[Paraview] visualization of neural network activity

[Benjamin Auffarth]

Thanks a lot, Jeff. I will think over, which option to use. Using titan I
could even do visualization at runtime (for analysis of the network) and for
bigger networks I could just store the network state and visualize offline.
Now I have somewhere to start. That helped a lot.

----
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


On Tue, Nov 16, 2010 at 4:56 PM, Jeff Baumes <jeff.baumes at kitware.com>wrote:

> 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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