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SNT: Reconstruction Viewer

1,817 bytes added, 18 July
Analyze and Measure
==Manage and Customize 3D Meshes==
[[Image:reconstruction-viewer-mesh-controls.png|right|thumb|400px|]]
[[Image:reconstruction-viewer-customize-mesh-controls.png|right|thumb|400px|{{bc|Customize|All Parameters...}}]]
*'''Import OBJ File(s)...''' Allows import and rendering of Wavefront OBJ files, commonly used to represent surface meshes of anatomical structures.
*'''Customize''' sub-menu providing control over rendering parameters of surface meshes.
<div align="left">
<ul>
<li style="display:inline-block;"> [[Image:reconstruction-viewer-obj-transparency-5.png|none|thumb|200px300px|Transparency = 5%]] </li><li style="display:inline-block;"> [[Image:reconstruction-viewer-obj-transparency-95.png|none|thumb|200px300px|Transparency = 95%]] </li>
</ul>
</div>
**'''Larva L1''' Drosophila 1st instar larval stage
**'''Larva L3''' Drosophila 3rd instar larval stage
*'''Mouse (Adult): Allen CCF Navigator''' Import and navigation system for the Allen Adult Mouse Common Coordinate Frameworkv3. Selecting this option imports the Whole Brain referencemesh, and presents a GUI allowing search , information, and import of Mouse Brain ontologies contained in the Allen Common Coordinate Framework v3.<div align="left"><ul> <li style="display:inline-block;"> [[Image:reconstruction-viewer-allen-ccf-ontology.png|none|thumb|200px|Allen CCF Navigator]] </li><li style="display:inline-block;"> [[Image:reconstruction-viewer-allen-ccf-thalamus-info.png|none|thumb|200px|Allen CCF Ontology Info]] </li></ul></div>
*'''Zebrafish (Embryonic)'''
**'''Max Planck ZBA''' Max Planck Zebrafish Brain Atlas
<div align="center">
<ul>
<li style="display:inline-block;"> [[Image:reconstruction-flycircuit-reference.png|none|thumb|300px|FlyCircuit Drosophila (Adult)]] </li>
<li style="display:inline-block;"> [[Image:reconstruction-viewer-whole-mouse-thalamus.png|none|thumb|300px|Allen Adult Mouse Whole Brain + Thalamus]] </li>
<li style="display:inline-block;"> [[Image:reconstruction-viewer-zebrafish-reference.png|none|thumb|300px|Max Planck ZBA]] </li>
</ul>
</div>
{{clear}}
==Analyze and Measure==
This menu houses several functions to measure and analyze loaded reconstructions.
*'''Measure''' Shows a table of summary statistics for selected reconstructions. If measuring multiple tracings, the table can be sorted by column.
<div align="left">
<ul>
<li style="display:inline-block;"> [[Image:reconstruction-viewer-measurements-AA0100.png|none|thumb|900px|AA0100 Measurements]] </li>
</ul>
</div>
*'''Distribution Analysis...''' Plots a histogram of the selected metric. If multiple reconstructions are selected, a single analysis is conducted on the group.
<div align="left">
<ul>
<li style="display:inline-block;"> [[Image:reconstruction-viewer-AA0100-distribution-analysis.png|none|thumb|200px|AA0100 Branch Order Histogram]] </li>
</ul>
</div>
*'''Sholl Analysis...''' Runs the [[Sholl_Analysis|Sholl Analysis]] plugin found in {{bc|Analyze|Sholl|Sholl Analysis (From Tracings)}}. Note only one reconstruction may be analysed at a time.
<div align="left">
<ul>
<li style="display:inline-block;"> [[Image:reconstruction-viewer-AA0100-sholl-table.png|none|thumb|200px|AA0100 Sholl Table]] </li>
<li style="display:inline-block;"> [[Image:reconstruction-viewer-AA0100-sholl-plot.png|none|thumb|200px|AA0100 Sholl Plot]] </li>
</ul>
</div>
*'''Strahler Analysis''' Conducts Strahler Analysis on the selected reconstruction. Note only one reconstruction may be analysed at a time.
<div align="left">
<ul>
<li style="display:inline-block;"> [[Image:reconstruction-viewer-AA0100-strahler-table.png|none|thumb|200px|AA0100 Strahler Table]] </li>
<li style="display:inline-block;"> [[Image:reconstruction-viewer-AA0100-strahler-plot.png|none|thumb|200px|AA0100 Strahler Plot]] </li>
</ul>
</div>
==Tool and Utilities==
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