Stack Run

A stack run displays a sequence of stacks with their associated spines. Each spine is tagged with a number, spines with the same number indicate the spine is persistent across imaging sessions.

Display a stack run. In a Map window, right click a  spine and select ‘display spine run +/- 1’. This will display the selected spine (teal box) in the center window. The previous (-1) and next (+1) stacks will also be shown with the same spine selected (teal square).

If the spine is not in either the previous or next stack, you will be shown the same region of the image (same distance along the backbone line) but there will be no (teal) selection.

You can quickly determine spine connectedness by their numbers. For example, spine 6 is present in all three stacks (as well as spine 7,21, 22, 23, and 24). Spine 39 is new in the middle stack.

Spine Labels

  • Green :   New Spine (#39 in the center window, note that spine is out of viewed focal plane).
  • Yellow : Persistent spines
  • White :   Bad spines


You can add new spines and modify the connection point and the position of a spine using the same interface as you used when originally marking spines.

You can modify the dynamic of the spines: Addition, Subtraction, Persistence, and Bad

  • Addition: Select a spine and press [+ button]
  • Subtraction: Select a spine and press [- button]
  • Persistent: Select a sequence of spines (in sequential stacks) and press [Persistent button]
  • Bad: Select a spine and press [Bad button]

As you make edits to spine dynamics (Addition, Subtraction, Persistent), the Map will be updated.

Bad Spines

As you edit spines using the Stack Run interface there is a new property, Bad. Marking a spine as Bad will exclude it from further analysis. Bad spines are indicated in a Stack Run with a white label and in a Map with a white circle.

The database of spines is updated as you mark spines +/-/Persistent, but it is your job to maintain the database as yo mark spines Bad. You can leave Bad spines connected to other Bad spines but need to be sure that Bad spines are not connected to non Bad (Good) spines.

[New Feature] The Search window allows you to find Bad spines that are connected to Good and to fix this situation.


Any edits you make to spine dynamics (+/-/Persistent) will be marked in a map with an open circle. Just as a spine has an Auto or Manual connection to the backbone (see Marking Spines), spine dynamics are also marked as Auto or Manual. When you are editing +/-/Persistent with a Stack Run, these edits are stored and will display in the Map as open circles (same color scheme).

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