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The Main Window

The main window (shown below) provides easy access to the capabilities of the program. On the right side of the window are the tools and view panel which allow you to switch modes of operation or switch the viewing direction by clicking the appropriate button. This can also be accomplished by using the main menu.

The status bar at the bottom of the window displays information such as cursor coordinates, zoom factor, measurement output, etc.

NeuronStudio Interface

Buttons

Zoom Tool The zoom tool is used to zoom in or out of the 2D display.

TIP: If your mouse has a scroll wheel it may be used to quickly zoom in and out of the display, regardless of which tool is active.

Move Tool The move tool is used to translate the display for the current view. It is also used to translate and rotate selected parts of the model.

Seed Tool The seed tool is used to select starting locations for automatic tracing.

Measure Tool The measurement tool is used to sample the image data to determine such information as diameter(width) and length. It is also used to select measurements and manually create new sections of the model.

Spine Tool The spine tool is used to manually add new spines and to select spines for editing.

Neurite Tool The neurite tool is used to create new sections of the model by semi-manual tracing. It is also used to select vertices of the model for editing.

ROI Tool The R.O.I. tool is used to adjust the region of interest for the current dataset, allowing for faster visualization of the data contained within it, since data outside of the region is ignored. In addition, it is used to limit analysis to a specified cuboid section of the data for some operations.

Magnet Tool The magnet tool is used to quickly select vertices of the model for editing and translation. It can also be used to translate the display for the current view.

Forward View Sets the 2D display to the forward view. The line of sight is parallel to the Z (optical) axis.

Side View Sets the 2D display to the side view. The line of sight is parallel to the X axis.

Top View Sets the 2D display to the bottom view. The line of sight is parallel to the Y axis.

Menus

(c) indicates an option that can be toggled on or off. (s) indicates a sub-menu.

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Send questions or comments to: alfredo.rodriguez@mssm.edu