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 main 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 ).

• 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: Use in conjunction with the monochrome Lucivid. It is possible to switch back to color for editing and visualization when using the computer monitor.

• Dim Monochrome: Use when the bright monochrome display overpowers your image. This is useful when using the Lucivid to trace 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).