• Atlas definition:
  • Collection of annotations within a coordinate system (ontological)
  • Canvas on which you pin information including the tools and protocols for integrating the information (functional)
  • Spatially defined data repository-metadata-viewers (structural or content)
  • Space is used as an index for informing search/retrieval + tools for converting different representations of space (main feature)
  • A way to organize the community (social)

This sort of atlas could contain image data, electrophysiological data, behavioral data, etc.

• Image/atlas visualization: Examined the functionality of the image/atlas visualization of the following
  • SmartAtlas^?
  • SHIVA
  • NBIAS
  • MBL and atlases
  • Structural function within Amira

Discussion about what is going on for SFN vs. what we want in the long term. Discussion of how to make things interoperable and what that means. Debate between portal and stand alone version.

• Bill: Registration pipelines by Drexel
• Processing pipelines/workflows using neuroterrain. Specialized for MBL
  • Platform independence (linux, osX, old Mac)
  • Network authenticated/network based
  • Defining (ontologically) a pipeline
  • Must be database driven
  • Mostly automated (80-90%) must accommodate manual too

• David: Registration Pipeline by LONI
  • Modular and put things together for a particular type of data.
  • Processing on remote host or locally
  • Grid enabled
  • Technical

Discussion of what happens with these registration tools in the future:

• • This would be behind the scenes and viewable to the user as some sort of wizard, including tools that tell you what is going on and what has been done with your data to get your results.
  • Giving the potential for a user to put their data into the viewer and have a rough estimate of what their data looks like relative to the atlas.

• Seth: Edinburgh tools showed some of the functions of EMAG and EMAP:
  • Atlases of embryos at different days (browses their database)
  • Can browse by gene, by region, by structure, by stage, by expression (or not expressed)
  • Gene information that is available at those days, and by structure, and can call up images that show what genes are available from your query
  • Predefined regions are used as a search or you can paint a new region. Clicking a region drives a query
  • Similar type of interface, plus links to images, ontologies, pubmed

Next couple of years, Rob would like to see the iScope stacks added to the BIRN infrastructure (iScope shows tissue on a microscope, and acts both as a client and server), creates Z axis movies, and can be registered to the larger 2D images. Shows the fine-grained histology from that area. Potentially embed some functionality into an atlas to find these image stacks and do some cell counting.

The other stuff is really necessary to drive these things… What can or can’t be done will written up by Bill and Willy. Bill: Data: MBL aligned to Drexel, and in SRB

Data set for SFN, and protocols