DTI-Circuit Requirements

Brain-Circuit Diagram Requirements

Some background: 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

Multiple species support for collaborators

1. Rat/Mouse
2. Human
3. Macaque

Curated data

1. Brain atlases (Allen, Paxinos, etc.), spatial coordinate systems (e.g., MNI)
2. Histology/plates
3. Functional brain connectivity

Experimental data

1. fMRI time-series - Badre has data of this nature

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

Accessibility

1. Easy to learn and use
   1. One idea is to build off "canonical" brain diagrams that are familiar to neuroscientists, and use these as scaffolding for drawing other curated data (e.g., projections), like Radu's protein pathway viewer
2. Easy to deploy to end-users (we should not preclude the CAVE if possible, though it is not the target display)
3. Supports fast prototyping for new features, designs

Scale

1. Must support 3D brain data: coordinate system for areas/nuclei/regions, shape of fiber bundles (tractography), volume rendering of regions
2. Must support multi-scale brain understanding (single cell up to whole brain)
3. Support for viewing subregions/substructures, systems and global view

The Schnitzer group described their desired tool as a 3D visual database of functional (neuron projections) brain connections. Presumably, the "3D" part means they're interested in studying these connections w.r.t. anatomical coordinates of the neuron terminus.

Interaction

Here is the current interaction Jeff does when performing a "circuit query". The high-level goal should be to simplify this process and make new types of interactions/queries available.

"I'm interested in a few areas: namely the projection from visual/sensory areas to forelimb motor and prelimbic.
So the way I do my search is:
1. go on the bams website.
2. choose brain parts
3. put "primary motor", "Secondary motor" and "prelimbic" in "Full text serach of brain parts annotations" in 3 different searches
4. choose the rats database, Swanson 1998
5. Then in the search, look for primary motor again (this shows how inefficient the search on BAMS is, because I searched for primary motor and it returns a million irrelevant search results)
5. Click on "Primary motor"
6. click on ""Efferent projections of Primary Motor Area" -- those are the areas that primary motor area sends projections to
7. click on ""Afferent projections of Primary Motor Area" -- those are the areas that primary motor area receives projections from
8. That's how I find out the connectivity data from the database. It's not totally clear and not very intuitive to use.

Like I said, I also repeat the search with Secondary Motor and Prelimbic as keywords."

SVL Project Requirements

Here's a short list of software deliverables from the SVL proposal:

1. A descriptive and predictive language for generating symbol-based visualizations of 3D tensor fields
   1. Theory and experiment needed to define symbol space and the "visual variables" that the language expresses and can perturb. (Is "symbol-based" a hard requirement? In practice, is that a simplification or something that will hold us back?)
2. Testbed tools for evaluating and optimizing visualizations
   1. Can we score a visualization automatically without humans using a model of perception/human information processing?
   2. Can we locally optimize visualizations using that model and a hill-climbing algorithm?
3. Application development for DTI/BioFlow

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