Skip to content, Skip to search

Changes

SNT: Reconstruction Viewer

8,087 bytes added, 18 July
Analyze and Measure
*'''Fit to Visible Objects''' Computes a bounding box containing all objects of the scene and adjusts the zoom level to ensure all objects are within the camera view.
*'''Stretch-to-Fill''' Stretches the projection on the whole viewport.
<div align="left">
<ul>
<li style="display:inline-block;"> [[Image:reconstruction-viewer-not-stretched.png|none|thumb|200px|Stretch-to-Fill - disabled]] </li>
<li style="display:inline-block;"> [[Image:reconstruction-viewer-stretched.png|none|thumb|200px|Stretch-to-Fill - enabled]] </li>
</ul>
</div>
*'''Impose Isotropic Scale''' Squares the aspect ratio of the selected dimensions, leaving the others unchanged.
<div align="left">
<ul>
<li style="display:inline-block;"> [[Image:reconstruction-viewer-aspect-ratio-none.png|none|thumb|200px|Impose Isotropic Scale - None]] </li>
<li style="display:inline-block;"> [[Image:reconstruction-viewer-aspect-ratio-ZY.png|none|thumb|200px|Impose Isotropic Scale - ZY]] </li>
</ul>
</div>
*'''Reload Scene''' Resets the zoom level to the default, fitting and centering all scene objects into the camera view. The current rotation setting remains unchanged. Note if some drawables in the 3D scene are not being rendered properly when this option is selected, it will prompt to rebuild the scene completely.
*'''Rebuild Scene''' Clears all objects from the scene then rebuilds them from scratch.
**'''Assign Color...''' Assigns the chosen homogeneous color to all selected reconstructions.
**'''Color Coding (Individual Cells)...''' Applies morphometric color mapping to selected reconstructions. The chosen LUT is used to assign a metric-based color gradient to each reconstruction.
<div align="left">
<ul>
<li style="display:inline-block;"> [[Image:reconstruction-viewer-color-mapping-individual.png|none|thumb|200px|Branch Order and Ice LUT]] </li>
</ul>
</div>
**'''Color Coding (Group of Cells)...''' Applies morphometric color coding to a selected group of reconstruction. Note that this option uses the chosen LUT to assign a homogeneous color to each reconstruction in the group based on the chosen metric.
<div align="left"><ul><li style="display:inline-block;"> [[Image:reconstruction-viewer-color-mapping-group.png|none|thumb|200px|No. Branch Points and Ice LUT]] </ul></div>**'''Color Each Cell Uniquely''' Applies a unique and homogeneous color to each selected reconstruction. Note this option will override any previously applied color mapping to the selected reconstructions.<div align="left"><ul> <li style="display:inline-block;"> [[Image:reconstruction-viewer-color-mapping-unique.png|none|thumb|200px|Unique Color Coding]] </li></ul></div>
**'''Thickness...''' Specifies a constant thickness to be applied to the selected reconstructions. Note this value will only affect how Paths are displayed in the Reconstruction Viewer.
<div align="left">
<ul>
<li style="display:inline-block;"> [[Image:reconstruction-viewer-thickness-1.png|none|thumb|200px|Thickness = 1.0]] </li>
<li style="display:inline-block;"> [[Image:reconstruction-viewer-thickness-5.png|none|thumb|200px|Thickness = 5.0]] </li>
</ul>
</div>
**'''Translate...''' Specifies a translation to be applied to the selected reconstructions. To avoid overwriting data from a tracing session, this command is only available in the standalone viewer.
*'''Remove Selected...''' Deletes the selected reconstructions from the scene.
*'''Remove All...''' Deletes all reconstructions from the scene.
 
==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.
**'''All Parameters...''' Allows adjustment of the color and transparency of the selected mesh(es) and their computed bounding boxes in a single menu.
**'''Color...''' Sets the color of the selected mesh(es).
**'''Transparency...''' Sets the transparency of the selected mesh(es).
*'''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.
663
edits