2005 AHM Planning: Atlas Tools

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Who should attend Scientists interested in atlasing neuroanatomical images and in integrating different types of imaging data in animal studies, particularly rodents.

Workshop Goals

Theoretical and practical aspects involved in atlasing neuroanatomical images of the mouse brain.

Exploration of the various meanings investigators attach to the term "atlasing," experimental design and how these shape the atlasing effort at the Mouse testbed of the Biomedical Informatics Research Network (BIRN).

Examination of tools and functions currently in use and the lessons learned in atlasing rodent images and data.


Workshop Logistics

  • The day-long workshop will be held on Thursday, Oct. 20 at the UC San Diego campus. Directions and the room designated for the workshop will be posted in the near future.
  • Sign up procedure: Please contact jyl.boline@loni.ucla.edu for information
  • The maximum enrollment for this workshop is TBA.


  • The workshop room does not permit food. Lunch will be served.

Workshop Participants

Preparation for Workshop -- Important Information for all attendees

All attendees are required to complete the following items prior to the workshop. Support will be provided as requested.

  • Mailing List: TBA
  • Software Installation: TBA.
  • Data to Download: TBA.

Tentative Agenda

9:00 AM - 3:00 PM

Agenda:

  • 9:00 - 9:15 AM GOALS OF WORKSHOP
    • Introduction to the Workshop and People-Introductions
    • Description of what atlasing means (i.e. what is where?)
    • Presentation of current mouse BIRN atlasing interface (time for playing with current version)
    • Continue by examining functions available in the tools used by mouse BIRN participants
  • We want to end up with:
    • Most important functions (prioritize functions)
    • Most liked interfaces for certatin functions
    • Additional external resources (workbench)
    • Feedback on current look and feel-suggest changes


  • 9:15 – 10:15 IMAGE/ATLAS VISUALIZATION
    • Image viewing
    • Images included with the software tools
    • Information about images
    • Image conversion
    • Locating/identifying structures within an image
  • ** *** Each presenter ~5-10 minutes each:
        • Maryann: SmartAtlas
        • Bill: NBIAS
        • Rob: MBL and atlases
        • David: SHIVA
        •  ?: Mouse BIRN Atlas Environment


  • 10:15 – 11:30 ADDING DATA TO MOUSE BIRN INFRASTRUCTURE
    • Registration tools
    • Visualization of registered image and Atlas
    • Adding image data set to mouse BIRN database
  • ** *** Each presenter ~10-15 minutes each:
        • Maryann: SmartAtlas
        • Bill: Drexel tools
        • David: Pipeline
        •  ?: Mouse BIRN Atlas Environment
  • 11:30 - 12:30 Lunch on own


  • 12:30- 1:30 DATA ACCESS AND QUERY (all locally and/or remotely)
    • Access to and query of atlases/image data sets
    • Access to and query of ontology information
    • Access to and query of higher resolution image data
    • Access to and query of other types of information
  • ** *** Each presenter ~10-15 minutes each:
        • Maryann: SmartAtlas
        • Bill: NBIAS
        • Seth: EMAP/EMAGE
        • Rob: GeneNetwork-highlight based on what's been going on the last 4 months
        • David: SHIVA
        •  ?: Mouse BIRN Atlas Environment


  • 1:30- 2:30 ANALYSIS/ADDITIONAL PROCESSING TOOLS
    • Measurement of signal intensities
    • Reslicing image
    • Image delineation or labeling
    • Measurements within an image
    • Comparisons between images
  • ** *** Each presenter ~10-15 minutes each:
        • Maryann: SmartAtlas
        • Bill: NBIAS
        • Seth: EMAP
        • Seth: AMIRA
        • Rob: iScope
        • David: BrainSuite2 and SHIVA
        •  ?: Mouse BIRN Atlas Environment


  • 2:30-2:50 EXPERIMENTAL DESIGN
    • Rob Williams: Discuss experimental design and atlasing: considerations to keep in mind when setting up atlasing experiments. Batch effects, lab confounds, strain background, capturing metadata (litter, parity, time of year, etc.).


  • 2:50-3:00 WRAP UP
  • List of short-term goals (SFN)
    • Implement XML exchange something painted in SmartAtlas
    • Update programs to look more like one
    • Integrate Genenetwork data sets into atlasing interface
    • Accessing data on the SRB->that way we can also place the data we want to share at SFN
    • Launch viewer with data already loaded (possible?)
  • List of long-term goals (6 months, 1 yr)
    • Integrate Genenetwork data sets into atlasing interface
    • Accessing data on the SRB->that way we can also place the data we want to share at SFN
    • Launch viewer with data already loaded
    • Embed viewer in portal instead of separate window? Want this?