Preferences: Tracing

Require shift key to display trace information pop-ups: Check the box to prevent information pop-ups from appearing unless you depress the Shift key when hovering on a tracing element. When you are in edit mode in the 2D window, the default behavior is for trace information pop-ups to display when you hover the cursor on a traced structure, portion of a traced structure, or marker.

Double-click closes contour: Check the box to close contours with a double-click instead of right-clicking or selecting an ending type from the Trace ribbon.

Display line thickness: Displays the thickness of the lines used to trace contours or trees.

Select one of four rendering methods: tapered thickness, next point’s thickness, thickness ratio (larger), thickness ratio (smaller).

To control line thickness, there are three options:

• Go to File > Preferences > Cursor and modify the cursor diameter under Settings.

• Use the + and - keys on the numeric keyboard.

• Scroll the mouse wheel.

The lines you see are representations of three-dimensional cylinders and frusta A frustum is a section of a cone, like a cylinder, but tapered.. When the 3-dimensional tracing is displayed on the flat screen, the result is a thick line if thickness is turned on.

Place points in continuous tracing: This adjustment controls how smooth the tracing is when using continuous tracing mode (see Tracing modes (2D)).

• More: Smoothest curves, but places more points in the data set.

• Fewer: Fewer data points for a given curve, but the curve is not as smooth.

The smoothness of the traced curve must be balanced against the overhead of more data points. Curves with many points are harder to edit.

Show drawn objects in:

• Color: Objects are drawn using the colors that you select.

• Monochrome: Objects are drawn using in monochrome colors.

• Dim Monochrome: Use when the bright monochrome display overpowers your image. This is useful when tracing very dim structures, such as weak fluorescent stains.

Tracing transparency: Adjust the transparency to see the object you are tracing while tracing.

Warn me when Z changes exceed: The Z deviation warning is intended to detect problems in tracing dendritic structures. Tracing branched structures involves many steps during which mistakes can introduce large jumps in Z. Since Z is the dimension going into and out of the screen it is not always clear that points are not close to each other in Z. The warning discriminant is a micron value. A warning is flagged if the difference of the Z coordinates of two sequential points exceeds this discriminant.

Use Selected Image/Z Meter for Z position adjustment: Choose one of the following from the dropdown menu:

• Selected Image: The Z value of points placed in a traced object will match the Z value of the image plane the point was traced on. For example, if you have an image stack with a Z step size of 0.5 µm and you place a point of a traced object on the 4th plane down of the image stack, the Z value of the point will equal -1.5 µm.

• Z Meter: The Z value of points in a traced object will match the Z value that is currently shown in the Z-meter. For example starting on the first plane of an image stack with a starting point of 0.0 µm on the Z meter, if you have the focus movement of the mouse wheel set to 0.6 µm and an image stack with a Z step size of 0.5 µm, and you place a point of a traced object 3 mouse clicks down, you will be placing that point on the 4th image plane of the image stack and the Z value of the point will equal -1.8 µm (not an interval of the Z step size).

Display Using Channel Colors: Check to display puncta in the color of their assigned color-channel (i.e., the channel selected in the Channel panel when the puncta are detected).

The default Neurolucida 360 software behavior is to assign random colors to puncta as they are detected.

Puncta size: Choose one of the following options for puncta sizing:

• In pixels = The size is fixed; zooming in or out, or changing the lens has no effect on the display size of the puncta.

• In micrometers = The size of the puncta depends on the lens selected or the scaling of the image being viewed. The size of the puncta is adjusted as you zoom. The puncta are scaled along with the tracing.

  If a low power lens is selected, or you are zoomed out on an image, you may not see the puncta since they are scaled as small as possible.

• Intrinsic: The intrinsic size for each punctum is defined by the diameter of the circular cursor when the punctum was placed. The intrinsic setting allows each individual punctum to be displayed at a different size. Since this size is defined in actual micron values, the displayed size depends on the lens selected or the scaling of the image being viewed. If a low-power lens is selected, or you are zoomed out on an image, you may not see the puncta since they are scaled as small as possible.