To trace on an image currently open in ImageJ, use From Open Image…. Specifies the image to trace on without having to restart SNT. Note that clicking on the headings separating the different widgets will point your browser to the relevant section of this manual! Menu Commands File › Tracing Channel Specifies the image channel to trace on (this option is ignored with single-channel images). The default setting provides the XY, ZY, and XZ views and allows for more accurate node placement but requires more RAM. User interface Specifies which views to display for 3D images. json) in the image directory and retrieving the filename closer to Image file. SNT will automatically try to fill this field by looking at all the reconstruction files (.traces. Reconstruction file The path of the reconstruction file to be imported. If no image is chosen, SNT will create an empty display canvas from the computed bounding box of the reconstruction file (if provided). Alternatively, an image path may be specified by clicking Browse and choosing an image file. The drop-down menu will list all images currently open in ImageJ. Image/ Image file The image to be traced/analyzed. 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. SNT is initialized by running Plugins › NeuroAnatomy › SNT…. Reconstruction Plotter A utility for rendering 2D illustrations of reconstructions (including vector formats) without having to load other interfaces Startup Prompt Viewer A fast, streamlined 3D viewer for analysis and quantification of existing neuroanatomical data SNT… The main interface, from which tracing and path editing operations are done
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