Preferences: Neurons

Purpose

Use Neurons preferences to customize tree colors and adjust structure visibility and display characteristics.

To access Neurons preferences:

• Go to File > Preferences > Tracing > Neurons.

  OR

• In the 2D window, enter Neuron tracing mode, then click the cog icon in the Neurons section of the Trace ribbon.

Neurons

Fill cell bodies: Check the box to display cell bodies as filled contours. If the box is not checked, the cell bodies are displayed as wire frame contours.

Color by branch order: Check the box to color-code tree branches by order. (See also Branch Ordering.) The colors indicated in the Neuron Structure Colors box are assigned to each branch order. If the box is not checked, all branches in a tree have the same color.

• There are 14 colors that the program cycles through to display branch orders. This means that the first and the 15th branch order have the same color.

• To change the color of a branch order, double click on the color square next to the branch order name and choose a new color from the color picker.

Show: Check a box to display that structure type: axons, dendrites, cell bodies, apical dendrites, ending labels, and nodes. You may decide to conceal neuronal structures to reduce the clutter in the tracing window. Even when structures are not displayed, you can view them by using Reveal hidden objects.

• Ending labels: Show ending labels displays text labels for branch endings are displayed. The endings include: N = normal, I = incomplete, L = low, H= high, M = midpoint, O = origin, G = generated.

  Placing and displaying ending labels can be useful when stitching branched structures between sections (e.g., lows can be matched to highs). (See Tracing trees: endings)

• Nodes: Show nodes displays a small filled or open circle at the location of nodes (branch points) the same color as the branch. If you can't see the node, increase its size under Node Size.

  Displaying a node helps to visualize where branched structures are joined, but the nodes may obscure small structures and other details that lie close to the nodes.

Hide: Check a box to hide spines or branches. (See also Hidden objects.)

Node style: Choose a node style from the dropdown menu to display nodes as closed circles or open circles.

Node size: Enter a pixel value into the text box to adjust the display size of nodes.

Varicosity marker: Click Change to choose a marker style for varicosities.

Neuron Structure Colors: This table contains the list of tracing structures and their corresponding colors.

• There are 14 colors that the program cycles through to display structures. This means that the first and the 15th structure have the same color.

• To change the color of a structure, double click on the color square next to the structure name and choose a new color from the color picker.

• To modify the color of each neuron structure after it has been traced, see Editing trees (2D).

Bright/Dark colors: Check a box to choose a color scheme.