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SNT: Manual

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Tiago moved page SNT: Overview to SNT: Manual: Improve naming consistency
(Return to the main {{SNTNavBar}}[[Category:SNT]] page)[[Category:Neuroanatomy]]<div class="toclimit-32">
=Startup Prompt=
[[Image:SNT-Startup-Prompt.png|right|thumb]]
Each of these SNT is initialized by running {{bc|Plugins|NeuroAnatomy|SNT...}}. All the options may in the startup prompt can be changed set once SNT is opened, but the startup prompt provides the convenience of setting the most important parameters at once.* '''Image'''/'''Image File''' Allows selection of the The image to display in the viewsbe traced/analyzed. If an image is already displayed in ImageJ, it may be selected in the The drop-down menuwill list all images currently open in ImageJ. Alternatively, an image path may be specified by clicking ''Browse'' and choosing an imagefile. If no image is chosen, SNT will create an empty display canvas from the computed bounding box of the reconstruction file (if provided). If no reconstruction is provided, no placeholder image is created.* '''Reconstrucion Reconstruction file''' The path of the reconstruction file to importbe imported. If an image SNT will automatically try to guess if there is loaded, the a reconstruction is rendered on file associated with the chosen imageby looking at all the reconstruction files (<tt>. Otherwisetraces</tt>, <tt>.(e)swc</tt>, it is rendered or <tt>.json</tt>) in an empty display canvasthe image directory, and choosing one that more [https://en.wikipedia.org/wiki/Levenshtein_distance closely matches] the image filename.* '''User interface''' Specifies which views to displayfor 3D images. The default setting provides the XY, ZY , and XZ views. Memory and screen space can be saved by choosing the ''Only XY view'' optionallows for more [[SNT:_Step-By-Step_Instructions#Accurate_Point_Placement|accurate node placement]] but requires more RAM.* '''Tracing Channel''' Specifies the image channel to trace on. If tracing on a (this option is ignored with single-channel image, leave this option as the default value (1images).
=Main Dialog=
===File===
Lists commands for I/O operations. Most are self-explanatory. Noteworthy:
[[Image:SNT-From-Open-Image-Prompt.png|right|thumb|200px|]]* {{bc|Choose Tracing Image|&nbsp;}} Specifies the image to trace onwithout having to restart SNT. To trace on an image currently open in ImageJ, use ''From Open Image...''. A prompt with the currently open images will appear, allowing selection of one. To browse for an imagefile, use ''From File...''. You should toggle the ''validate spatial calibration'' checkbox to ensure the image to be imported is compatible with the existing one.  * {{bc|Import| Labels (AmiraMesh)...}} This option assumes you are tracing on the same spatial coordinates of an annotated neuropil, for which compartments have been segmented (''labeled'') and stored in an [https://amira.zib.de/ Amira] labels file. Once loaded, SNT will report the name of the compartments in the ImageJ status bar when hovering over the image. [[Image:SNT-FromMouseLight-OpenRemote-ImageLoader-Prompt.png|leftright|thumb|"From Open Image200px|]]* {{bc|Import| Remote Databases|&nbsp;}} Allows import of neuronal reconstructions from the [http://www.flycircuit.tw/ FlyCircuit], [https://ml-neuronbrowser.janelia.org/ MouseLight] and [http://neuromorpho.org/ NeuroMorpho] remote databases.  * {{bc|Export (All Paths)|&nbsp;}} Allows export of all traced paths in the [[SNT:_FAQ#swc|SWC]] file format, the most common format for representing neuronal reconstructions. Note that you can also export subsets of paths using the [[#Path Manager|Path Manager]]. Additionally, useful numeric properties of paths can be stored in a CSV file by choosing the ''CSV Properties...'' export option.<div align="left"><ul> <li style="display:inline-block;" prompt> [[Image:SNT-Path-CSV-Properties-Example-Spreadsheet.png|none|thumb|600px|OP_1 CSV Properties snapshot in LibreOffice]]</li></ul></div>
