailing list and you know the answer, please speak up and help them!

Working Groups

  • XML Spec
    • It was decided that several labs would attempt to characterize their hardware in OME-XML to verify all fields are properly supported. The deadline for this characterization is Friday, May 19th. The following hardware will be characterized:
      • Madison (Kevin & Curtis): Bio-Rad Radiance, an Olympus Fluoview, and a conventional DIC microscope
      • Dundee (Jean-Marie): Bio-Rad Radiance (different characteristics)
      • Baltimore (Ilya): Deltavision scope
      • MIT (Jeremy): Deltavision scope (different characteristics)
    • A number of additions and other potential changes to OME-XML were also discussed — see OME-XML Evolution for details
  • ROIs
    • See ROI5D Proposals for details on this discussion.
  • Release Planning
  • Overlays
  • Web Page

April 23: Meet in Penthouse of BockLabs (1525 Linden Drive)

Morning: Using OME

Some breakout sessions, to cover more specific issues....currently these are suggestions, please add more.
9:00 - 11:30Designing and Publishing APIsTBD
9:00 - 11:30Defining Future UIsTBD Need to define integration between UI efforts at MIT and Dundee
11:30 - 12:30 Building Better DocumentationTBD Define Doc Policy, Review
12:30 - 1:30Lunch

Afternoon: Coding breakout

Good time for exchanging ideas on usage, install

April 24: Funding/Managing OME Meet in Penthouse of BockLabs (1525 Linden Drive)

Kevin, Ilya, Jason, and Peter go hide and draft grants (also 23 April PM?)

Working Groups (cont.)

  • Most of the morning was spend working on the various group projects from the day before. The OME Tiki has been updated with various pages to reflect the status of these current endeavours.
  • Some discussion about building a forum for the community and what the forum would look like.
  • After a lengthy discussion about an OME/OMERO integration, the group concluded that better communication and documentation within Tiki would help the group make assessments about how to implement a merge. Please take the time to examine the OMERO / Java documentation and provide feedback if you need further details. The group then decided that a future date (perhaps around the alpha release at the end of the summer 2006) would be a good time to look at how a functionality merge could be handled.


This basic roadmap covers what to expect in the next 12 months for the various OME related projects.

Data ManagerMulti-Dimensional ROIsPlug-in AgentIntegrationTable Browsing / Public BrowsingBetter Meta-data support
HiViewer(viewer)Meta-Data SupportPlate BrowserImport files from ClientLimited overlay support
Annotator (ROIs, etc)Additional DimsTony’s Delta ViewerUCSB’s functionality / Ajax
Chain BuilderInteroperability with Matlab, OME, ImageJTeraNode IntegrationPersonalised Templates
Quasi Hierarchy NavigatorScripting Visual of Analysis Results
Performance Reports / Final View of Analysis
Classifier front-end
Screening support
Customized Search


  • Current Issues
    • Default “World Access” is unacceptable
    • ACLs for data access and operations
    • Front end of management
    • Encryption / secure logins
    • Public viewing facility / External public links
    • Improved sessions key semantics
    • Strengthen password hashing algorithm


  • MEX is OK
  • Deletes on ST Headers, Chains, Projects, Datasets
  • Needs a front-end
  • Delete privileges flag
  • Trash Bin / Purge


  • Install Logging

Presentations from the 2006 OME Developers Meeting

These are PDFs and PPTs from the meeting of OME Developers held April 21-24, 2006 at the University of Wisconsin, Madison WI.

April 21

Josiah Johnston (Baltimore) OME Web UI
Harry Hochheiser (Baltimore)Integrating with MGI
Chris Allan (Dundee) OMERO Server
Jean-Marie Burel (Dundee)Shoola
Curtis Rueden (Madison)VisBio (missing)
Josiah Johnston (Baltimore) Signatures, ROIs, and MATLAB, Timing Results
Sheldon Chan & Tony Scelfo (MIT) External Analysis & Visualization

April 22

Mike McCaughey (Vanderbilt)OME at Vanderbilt
Kris Kvilekval (UCSB)UCSB Bioimaging and OME
Bernd Jagla (Columbia)HCS with OME, InCell3000, Partek
Catriona Macaulay (Dundee)Usable Access for the Open Microscopy Environment

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