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SNT: Reconstruction Viewer

5,893 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.
*'''Remove Selected...''' Deletes the selected mesh(es) from the scene.
*'''Remove All...''' Deletes all imported mesh(es) from the scene.
<div align="left">
<ul>
<li style="display:inline-block;"> [[Image:reconstruction-viewer-obj-transparency-5.png|none|thumb|300px|Transparency = 5%]] </li>
<li style="display:inline-block;"> [[Image:reconstruction-viewer-obj-transparency-95.png|none|thumb|300px|Transparency = 95%]] </li>
</ul>
</div>
{{clear}}
 
==Reference Brains==
This menu contains several Drosophila and Mouse reference brains.
[[Image:reconstruction-reference-brains-menu.png|right|thumb|400px|]]
*'''Drosophila (Adult)'''
**'''FlyCircuit''' FlyCircuit Drosophila reference brain
**'''JFRC2 (VFB)''' Janelia Farm Research Campus Virtual Fly Brain
**'''JFRC3''' Janelia Farm Research Campus Drosophila reference brain (Version 3)
**'''Adult VNS''' Adult Drosophila ventral nervous system reference
*'''Drosophila (Embryonic)'''
**'''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 Framework v3. Selecting this option imports the Whole Brain reference mesh, 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==
[[Image:reconstruction-viewer-measurement-menu.png|right|thumb|400px|]]
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==
[[Image:reconstruction-viewer-tools-menu.png|right|thumb|400px]]
*'''Debug Mode''' Logs detailed information about plugin usage to the Console.
*'''Take Snapshot''' Saves a PNG image of the current scene to disk. The default directory may be changed in the Reconstruction Viewer ''Preferences''.
*'''Record Rotation''' Animates a rotation of the current scene and saves each frame to disk. The save directory, rotation degree, duration and frames per second may be adjusted in the Reconstruction Viewer ''Preferences''.
*'''Color Legends''' Contains options relating to the adding and management of LUT-based color legends.
*'''Keyboard & Mouse Sensitivity''' A sub-menu with options for sensitivity of mouse and keyboard scene interaction. Note that a default shared sensitivity parameter can be specified for panning, zooming and rotating (using hotkeys) in the Reconstruction Viewer ''Preferences''.
**'''Pan Accuracy''' Sets the responsiveness of panning. A lower step size is more responsive.
**'''Rotation Steps'''Sets the number of degrees of a single rotation step. Note this preference only applies to rotations made with the Left/Right Arrow keys.
**'''Zoom Steps''' Sets the percentage of a single zoom step.
*'''Keyboard Shortcuts...''' Shows a list of all Reconstruction Viewer keyboard shortcuts.
*'''Preferences...''' Configurable preferences for snapshot recordings, keyboard and mouse controls, and the preferred scripting language for the Viewer. Preferences persist across plugin sessions.
*'''Script This Viewer...''' Opens an instance of the Script Editor with pre-loaded extensible boilerplate code for advanced scripting of Reconstruction Viewer. For an example of the scripting capabilities of Reconstruction Viewer, see ''Reconstruction Viewer Demo (Python)'' at {{bc|Templates|Neuroanatomy|Analysis}} in the Script Editor.
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