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 ===Utilities===* {{bc|ImportQuick Measurements| Labels (AmiraMesh)}} Allows import and rendering of AmiraMesh filesShows a table with summary statistics for all existing paths. To measure only selected paths, use {{bc|Analyze|Measure}} in the native file format of the Path Manager. * {{bc|Sholl Analysis...}} Shows a help menu which describes how to conduct [[Simple_Neurite_Tracer:_Sholl_analysis|Sholl Analysis]] from within SNT on existing paths.<div align="left"><ul> <li style="display:inline-block;"> [[httpsImage:SNT-Sholl-Analysis-How-to-Menu.png|none|thumb|200px]] </li></amiraul></div>* {{bc|Strahler Analysis}} Conducts Strahler Analysis on existing paths, producing a table of analysis results and a Strahler plot.zib<div align="left"><ul> <li style="display:inline-block;"> [[Image:SNT-Strahler-Analysis-Table.depng|none|thumb|200px|Strahler Analysis table for OP_1]] </ Amirali><li style="display:inline-block;"> [[Image:SNT-Strahler-Analysis-Plot.png|none|thumb|200px|Strahler Analysis plot for OP_1]] data visualization software</li></ul></div>* {{bc|Reconstruction Plotter. ..}} Plots a dynamic 2D projection of all existing paths. A control panel is included which allows adjustment of the spatial orientation of the tracing. If paths are assigned color tags, use {{bc|Actions|Render final (colorized) plot}} from the control panel to render the (static) plot with color-mapped paths, with the final orientation matching that of the dynamic plot.<div align="left"><ul> <li style="display:inline-block;"> [[Image:SNT-AmiraReconstruction-MeshPlotter-Example.png|none|thumb|200px]] </li><li style="display:inline-block;"> [[Image:SNT-Reconstruction-Plotter-Controls.png|none|thumb|200px]] </li><li style="display:inline-block;"> [[Image:SNT-Reconstruction-Plotter-Colored.png|none|thumb|200px]] </li></ul></div>* {{bc|Compare Reconstructions...}} Given two input reconstruction files, runs ''Quick Measurements'' on both and generates a plot with summary statistics, allowing for quick morphometric comparisons.<div align="left"><ul> <li style="display:inline-block;"> [[Image:SNT-Compare-Reconstructions-Table.png|none|thumb|AmiraMesh Fly brain600px|Comparison of OP_1 and OP_2]]</li></ul></div>
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* {{bc|Import| Remote Databases|}} Allows import of neuronal reconstructions from the [http://www.flycircuit.tw/ FlyCircuit], [http://ml-neuronbrowser.janelia.org/ MouseLight] and [http://neuromorpho.org/ NeuroMorpho] remote databases.
[[Image:SNT-MouseLight-Remote-Loader-Prompt.png|left|thumb|MouseLight reconstruction loader prompt]]
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* {{bc|Export (All Paths)}} Allows export of all traced paths in the [http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html SWC] file format, a widely used standard for representing neuronal reconstructions which is supported by most annotation and visualization software. Additionally, useful numeric properties of paths can be stored in a CSV file by choosing the ''CSV Properties...'' export option.
===Utilities===
* {{bc|Choose Tracing Image|}} TBD
* {{bc|Import| Labels (AmiraMesh)}} TBD
* {{bc|Import| Remote Databases|}} TBD
* {{bc|Export (All Paths)}} TBD
===Scripts===
TBD
Contains commands for organizing tracing views on screen, plus commands for displaying cached data used for auto-tracing.
* '''Arrange Views''' Resets the view pane on-screen positions to their default.
* '''Hide Tracing Canvas''' Allows toggling of the visibility of the three view panes as well as the Legacy 3D View window.
