= 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 VRML 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=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]],
- [[http://www.3dbar.org:8080/getReconstruction?cafDatasetName=aba2011&structureName=VPL&qualityPreset=high&outputFormat=vrml|Ventral posterolateral nucleus of the thalamus]].
Download also [[attachment:framedata0051.vtk.zip|a model of a of the barrel cortex column]]. Unwrap downloaded archives.

== Visualisation ==
Run [http://www.paraview.org ParaView] software (description for version 4.0.1). 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 ''Properties'' tab 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 ''Solid Color''. Click ''Coloring: Edit'' and select color to:
- Red = 250, Green: 245, Blue: 255 for ''scene_SSp_bfd1.wrl'',
- Red = 153, Green: 163, Blue: 255 for ''scene_SSp_bfd2Slash3.wrl'',
- Red = 74, Green: 77, Blue: 128 for ''scene_SSp_bfd4.wrl'',
- Red = 171, Green: 177, Blue: 255 for ''scene_SSp_bfd5.wrl'',
- Red = 145, Green: 149, Blue: 213 for ''scene_SSp_bfd6a.wrl'',
- Red = 177, Green: 170, Blue: 255 for ''scene_SSp_bfd6b.wrl''.

[[Screenshot(18,width=400,height=300,description=$description,align=center,format=png)]]

Click ''Coloring: Edit'' for the ''framedata0051.vtk'' model (ensure that ''Coloring'' is set to ''voltage''). Click the "Gear" icon to edit ''Color Scale''. Set ''Color Space'' to ''CIELAB''; set the left color point to Red = 59, Green = 76 and Blue = 192 and the right to Red = 255, Green = 255 and Blue = 0. Add two color points: at ''Color Scalar Value'' = -40 (Red = 150, Green = 150 and Blue = 0) and at ''Color Scalar Value'' = 18 (Red = 190, Green = 35 and Blue = 21). Click the ''Apply'' button, then close the ''Color Scale Editor'' window.

[[Screenshot(19,width=400,height=300,description=$description,align=center,format=png)]]


Apply the ''Transform'' filter (''!Filters/Alphabetical/Transform'' from menu) to the ''framedata0051.vtk'' model. In the ''Properties'' tab set the transformation matrix to:

||=Translate =||-3.71011222757522 ||-0.955791920040867 ||-0.855289018330382 ||
||=Rotate =||40.2025580192141 ||-63.976105129058 ||76.2999549515704 ||
||=Scale =||0.58 ||0.58 ||0.58 ||

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Click the ''Apply'' button.

[[Screenshot(21,width=400,height=300,description=$description,align=center,format=png)]]

Choose an appropriate viewport and export the scene or a screenshot if you wish.

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