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.
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.
The seed tool is used to select starting locations for automatic tracing.
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.
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.
Sets the 2D display to the forward view. The line of sight is parallel to the Z (optical) axis.
Sets the 2D display to the side view. The line of sight is parallel to the X axis.
Sets the 2D display to the bottom view. The line of sight is parallel to the Y axis.
() indicates an option that can be toggled on or off. () indicates a sub-menu.
|Open... Ctrl+O||Open a 3D image or 2D image sequence.|
|Close||Clears the model and closes the current image.|
|Save Neurites Ctrl+S||Save the model to an existing or new file.|
|Save Neurites As...||Save the model to a new file.|
|Save Spines...||Save the spines to a file.|
|Save Labeling...||Save the edge labeling to a file.|
|Save Measurements...||Save measurements to a file.|
|Save Image...||Save the image (or ROI) into a new file or file sequence.|
|Save Projections...||Save the projections as image files.|
|Import SWC...||Add a model stored in SWC format into the current model.|
|Import Spines...||Add spines to the current workspace.|
|Image Info...||Display information about the current image.|
|Model Info...||Display information about the current model and spines.|
|Delete Neurites X+N||Delete the dendrites.|
|Delete Spines X+S||Delete all spines.|
|Delete Measurements X+M||Delete all measurements.|
|Delete All X+A||Delete model, spines, and measurements.|
|Delete Selected Delete||Delete the selected elements depending on the current mode.|
|Join / Unjoin 2-Selected J||Add or remove an edge between 2 selected vertices. Neurite tool must be active and only 2 vertices selected.|
|Set 1-Selected as Origin||Set the selected vertex as an origin. Only 1 vertex must be selected.|
|Select All Connected||Select all vertices in the same connected component of any selected vertices.|
|Select Sub-Trees||All vertices within the same sub-tree as a selected vertex also become selected.|
|Select by Type / Function ()||A sub-menu for selecting objects by type or function.|
|Select Spine Stems||Select spines that may be created due to inadequate resolution of spine necks.|
|Select Spines on Selected Neurites||Selects spines that are attached to any currently selected neurites.|
|Select Spines with Invalid S.A.||Selects those spines with an attachment area that is greater than their surface area.|
|Create Neurite Selection Paths||Selects all vertices along paths between any currently selected vertices.|
|Set Order of Selected Neurites||Opens a dialog box for manually setting the branch order of any selected neurites.|
|Add Selected Spines to Classifier||Adds any selected spines to the current neural network classifier.|
|Transpose Children of Selected Vertices||Reverses the layout in memory of edges for selected vertices. Useful for rearranging section labeling.|
|Hide Selected||Hides any selected vertices.|
|Unhide All||Unhides any vertices that were previously hidden.|
|Select All Ctrl+A||Selects all elements depending on which tool is active.|
|Deselect All Esc||Deselects any selected elements.|
|Convert Measurements C||Converts measurements into a section of the model.|
|Mode ()||A sub-menu for setting the current mode (tool).|
|Settings...||Open the settings dialog.|
|Spine Classifier...||Open the spine classifier dialog.|
|Build Neurites N||Start the automatic tracing procedure.|
|Build Spines S||Start the spine detection and analysis procedure.|
|Recompute Spine Attachments||Recompute the points where the spines attach to the model.|
|Recompute Manual Spines||Recompute various spine attributes for manual spines only.|
|Visualize R.O.I. F9||Accepts the current region of interest. The projections and volume rendering (if active) are automatically regenerated.|
|Image Filter ()||A sub-menu for various image processing routines.|
|Projections ()||A sub-menu for various options for generating projections.|
|Edge Labeling ()||A sub-menu for various ways of labeling edges.|
|Sholl Analysis||Runs and saves a sholl analysis on the current model.|
|Number of CPU's ()||Specify the number of CPU's for your machine.|
|Image ()||Toggle display of the image.|
|Palette ()||Set the current palette for the 2D and 3D displays.|
|Line/Point Size ()||Set the line and point size (in pixels) for various rendered elements.|
|Colors...||Open the colors window to set the colors of various elements of the display.|
|3D Viewer...||Open the 3D view window.|
|XY Slice Viewer ()||Start the slice viewer display.|
|XY Projection (Axial) ()||Set the 2D display to the forward view.|
|ZY Projection (Side) ()||Set the 2D display to the side view.|
|XZ Projection (Side) ()||Set the 2D display to the bottom view.|
|Fit Image F||Adjust the zoom factor so that the image fits completely within the 2D display window.|
|Actual Pixels A||Set the zoom factor to 100% (no magnification).|
|Center & Limit Image ()||Toggle activation of centering and limiting the image display.|
|Seed Always Visible ()||Toggle whether to display the current seed no matter which mode is active.|
|R.O.I. Always Visible ()||Toggle whether to display the current region of interest no matter which mode is active.|
|Spine Axes ()||Toggle whether or not to show the attachment axis of the spines.|
|Spine ID's (2D Only) ()||Toggle the display of the spine ID numbers in the 2D window.|
|Edge Order Numbers (2D Only) ()||Toggle the display of the edge order numbers in the 2D window.|
|Edge Section Numbers (2D Only) ()||Toggle the display of the edge section numbers in the 2D window.|
|Sholl Spheres (2D Only) ()||Toggles the display of the sholl analysis spheres in the 2D window.|
|Projection Axes ()||Togglw whether or not to show the current axes of the projection in the 2D window.|
|Flash Model F4||Temporarily displays only the dataset.|
|Flash Hidden F3||Temporarily displays any hidden objects.|
|Neurite Vertex Shape ()||A sub-menu for various ways of displaying the vertices of the model.|
|Neurite Vertex Color ()||A sub-menu for various ways of coloring the vertices of the model.|
|Neurite Edge Shape ()||A sub-menu for various ways of displaying the edges of the model.|
|Neurite Edge Color ()||A sub-menu for various ways of coloring the edges of the model.|
|Spine Shape ()||A sub-menu for various ways of displaying spines.|
|Spine Color ()||A sub-menu for various ways of coloring spines.|
|Model Shape (Neurite, Edge, Spine) ()||A sub-menu for various ways of setting the shapes of the neurites, edges, and spines with a single click.|
|Flicker Free (Slower) ()||Toggle synchronized drawing of the 2D and 3D windows.|
|Contents... F1||Access this help documentation.|
|About...||Display a dialog box with various information about NeuronStudio's version and license.|