* '''Show Cached ''Filtered Image''''' Displays the cached filtered image in a separate window. Note a filtered image must be loaded in order to use this feature. The process of loading a filtered image is detailed in [[SNT:_Step-By-Step_Instructions#Generating_Filtered_Images|Generating Filtered Images]].
* '''Show Cached ''Hessian Tubeness Image''''' Displays the cached ''Hessian (Tubeness) image'' in a separate window. Note there are two ways to enable this feature. Either 1) enable ''Hessian-based analysis'' then run the ''Cache All Hessian Computations'' command from the "Auto-tracing" gear drop-down menu or 2) use the ''Load Precomputed "Tubeness" Image'' option in the same gear menu. These features are detailed in the "Auto-tracing" section of the [[SNT:_Overview#Main_Dialog|Main Dialog]] overview guide.
==Main Tab==
Other options are also available in the ''gear'' drop-down menu:
* '''Cache All Hessian Cached Computations(Main/Secondary Image)''' By default SNT computes the Hessian matrix on a "compute-as-you-go" basis, which saves memory but increases the pathfinding time. If you have enough RAM, you can use this option set of options to compute once the matrix and once for the full image and cache the result, which in certain cases, can lead to almost-instantaneous searches. Note that this computation adopts the current values of sigma and max. reported in the widget, so you should adjust those before running this command. 
* '''Flush Cached Data''' Removes cached data from memory
* '''Load Precomputed "Tubeness Image"''' This (advanced) option prompts you to load a file of a ''Tubeness image'' generated elsewhere. This is useful if e.g., you want o experiment algorithms from other software packages, or your own. Note that loaded image is assumed to have compatible dimensions with the image currently being traced.
* '''Show Cached "Tubeness Image"''' Displays the ''Tubeness'' data currently cached. Useful for debugging purposes. Also mirrored in {{bc | View | Show Cached/Loaded Hessian (Tubeness) Image}}.
[[File:original-hessian-side-by-side.png|center|thumb|600px400px|Original (left) and Hessian (right) TBD: Replace with MIPsOP_1 "Tubeness" image overlay at 80% opacity]]
===Tracing on Filtered Secondary Image===This is one of SNT's most advanced features. [[#Auto-tracing|Hessian-based analysis]] provides a convenient and easy way to perform auto-tracing on pre-process processed data in which voxels defining the traced structure are scored by their likelihood of ''belonging'' to a tube-like structure. However, it is just one approach for "tubeness" classification. What if your data requires different filtering?, or you want to experiment with other approaches?, or the perfect pre-processing algorithm for your images is not yet available in ImageJ? ''Tracing on Filtered Secondary Image'' is the answer to these questions: It allows you to feed SNT with pre-processed data on which the A*star search will operate. Here are two specific usages for this option:
*'''Frangi ''Vesselness'' filtering''' For certain datasets Frangi filtering ([https://link.springer.com/content/pdf/10.1007%252FBFb0056195.pdf Frangi et al. 1998]) is more effective than [[Tubeness]] at enhancing tube-like structures in the image. However, it is more computation intensive, and thus, less suitable to be adopted by the "compute-as-needed" approach used in Hessian-based analysis. Thus, one can import a pre-computed Frangi-filtered image using this option.
*'''Hessian-analysis at multiple scales''' Let's consider a structure formed simultaneously by very thick and very thin processes(e.g. axons and dendrites). To trace it one would need to adjust continuously the sigma parameter while tracing. Instead, to trace structures of variable diameters more effectively, one could load a copy of the Hessian current image associated with the second sigma could be loaded as ''Filtered Imagesecondary image'', and assign different hessian parameters to both images.
*'''Adopting probability maps''' Pre-classified images (using e.g., machine learning) could also be loaded here.
Importantly, this option can be toggled at will, during tracing. Indeed, one can ping-pong between ''filtered secondary image'' and tracing main image simply, by pressing {{key|I}}, the shortcut for the ''Trace on filtered Secondary '''I'''mage'' checkbox.
