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 a model of a of the barrel cortex collumn . 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).

Loaded models.

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.

Color and opacity settings.

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.

Voltage to color mapping.

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	855289018330382
Rotate	40.2025580192141	-63.976105129058	76.2999549515704
Scale	0.58	0.58	0.58

• 1 - Open Grayscale Image... - Tutorial: How to use labeled volumes?
• 2 - Choose NIfTI volume you extracted - Tutorial: How to use labeled volumes?
• 4 - Choose 'Segmentation', then 'Load from image' - Tutorial: How to use labeled volumes?
• 5 - Select the same NIfTI file - Tutorial: How to use labeled volumes?
• 7 - "Segmentation", "Load Label Descriptions..." - Tutorial: How to use labeled volumes?
• 8 - Select file with the lookup table - Tutorial: How to use labeled volumes?
• 9 - - Tutorial: How to use labeled volumes?
• 10 - Click 'update mesh' button - Tutorial: How to use labeled volumes?
• 11 - "Segmentation", "Export As Surface Mesh" - Tutorial: How to use labeled volumes?
• 12 - - Tutorial: How to use labeled volumes?
• 13 - Downloading labeled volume from 'Atlas Details' tab - Tutorial: How to use labeled volumes?
• 14 - Downloading labeled volume from 'Live preview' tab - Tutorial: How to use labeled volumes?
• 15 - You have to be logged in in order to access the Custom Reconstruction Wizzard. Structures loaded in Live preview window are automatically transferred to the reconstruction wizard. - Accessing the Custom Reconstruction Wizzard
• 16 - Accessing the reconstruction wizzard from the Reconstructions tab. - Accessing the Custom Reconstruction Wizzard
• 17 - Visualisation01 - Loaded models.
• 18 - Visualisation02 - Color and opacity settings.
• 19 - Visualisation03 - Voltage to color mapping.
• 20 - Visualisation04 - The transformation filter.
• 21 - Visualisation05.png - A complete scene.
• 22 - Visualisation06.png - The complete scene at another viewpoint.
• 23 - Visualisation07.png - The complete scene - focus on the model of barrel cortex column.