The map window displays a schematic of spines across multiple stacks: their position along the dendritic backbone and their dynamics (added, subtracted, persistent).

Each dendritic backbone is represented as a vertical black line (one dendrite per stack). Each spine is a circle, its position along the black line denotes its position on the dendritic backbone.

The dynamics of spines are encoded with color:

  • Green            Addition
  • Yellow          Persistent
  • Red                Subtraction
  • White            Bad (spines marked bad by user)
  • Black-lines Spines that are connected across stacks (e.g. are the same spine)


Left Mouse-Click. To select a spine.

Selecting a spine (yellow box) will select other spines connected to it (blue line) and propagate the spine selection to other open stack and stack run windows.

Conversely, selecting a spine in an open stack or stack run window will select the same spine in the map window.

Right Mouse-Click to display a contextual menu that allows you to

  • Plot Stack Index: Display the Stack the spine is in.
  • Plot Spine #n: Display the selected spine in its Stack.
  • Plot Spine Run +/-1: Display the selected spine in a Stack Run. The stack run will show the selected spine in the middle window with the previous stack(s) to the left and the next stack(s) to the right.
  • Connect to next… Will automatically connect spines from the selected stack to the next. [Dec 2013, you need to close and reopen the map to see the new connections].
  • Connect Entire Map… Will automatically connect spines across the entire map.
  • Regenerate Spine Labels [depreciated]
  • Unload All Stacks [depreciated]
  • Cancel Map Selection [depreciated]


Drag a marquee and right click to set a property for a group of spines. For example you can set all spines in a marque selection as bad. Remember, bad spines are white.

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