Preferences: Tracing

You need a reference point to be able to modify these parameters.

View

When you are in edit mode in the Main, 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. Check the box to prevent information pop-ups from appearing unless you depress the Shift key when hovering on a tracing element.

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

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. When the 3-dimensional tracing is displayed on the flat screen, the result is a thick line if thickness is turned on.

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.

  • 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.

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

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.

Contours

See Preferences: Contours

Markers

See Preferences: Markers

Neurons

See Preferences: Neurons

Spines

See Preferences: Spines

Branches

Click the Customize... button for options. In the Customize Branches window that opens, you can specify names and colors for branches, and choose to show or hide them.

Puncta

Click to check/clear the Display Using Channel Colors checkbox.

  • The default Neurolucida software behavior is to assign random colors to puncta as they are detected. When the Display Using Channel Colors checkbox is checked, puncta are instead displayed in the color of their assigned color-channel (i.e., the channel selected in the Channel panel when the puncta are detected).