[Paraview] visualization of neural network activity

[Jeff Baumes]

VTK/Titan may have most of the components that you need, but they are not
currently available in ParaView. Titan (titan.sandia.gov) has a generic hdf5
reader that loads data into a vtkTable that may suit your needs. There are
also utilities for converting a vtkTable into a vtkGraph which can then be
visualized in vtkGraphLayoutView, which can do 2D or 3D layout. As far as
animation goes, graph layout on time-changing graphs is a tricky problem
since it's easy to lose your frame-of-reference if you redo layout each
time. But if you want to do the layout once, fix the node positions, then
just animate properties like colors, that is more doable.

The other option is to manually get the data into one of the several
geometry formats ParaView supports, then you could use ParaView directly.
For example, you could produce a legacy vtkPolyData format where you define
neurons as points and connections as lines, then you load it in ParaView and
do things like glyph the points with spheres, color lines by attributes,
etc.

Jeff

On Tue, Nov 16, 2010 at 4:54 AM, Benjamin Auffarth <auffarth at csc.kth.se>wrote:

> Hi all,
>  my question is about suitability of ParaView for visualization of neural
> network models. I saw the gallery, looked at the supported file formats,
> available tools and filters, and looked over the user guide (1.7). My
> impression is that ParaView is typically used for visualization of data
> that is layed out in a grid, say 3D matrices, especially particles, however
> I noticed there is the possibility to interactively create 3D objects and
> output them to povray and I I saw that ITK R4 at one point had support for
> neural network visualization (http://www.paraview
> .org/Wiki/ITK_Release_4/Discussion_Points#Neural_Networks).
>  Our aim is to visualize a network model consisting of neurons and
> connections between neurons and show time dynamics of evolving attractors,
> etc. The visualization should basically colorcode neurons and synapses,
> possibly in 3D and possibly raytraced. We run our simulations in parallel
> and would like to use a binary format like hdf5 or netcdf to store data of
> neural activations and connection strengths. These should then be used to
> create a 3D representations (images and videos). I think Povray (+ pevious
> binary2text conversion) could be simply setup to do network visualization
> for our purpose. Can this visualization be done in ParaView? (If yes,
> how?)
> thanks,
> Benjamin.
>
>
> ----
> Benjamin Auffarth
> KTH, Computational Biology and Neurocomputing (CBN),
> Albanova Universitetscentrum, Roslagstullsbacken 35,
> S-100 44 Stockholm, Sweden
> room 162:021B, tel. +46 8 790 8699
>
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-- 
Jeff Baumes, Ph.D.
Technical Lead, Kitware Inc.
(518) 881-4932
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