DTI-Circuit Requirements: Difference between revisions
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===Data=== | ===Data=== | ||
We should clarify which species (rat, human) and current datasets/nomenclatures our collaborators are using. | |||
For the last project, the Stanford group was using the [http://brancusi.usc.edu/bkms BAMS database], and specifically looking at the connections in the rat brain. This data is serialized and available [http://brancusi.usc.edu/bkms/bamsxml.html as XML]; previously, we parsed the Swanson-98 XML to build the connection graph. | |||
===Visualization=== | ===Visualization=== | ||
Revision as of 00:48, 21 June 2011
Functional Connectivity (Schnitzer Group) Requirements
We made some progress in the fall on an interactive visualization that overlays a node-link diagram of functional brain connections above a anatomical map of these regions. For a starting point, this was in 2D (i.e., the spatial layout of the nodes was simply mapped over a single, static, sagittal view of the brain). In our talks with the Stanford group, it seems they are ultimately looking for a 3D "database" of these connections. In other words, they want to view connections in the context of the full brain volume.
A demo video of that tool is available here [ Media:Steve_2dcircuit_prototype.mp4 ]. Jeff Law, who was/is a post-doc in that group, hints at some reqs for the next design in his feedback to that video:
"The movie looks REALLY COOL. And a working version of this would be very helpful for us! But just to clarify what you've done:
So you basically loaded the database from the Allen atlas (the pdf file) and combined it with the connectivity information you got from BAMS. Am I right? One thing that would be really nice is instead of searching for specific area and show the connections (which is very useful), the software let the user to choose the area of interest by moving the cursor (and the tag would show the name of the area), and the connections to/from that area would be shown interactively. Do you get what I mean?"
Data
We should clarify which species (rat, human) and current datasets/nomenclatures our collaborators are using.
For the last project, the Stanford group was using the BAMS database, and specifically looking at the connections in the rat brain. This data is serialized and available as XML; previously, we parsed the Swanson-98 XML to build the connection graph.
Visualization
bar
Interaction
baz
SVL Project Requirements
Previous Efforts
NSF Expeditions Pre-proposal (September 2010) -- Media:NSF_expedition_pre_circuits.pdf
NSF SI-S2 Proposal (June 2010) -- Media:SI2-SSI-submission_circuits.pdf
Reviews for both collected by DHL -- Media:NSF_circuit_prop_reviews.pdf