'''Filtered Secondary Image options''' can be specified in the ''gear'' drop-down menu, including commands for Loading/displaying the image file and the powerful ''Generate Filtered Secondary Image'' command:
TBD[[Image:SNT-Tracing-On-Filtered-Image-Gear-Options.png|right|thumb|200px]][[Image:SNT-Generate-Filtered-Image-Prompt.png|right|thumb|200px]]* '''Load Specified File''' Loads the filtered image specified in the ''File'' textbox. * '''Generate Secondary Image''' Enables processing of the currently open image directly from SNT. Three routines are currently supported: ''Frangi'', ''Frangi (without Gaussian)'' and ''Tubeness''. Supports saving and display of the resulting image. To use the currently open image as the secondary image, choose ''None. Duplicate Primary Image''. Noteworthy: It is assumed that the current sigma value in the Auto-tracing widget reflects the size of structures to be filtered. If that is not the case, the sigma should be adjusted before running this command.* '''Adjust Min-Max''' Sets the range of pixel intensities used by A* search. * '''Show Cached image''' Displays the currently loaded filtered image in a separate window.* '''Show Path in File Explorer''' Opens the directory containing the filtered image specified in the ''File'' textbox in the File Explorer GUI.
See the [[SNT:_Step-By-Step_Instructions#Generating_Filtered_Images|Generating Filtered Images]] walk-through for more details.
{{clear}}
===Filters for Visibility of Paths===
By default, all the entire nodes of a path is are projected onto the current Z-slice. This is useful to see how much has been completed and gives a sense of the overall structure of the reconstruction. However, SNT provides 3 three additional visibility options for paths:
[[File:Path-visibility-filters.png|right|thumb|"Filters for visibility of paths" widget]]
# '''Only selected paths (hide deselected)''' Only show paths that have been manually selected in the Path Manager or with the {{Key|G}} key ({{Key|Shift}}+{{Key|G}} to select multiple paths).
# '''Only nodes within X nearby Z-slices''' Only highlight nodes within X number of Z-slices on either side of the current slice. The projected skeletons of all paths remain visible.
# '''Only paths from active channel/frame''' If tracing on a multichannel image or an image with a time axis, only show paths from the active channel or frame.
Any combination of these options may be toggled simultaneously. Note that these options do not apply to [[SNT:_Reconstruction_Viewer|Rec. Viewer]] and [[SciView]].
===Default Path Colors===
By default, finished paths are colored by their selection status (only selected paths can be edited, or extended). The default colors are <font color="#00FF00">Green</font> (selected paths) and <font color="#FF00FF">Magenta</font> (deselected). Default colors can be customized by pressing the respective button in the widget and using the [https://en.wikipedia.org/wiki/CMYK_color_model CMYK color chooser]. For customizing unconfirmed and temporary paths, see the ''Colors'' option in the [[#UI_Interaction|UI Interaction]] widget.
'''Enforce default colors (ignore color tags)''' If active, SNT will force all paths to conform to the default "Selected" and "Deselected" color buttons. Any custom color tags will be ignored until the option is toggled off. Note that this options does not apply to [[SNT:_Reconstruction_Viewer|Rec. Viewer]] and [[SciView]].
{{Tip| id = coloring-paths|tip = The [[#Path Manager|Path Manager]] offers several ways to colorize Paths: 1) Using {{bc | Tag | Color}} swatches (custom colors can be temporarily assigned to empty swatches, by right-clinking on them) or 2) Using {{bc|Analyze|Color Coding}}, providing morphometric-based [[SNT:_Overview#Analyze|color mapping]]. Note that Path Manager commands are applied to all paths if no no path(s) are selected.
=Fill Manager=
Provides controls for all filling operations. It is described in more detail in the [[SNT:_Step-By-Step_Instructions#Filling|Filling: Step-By-Step Instructions]].
{{SNTNavBar}}
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