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SNT: Manual

11 bytes removed, 8 May
WIP: minor improvements to text/layout
(Return to the main [[SNT]] page)
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=Main Dialog=
==Main Tab==
===Cursor Auto-snapping===
'''Enable Snapping checkbox''' If active (the default) the cursor snaps to the brightest voxel in its vicinity (Toggling shortcut: {{Key|S}}). To accomplish this, SNT takes the cuboid of the specified dimensions (in pixels) centered on the current cursor position and searches quickly for local maxima in that neighborhood, moving the cursor to that position. The Z-plane in which the maximum was found is automatically selected if the "Z" parameter is greater than 0. Noteworthy:
* This feature assumes the signal is brighter than the background as typically found in fluorescent images.[[File:cursor-snap.png|right|border]]* If multiple maxima exist (e.g., when the signal is saturated), it snaps to their centroid.[[File:cursor-snap.png|right|border]]
* To streamline the computation: XYZ dimensions are constrained to even numbers and limited range.
* Snapping occurs in 2D (i.e., in the active plane) if Z=0.
===Auto-tracing===
[[File:SNT-auto-tracing.png|right|thumb|"Auto-tracing" widget]]'''Enable A* Star''' By default, SNT uses the [https://en.wikipedia.org/wiki/A*_search_algorithm A* search algorithm] to automatically trace paths between two manually selected points. To manually place nodes in a path, toggle this feature off. Note that it is also possible to enable other algorithms through the installation of further SNT addons. See [[SNT: Tubular Geodesics|Tubular Geodesics]] for more details.
'''Hessian-based analysis''' (Toggling shortcut: {{Key|H}}) A quick way to improve the quality and efficiency of the pathfinding is to enable this feature, in which paths are computed after filtering the image for tube-like structures. Upon such filtering, SNT will use a measure of [[Tubeness]] at each point of the image to define the best path through it, based on eigenvalues and eigenvectors of the Hessian matrix. The later can be used to infer the likelihood that a point in the image belongs to a a tube-like structure. This concept is also known as ''vesselness'' or ''neuriteness''.
'''Hessian options''' (Specified in the ''gear'' drop-down menu). Hessian analysis requires two parameters to be specified:
* '''Maximum''' The maximum pixel intensity on the ''Tubeness'' image beyond which the cost function for A* search is minimized.
These parameters may be chosen "Manually" (if you already have a quantitative understanding of the image) or "Visually" (generally more intuitive). If you choose "Visually", the dialog will prompt you to click on a representative region of the image which has meaningful structure. Once you click there, a 9-square palette is generated showing increasing values of sigma (from top-left to bottom-right) applied to that chunk region of the image. The palette is an image stack which can be scrolled through with the mouse wheel.
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===Filters for Visibility of Paths===
By default, the entire path is 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 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 Manger 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.
===Default Path Colors===
Path coloring in SNT indicates status of the path. The default color indicators for finished paths are: [[File:Default-path-colors.png|right|thumb|300px|"Default Path Colors" widget]]
[[File:CMYK-color-model.png|right|thumb|300px|CMYK color selection UI]]
* By default, finished paths are colored by their selection status (only selected paths can be edited, or extended). The default colors are <pre stylefont color="color: #00FF00;font-size:20px">Green</prefont> Selected* (selected paths) and <pre stylefont color="color: #FF00FF;font-size:20px">Magenta</prefont> Deselected (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, meaning see the path cannot be extended or edited until selected''Colors'' option in the [[#UI_Interaction|UI Interaction]] widget.
The '''Enforce default colors (ignore color for each path type can be changed tags)''' If active, SNT will force all paths to conform to any color in the [https://en.wikipedia.org/wiki/CMYK_color_model CMYK color model]. To do so for selected and deselected paths, press the default "Selected" or and "Deselected" button in the "Default Path Colors" widgetcolor buttons. For unconfirmed and temporary paths, see Any custom color tags will be ignored until the "Colors" option in the [[SNT:_Overview#UI_Interaction|UI Interaction]] widgetis toggled off.
{{Tip| id = coloring-paths|tip = The "Enforce default colors (ignore color tags)" option, if active, will force all paths to conform to the default colors specified by the "Selected" and "Deselected" color buttons. Any custom color tags will be ignored until the option is toggled OFF. Selected paths can be assigned color tags in the [[#Path Manager|Path Manager. To do so, go ]] offers several ways to colorize Paths: 1) Using {{bc | Tag | Color}} then choose the desired swatch. A path swatches (custom colors can be temporarily assigned a custom color to empty swatches, by right-clicking an empty swatch, which will bring up the CMYK palette. The chosen color will be temporarily saved in that swatch. Metric-based color mapping of paths can be done in the Path Manager through the clinking on them) or 2) Using {{bc|Analyze|Color Coding}} menu option. See , providing morphometric-based [[SNT:_Overview#Analyze|herecolor mapping]]. To change color of Note that Path Manager commands are applied to all paths, deselect all paths firstif no no path(s) are selected.{{Tip| id = color-swatches|tip = Hover the mouse cursor over a color swatch to display a tooltip with its RGB value.}}{{clear}}
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<li style="display:inline-block;"> [[Image:Path-manager-color-tag.png|none|thumb|260px200px|Color tagging]] </li><li style="display:inline-block;"> [[Image:Color-tag-result-2.png|none|thumb|260px200px|Arbitrary path coloring]] </li><li style="display:inline-block;"> [[Image:Color-tag-result-image.png|none|thumb|340px200px|Result]] </li>
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==Options Tab==
===Views===
[[File:SNT-views-widget.png|right|thumb|"Views" widget]]* '''Overlay MIP(s) at X% opacity''' Overlays the [https://en.wikipedia.org/wiki/Maximum_intensity_projection Maximum Intensity Projection] of the image onto "over" the current Z-slice image canvas at the specified opacity. Overlaid projection is only used as a visualization aid and is ignored by the auto-tracing algorithms. It is rendered using the LUT of the channel currently being traced. To reload the overlay (e.g., in case the image being traced changes during a tracing session) toggle the checkbox twice.{{clear}}<div align="leftcenter">
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<li style="display:inline-block;"> [[Image:OP1-without-MIP.png|none|thumb|300px250px|Image without MIP overlay]] </li><li style="display:inline-block;"> [[Image:OP1-with-MIP.png|none|thumb|300px250px|Image with MIP overlay at 30%]] </li>
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* '''Draw diameters in XY view''' Displays the stored diameter (if any) in the XY view for all existing nodes. Each diameter is drawn as a line segment with length = diameter, which is bisected by the orthogonal tangent vector to the path at that node.
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<li style="display:inline-block;"> [[Image:Draw-diameters-disabled.png|none|thumb|300px200px|Draw diameters in XY view - disabled]] </li><li style="display:inline-block;"> [[Image:Draw-diameters-enabled.png|none|thumb|300px200px|Draw diameters in XY view - enabled]] </li>
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* '''Apply zoom changes to all views''' If a zoom change is applied to any one of the XY, ZY or XZ views, apply the same change to the two other views if they are open. May Since in ImageJ zooming may resize windows.the image window, you can use {{bc|Views|Arrange Views}} to reset their positions
* '''Resize Canvas''' If using a display canvas to view reconstructions, reset its dimensions to the default. (Currently, this command is only available for display canvases, to resize an image go to IJ's command {{ bc | Image | Adjust | Canvas Size...}}
* '''Display ZY/XZ views''' If currently using the XY only view, display the ZY and XZ views as well.
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