Placing Markers

Purpose

Use markers to quickly mark structures of interest in your images.

A variety of marker types (i.e., circle shape, star shape, etc.) are available in the Markers toolbar in the main window.

Showing and hiding the Markers toolbar

By default, the Markers toolbar runs vertically along the left side of the main BrainMaker window.

Right-click in the status bar at the bottom of the main BrainMaker software window and check or uncheck Markers toolbar to show or hide the toolbar.

Using Markers

Placing markers

Click a symbol in the Markers toolbar to select the marker type.

Note that this puts you in Markers mode and disables tracing.
Click in the tracing window to place the marker.
- Continue clicking to place additional markers of the selected marker type.
- To switch to a different marker, select its symbol in the Markers toolbar and click in the tracing window to place it.
Exit Markers mode by clicking the highlighted marker type in the Markers toolbar.

Deleting markers

To delete the last marker placed, press CTRL-Z

To delete all markers of the same marker type, right-click over the marker type in the Markers toolbar and select Delete All Markers of This Type.

Editing markers

There are comprehensive marker-editing options in the main window; see Editing markers (2D)

There are also marker-editing options available in the ; see Editing markers (3D).

Using markers for colocalization

Colocalization markers combine 2, 3, or 4 markers into one marker. This feature is designed for annotating cells and structures that were labeled with two or more staining methods. See Colocalize markers for details.

Changing marker-type properties

Go to File > Preferences > Tracing > Markers or right-click a marker in the Markers toolbar menu to modify the selected marker type.

BrainMaker software applies the change to all markers associated with that symbol, including markers that have already been placed.

Customizing the Markers toolbar

Displaying marker summary and marker names in the Markers toolbar

Marker summary: Number of markers placed for a given marker type. Right-click in the Markers toolbar and select Show Marker Summary.
Marker names: Right-click in the Markers toolbar and select Show Marker Names.

Adding or removing marker types

Right-click over the Markers toolbar and select Customize Marker Bar.

Select markers in the Customize Toolbar window that opens and use the Add and Remove buttons to specify the marker types available in the Markers toolbar. Click Reset to return the Markers toolbar to include the default list of markers.

Hiding a marker type

Right click a marker in the toolbar and select Hide Marker; the marker becomes unavailable in the toolbar and markers of that type that have already been placed are hidden.

See Hidden Objects for information on hiding and revealing objects.

Repositioning the Markers toolbar

To move the Markers toolbar, hover your mouse on the top of the toolbar; the cursor will become a 4-pointed arrow. Drag the toolbar to move it.

Drag the toolbar to any edge of the tracing window to dock it.
Position the toolbar anywhere onscreen as a floating toolbar.