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SNT: Manual

1 byte added, 21:16, 18 May 2019
SNT is initialized by running {{bc|Plugins|NeuroAnatomy|SNT...}}. All the options in the startup prompt can be set once SNT is opened, but the startup prompt provides the convenience of setting the most important parameters at once.
* '''Image'''/'''Image File''' The image to be traced/analyzed (optional). The drop-down menu will list all images currently open in ImageJ. Alternatively, an image path may be specified by clicking ''Browse'' and choosing an image file. If no image is chosen, SNT will create an empty display canvas from the computed bounding box of the reconstruction file (if provided).
* '''Reconstrucion Reconstruction file''' The path of the reconstruction file to be imported (optional). SNT will automatically try to guess if there is a reconstruction file associated with the chosen image by looking at all the reconstruction files (<tt>.traces</tt>, <tt>.(e)swc</tt>, or <tt>.json</tt>) in the image directory, and choosing one that more [ closely matches] the image filename.
* '''User interface''' Specifies which views to display for 3D images. The default setting provides the XY, ZY, and XZ views and allows 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 (this option is ignored with single-channel images).