Point List

The point list panel displays a list of annotations for one stack.

To open a point list panel

  • Right-click a stack and select the menu ‘Windows … Point List’.
  • In a stack window, use the ‘Point List’ button in the left-panel. Open the left-panel with keyboard ‘[’.


Select individual annotations in the list and the selection will propagate to open stack windows, stack plots and map plot windows. The action performed when an annotation is selected can be specified in the ‘On Selection’ popup.

  • Select. Select the annotation .
  • Select + Snap Image. Select the annotation and snap to the (z) image plane.
  • Select + Snap Image + Zoom. Select the annotation, snap to the (z) image plane, and zoom in on the annotation. The amont of zoom is controlled in Options - Stack Display - Default Zoom Width/Height.

Choose the type of annotation to display with the ‘Object Type’ popup. For spine annotations, the list can be limited to one or all segments.

Keyboard 'b' will toggle the selected object between bad and good.

Edit User Type

Turn on the ‘Edit User Type’ checkbox and use keyboard 0-9 to set the value of ‘User Type’. Counts for each User Type are included for each segment in each segment report.


A left-click on a column header will sort the table by that column. Shit+click the column header to reverse sort. Columns can be turned on and off with a right-click in the column headers.

Here is a partial list of the meaning of each column. See intensity for a list of the meaning of additional columns.

Column Meaning
Idx The row in the table
roiType The type of annotation (spineROI, controlPnt, otherROI). Control the displayed types with the ‘Object Type’ popup.
channel The channel the annotation was created in.
isBad Bad annotations are shown as ‘1’. In single time-point analysis, set annotations bad with keyboard b.
parentID The segment number a spine annotation is attached to
z The z-image plane the annotation is in
nnDist Distance (um) to the nearest spine annotation.
pDist Only for spine annotation maps, the distance (plus or minus) away from the pivot point
cDate/cTime The creation date and time
mDate/mTime The modification date and time
userType The User Type for an annotation. User types can be edited by turning on ‘Edit User Type’ and using keyboard 0-9.
sLen2d The 2D length of each spine annotation
sLen3d The 3D length of each spine annotation


Right-click a column header and select Quick Plot to plot that stat versus its annotations index. The index of each annotation is the order they were created in.

Any two columns can be plotted as X and Y. Right click a column and select Set X Stat, then right-click another column and select Set Y Stat. Then use the main Plot button to plot X versus Y.

For example, to plot ‘spine length 3d’ versus ‘background subtracted spine sum’.

  • Turn on the intensity columns with a right-click on the columns header and select ‘Intensity’.
  • Right-click on ‘sLen3d’ column and select ‘Set Y Stat’
  • Right-click on ‘ubssSum’ column and select ‘Set X Stat’
  • Click the ‘Plot’ button.