Workspace ribbon

Purpose

The Workspace ribbon contains useful tools and windows that are essential to helping you get the most out of using Neurolucida. They include windows that help with navigation, panels that assist with acquiring, viewing and analyzing images, and tools for general analysis.

Workspace groups

Views

	The Macro View window provides an aerial view of the entire tracing (with or without images). The view is a top-down perspective along the X and Y axes (as in the main window). For more details, see Macro view.
	Use the Z meter to view the cursor location in the Z axis; it is helpful as you navigate or trace. See Z meter for more information.
	Use the orthogonal view to view tracing/image data from the side, along the XZ axes or the YZ axes. It is also useful for quickly moving the displayed portion of tracing/image data. For more instructions, see Orthogonal view .
	View your image or image stack, plus your reconstruction data in three dimensions, as a partial projection, or as cross sections. Use the 3D Visualization window to create video clips, and export your 3D representations. Edit trees, somas, spines, vessels, markers and contours that were placed in the main Neurolucida software window. See 3D visualization overview for detailed instructions.
	Click to display a grid in the main window. Displaying the grid may be useful for: camera alignment, checking lens calibration or stage movements, and visually dividing a region into fixed areas for further analysis. For more instructions, see Grid.
	Define the size of the AutoMove area in the main window. See AutoMove for more instructions.
	AutoMove is an automatic centering procedure. It acts in conjunction with the AutoMove area, represented as a dashed rectangle, to help enable you to trace structures larger than a single field of view. The tracing and the stage or image move together so that there is no loss in registration (there may be a momentary delay as the stage moves to its new location). See AutoMove for more information.

Acquisition tool panels

	The camera histogram displays a graphical representation of the dynamic range (visual brightness and contrast) of the live camera feed. See Camera histogram for more information.
	This is a generic interface for controlling the camera parameters that may vary slightly depending on the camera you have. For more details, see Camera settings.
	The Multichannel control window enables you to adjust and memorize camera settings for individual color channels in preparation for acquiring images in more than one color channel. See Multichannel control for more information.
	Acquire an image stack from the current field of view. This creates a single image file comprised of a series of stacked image planes that represent z-planes of the specimen. For more detailed instructions, see Acquire an image stack.

Image

	The Image Organizer displays the location and status of each image that is open in the main window and provides options for manipulating image appearance. For more details, see Image organizer.
	The Image Adjustment panel enables you to change how the current image looks on screen. You can save these adjustments with the image if you choose; you'll be prompted to decide when you close the file or exit the software. See Image adjustment for more information.
	The Luminance Histogram is a visual representation of luminance data collected from image data contained within a contour. Collect luminance must be activated to see data in the histogram. See Luminance histogram for instructions.

Tracing

	Use the Serial Section Manager to define the key parameters (i.e., initial section thickness, Z position, etc.) for each section. For in depth instruction, see Serial section manager.
	Contour measurements Analyses of all contours visible in your current tracing. The data are updated in real time as you trace new contours. For more details, see Contour measurements.

Arrangement

	Click to reset all docked windows to their default location.
	Click to close all dockable windows.