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 ‘[’.

Interface

Select individual annotations in the list and the selection will propagate to open stack windows, stack plots and map plot windows.

The behavior of selecting is defined by the ‘On Selection’ popup. Choose one of ‘Select’, ‘Select + Snap Image’, and ‘Select + Snap Image + Zoom’.

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 ‘userType’:

Counts for each of these user types are included for each segment in each segment report.

Plotting

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.

Columns

To make the table easier to read, columns can be turned on and off with a right-click in the column headers.

A left-click on a column header will sort the table by that column. Shit+click the column header to reverse sort.

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
parentID The segment number a point (spine) belongs to
dbIdx The row in the stack db
roiType The type of the point (spineROI, controlPnt, otherROI)
isBad A ‘1’ if the point is marked bad. Toggle this with keyboard ‘b’
intBad A ‘1’ if the point ismarked intensity bad
z The z-image plane the point is in
nnDist Distance (um) to the nearest spine.
dDist The distance (um) along the segment the point (spine) is attached to.
pDist Only for maps, the distance (plus or minus) away from the pivot point