DTI-Circuit Requirements - Revision history

Steven Gomez: /* Visualization */

2011-06-30T16:32:37Z

Visualization

← Older revision		Revision as of 16:32, 30 June 2011
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	# Easy to learn and use		# Easy to learn and use
	## 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		## 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
			## Conforms to [http://faculty.washington.edu/jtenenbg/courses/360/f04/sessions/schneidermanGoldenRules.html good UI design rules]
	# Easy to deploy to end-users (we should not preclude the CAVE if possible, though it is not the target display)		# Easy to deploy to end-users (we should not preclude the CAVE if possible, though it is not the target display)
			## Web deployment (e.g. Google Maps-style) if sufficiently powerful
	# Supports fast prototyping for new features, designs		# Supports fast prototyping for new features, designs

	Scale		Scale
	# ~~Must support~~ 3D brain data: coordinate system for areas/nuclei/regions, shape of fiber bundles (tractography), volume rendering of regions		# Supports 3D brain data: coordinate system for areas/nuclei/regions, shape of fiber bundles (tractography), volume rendering of regions
	# ~~Must support~~ multi-scale brain understanding (single cell up to whole brain)		# Supports multi-scale brain understanding (single cell up to whole brain)
	# ~~Support for~~ viewing subregions/substructures, systems and global view		# Supports viewing subregions/substructures, systems and global view
			## Internal and external connections to a systems, with filtering by system/region
	<br>		<br>
	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.		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.

Steven Gomez: /* Brain-Circuit Diagram Requirements */

2011-06-30T16:16:46Z

Brain-Circuit Diagram Requirements

@@ Line 64: / Line 64: @@
 <br>
 Like I said, I also repeat the search with Secondary Motor and Prelimbic as keywords."
 </blockquote>

Steven Gomez: /* Functional Connectivity (Schnitzer Group) Requirements */

2011-06-28T18:51:57Z

Functional Connectivity (Schnitzer Group) Requirements

← Older revision		Revision as of 18:51, 28 June 2011
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	{{stub}}		{{stub}}

	==~~Functional Connectivity (Schnitzer Group)~~ 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.		'''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.

Steven Gomez: /* Functional Connectivity (Schnitzer Group) Requirements */

2011-06-28T18:50:54Z

Functional Connectivity (Schnitzer Group) Requirements

← Older revision		Revision as of 18:50, 28 June 2011
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	==Functional Connectivity (Schnitzer Group) Requirements==		==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.		'''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:		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:
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	Experimental data		Experimental data
	# fMRI time-series - Badre has data of this nature		# fMRI time-series - Badre has data of this nature
			<br>
	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.		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===

			Accessibility
			# Easy to learn and use
			## 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
			# Easy to deploy to end-users (we should not preclude the CAVE if possible, though it is not the target display)
			# Supports fast prototyping for new features, designs

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

Steven Gomez: /* Data */

2011-06-28T18:35:06Z

Data

← Older revision		Revision as of 18:35, 28 June 2011
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	===Data===		===Data===

	~~We should clarify which~~ species (~~rat~~, ~~human~~) ~~and current datasets~~/~~nomenclatures our collaborators are using.~~		Multiple species support for collaborators
			# Rat/Mouse
			# Human
			# Macaque

			Curated data
			# Brain atlases (Allen, Paxinos, etc.), spatial coordinate systems (e.g., MNI)
			# Histology/plates
			# Functional brain connectivity

			Experimental data
			# fMRI time-series - Badre has data of this nature

	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.		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.

Steven Gomez: /* SVL Project Requirements */

2011-06-21T15:57:56Z

SVL Project Requirements

← Older revision		Revision as of 15:57, 21 June 2011
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	==SVL Project Requirements==		==SVL Project Requirements==
			Here's a short list of software deliverables from the SVL proposal:

			# A ''descriptive'' and ''predictive'' language for generating symbol-based visualizations of 3D tensor fields
			## 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?)
			# Testbed tools for evaluating and optimizing visualizations
			## Can we score a visualization automatically without humans using a model of perception/human information processing?
			## Can we locally optimize visualizations using that model and a hill-climbing algorithm?
			# Application development for DTI/BioFlow

	===Data===		===Data===

Steven Gomez: /* SVL Project Requirements */

2011-06-21T01:02:08Z

SVL Project Requirements

← Older revision		Revision as of 01:02, 21 June 2011
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	==SVL Project Requirements==		==SVL Project Requirements==

			===Data===

			===Visualization===

			===Interaction===

	==Previous Efforts==		==Previous Efforts==

Steven Gomez: /* Interaction */ added some background

2011-06-21T01:01:16Z

Interaction: added some background

@@ Line 24: / Line 24: @@
 ===Interaction===
-baz
+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.
 ==SVL Project Requirements==

Steven Gomez: /* Visualization */

2011-06-21T00:52:42Z

Visualization

← Older revision		Revision as of 00:52, 21 June 2011
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	===Visualization===		===Visualization===

	~~bar~~		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===		===Interaction===

Steven Gomez: /* Data */

2011-06-21T00:48:30Z

Data

← Older revision		Revision as of 00:48, 21 June 2011
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	===Data===		===Data===

	~~foo~~		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===