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SNT: Step-By-Step Instructions

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[[Category:SNT]][[Category:Neuroanatomy]]
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<li style="display: inline-block;"> [[Image:SNT-Edit-Path-Connect-To-Result.png|thumb|none|250px|4) Joined result<br>&nbsp;]] </li>
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==Tracing in the Legacy 3D Viewer==
It remains possible to trace in the legacy 3D Viewer.
[[File:SNT-3D-Dialog.png|right|thumb|"Legacy 3D Viewer" widget]]
===I.Starting the Viewer===
To open the viewer, select the ''3D'' menu tab in the SNT dialog and look for ''Legacy 3D Viewer''. You will see 3 parameters:
[[File:SNT-Image-Resampling-Factor.png|right|thumb]]
* Select ''New with image'' from the ''Viewer'' drop-down menu (selecting ''New without image'' would only allow you to look at reconstructions without the underlying signal). Note that you can recycle existing viewers you may have open by choosing there their window titles from the drop-down menu.
* Select the preferred rendering style from the ''Mode'' drop-down menu.
* Once you ''Apply'' the viewer choice, a prompt will appear asking you to choose the resampling factor for the image. Then, the viewer window will appear with the currently open image.
===II.Tracing and Navigation===
* '''Selecting points for tracing''' Select the "''Wand" tool '' ({{key|W}} [[SNT:_Key_Shortcuts#Legacy_3D_Viewer|shortcut]]) in the main Fiji ImageJ toolbar and click over the region you want to trace. Tracing works the same way as in the 2.5D view, i.e., click somewhere in the image to create a starting point, then click further along the structure of interest to find a path between the two points, then confirm or deny the temporary segmentas described [[#Tracing|above]]. Similarly, branching occurs as [[#Branching: Start A Path On An Existing Path|described for 2D canvas(es)]], etc..by holding the {{key|Alt|Shift}} modifier.* '''Rotation''' Either use the "''Hand" tool'' ({{key|H}} [[SNT:_Key_Shortcuts#Legacy_3D_Viewer|shortcut]]) tool and left-click while dragging the mouse ''or'' drag mouse while holding the scroll wheel.
* '''Translation''' Hold {{key|Shift}} and the scroll wheel while dragging the mouse.
* '''Adjusting zoom depth''' Scroll the mouse wheel.
Once you have selected each of these tools (Wand and Hand) once, you should be able to switch between them by pressing the {{key|Esc}} key. See [[SNT:_Key_Shortcuts#Legacy_3D_Viewer|Key Shortcuts]] for the list of all supported shortcuts.
[[File:Fiji-toolbar-wand-and-hand-2.png|center]]
The following key shortcuts also work in the 3D Viewer:
 
* {{key|Y}} confirm the temporary path segment
* {{key|N}} cancel the temporary path segment
* {{key|F}} complete the current path
* {{key|G}} select the current path under the mouse pointer
 
You can still create branches and joins in the 3D Viewer as you would in the 2D viewer. First, select the path you want to branch off, or join to by pressing {{key|G}} while the mouse pointer is over that path. (It should turn green.) Then create the join or branch by holding down the join modifier key ({{key|Alt}} and clicking at the right point on the selected path.
=Filling=
There is a simple facility in this plugin for "filling out" paths to volumes. This is not particularly sophisticated, but often good enough for a rough visualization of the shape of a neuron beyond what can be seen from the traced path.
=Accurate Point Placement=
This section describes methods to increase the accuracy of node placement.
===Step by Step===
When starting up, make sure that "Default: XY, ZY and XZ views" is selected:
{||-|Accurate node placement requires ''XY'', ''ZY'' and ''XZ'' views to be visible. You can do so at [[SNT:_Overview#Startup_Prompt|startup]], by making sure that ''Default: XY, ZY and XZ views'' is selected, or by clicking in ''Display ZY/XZ Views'' in the [[SNT:_Overview#Options_Tab|Options tab]] if you have already started SNT.|[[Image:SNT-Three-Pane-View-Enabled-Startup-Prompt.png]]|-|Find the approximate location of your start point by moving your mouse in the XY window, holding down {{key|Shift}} to synchronize the view in the other panes. At this point, you should enable cursor [[SNT:_Overview#Cursor_Auto-snapping|auto-snapping]] in the [[SNT:_Overview#Main_Tab|Main tab]] using suitable parameters for your image.|[[Image:SNT-Accurate-Point-Placement-Walkthrough-Updated-1.png|350px]]|-|When you press {{key|+}} to zoom in, all the panes will zoom in on the point that the crosshair is over, so each time you press {{key|+}}, make sure you move your mouse pointer so that it's still over the structure of interest. You may want to adjust in the [[SNT:_Overview#Views|Views]] widget ([[SNT:_Overview#Options_Tab|Options tab]]) whether all views should zoom synchronously.<br>At this point, you should adjust a suitable [[SNT:_Overview#Cursor_Auto-snapping|snapping neighborhood]] both in 2D (XY) and 3D (Z). Note that when Z-snapping is enabled, all views become synchronized,|[[Image:SNT-Accurate-Point-Placement-Walkthrough-Updated-2.png|350px]]|-|Locate the center of the structure to be clicked on. If [[SNT:_Overview#Cursor_Auto-snapping|cursor auto-snapping]] is enabled, simply mouse over the structure, otherwise, try moving the mouse and scroll wheel in each of the panes (holding down {{key|Shift}} so synchronize the views in all three panes). Note that you can toggle the cursor auto-snapping feature at will, by pressing the [[SNT:_Key_Shortcuts|shortcut]] {{key|S}}. Also, note that you can "click" on the [[SNT:_Key_Shortcuts#Tracing|brightest voxel]] of a voxel column, by pressing {{key|M}}.
Find the approximate location of your start point by moving your mouse in the XY window, holding down {{key|Shift}} to synchronize the view in the other panes: [[Image:SNT-Accurate-Point-Placement-Walkthrough-Updated-1.png|400px]] When you press {{key|+}} to zoom in, all the panes will zoom in on the point that the crosshairs is over, so each time you press {{key|+}}, make sure you move your mouse pointer so that it's still over the structure of interest: [[Image:SNT-Accurate-Point-Placement-Walkthrough-Updated-2.png|400px]] To make sure you're clicking in the center of the structure, try moving the mouse and scroll wheel in each of the panes (holding down {{key|Shift}} so synchronize the views in all three panes). When you're happy with the point under the crosshairs, left-click to start the path: |[[Image:SNT-Accurate-Point-Placement-Walkthrough-Updated-3.png|400px350px]]|-|Zoom out again with the {{key|-}} key, and similarly zoom in on the next point you want to be on your path to place it precisely: |[[Image:SNT-Accurate-Point-Placement-Walkthrough-Updated-4.png|400px350px]]|-|The path along the neuron may not follow the center line perfectly: |[[Image:SNT-Accurate-Point-Placement-Walkthrough-Updated-5.png|400px350px]]|-|... but you can later improve that with the {{bc|Refine/Fit|Fit Path...}} option in the [[SNT:_Overview#Path_Manager|Path Manager]], which tries to fix align the path to the midline and radius of the structure to sub-voxel accuracy: |[[Image:SNT-Accurate-Point-Placement-Walkthrough-Updated-6.png|400px350px]]|-|}
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