= Using atlas data as a spatial reference for a result of a realistic neural network simulation =

== Model download ==
From [[http://www.3dbar.org:8080/getPreview?cafDatasetName=aba2011;structureName=grey,VPL,SSp-bfd1,SSp-bfd2Slash3,SSp-bfd4,SSp-bfd5,SSp-bfd6a,SSp-bfd6b The Allen Mouse Brain Reference Atlas, 2011 Segmentation]] download the following VRLM high quality models:
- [[http://www.3dbar.org:8080/getReconstruction?cafDatasetName=aba2011&structureName=grey&qualityPreset=high&outputFormat=vrml Basic cell groups and regions]],
- [[http://www.3dbar.org:8080/getReconstruction?cafDatasetName=aba2011&structureName=VPL&qualityPreset=high&outputFormat=vrml Ventral posterolateral nucleus of the thalamus]],
- [[http://www.3dbar.org:8080/getReconstruction?cafDatasetName=aba2011&structureName=SSp-bfd1&qualityPreset=high&outputFormat=vrml Primary somatosensory area, barrel field, layer 1]],
- [[http://www.3dbar.org:8080/getReconstruction?cafDatasetName=aba2011&structureName=SSp-bfd2Slash3&qualityPreset=high&outputFormat=vrml Primary somatosensory area, barrel field, layer 2/3]],
- [[http://www.3dbar.org:8080/getReconstruction?cafDatasetName=aba2011&structureName=SSp-bfd4&qualityPreset=high&outputFormat=vrml Primary somatosensory area, barrel field, layer 4]],
- [[http://www.3dbar.org:8080/getReconstruction?cafDatasetName=aba2011&structureName=SSp-bfd5&qualityPreset=high&outputFormat=vrml Primary somatosensory area, barrel field, layer 5]],
- [[http://www.3dbar.org:8080/getReconstruction?cafDatasetName=aba2011&structureName=SSp-bfd6a&qualityPreset=high&outputFormat=vrml Primary somatosensory area, barrel field, layer 6a]],
- [[http://www.3dbar.org:8080/getReconstruction?cafDatasetName=aba2011&structureName=SSp-bfd6b&qualityPreset=high&outputFormat=vrml Primary somatosensory area, barrel field, layer 6b]].
Download also [[attachment:framedata0051.vtk.zip|a model of a of the barrel cortex collumn]]. Unwrap downloaded archives.

== Visualisation ==
Run [[http://www.paraview.org ParaView]] software. Open downloaded *.wrl and *.vtk files. Click the ''Apply'' button (in the tab ''Properties'').
[[Screenshot(17,width=400,height=300,description=$description,align=center,format=png)]]

In the tab ''Properties'' set ''Styling: Opacity'' to 0.1 for ''scene_grey.wrl'' model. For every ''scene_SSp_bfd*.wrl'' model
set ''Styling: Opacity'' to 0.3, then change ''Coloring'' from ''VRMLColor'' to ''SolidColor''. Click ''Coloring: Edit'' and select color:


[[ScreenshotsList()]]