Marking Spines

Marking and editing spines in a stack is easy. The hard part is deciding what is a spine and what is not a spine. Please see Spine Scoring Strategies.

On the right is a zoomed in stack window showing some marked spines (scale bar is 2 um). Spines are labelled with their ‘spine index’, the backbone line and radius is a red dotted line, user spine selection is shown as a yellow box. The properties of a selected spine is shown in the SpineInfo window.

Creating Spines

Shift-click to create a new spine. The (x,y,z) positon of a spine is determined by the mouse position (x,y) and the slice you are currently viewing (z).

Selecting spines

Left-click on a spine to select it (yellow box appears). If you are viewing the SpineInfo window (shift-?), it will be updated.

Editing Spines

Right-click a spine and you will get a contextual spine menu.

  • Auto Connect. Default behavior. Draws a spine line between the spine head and the backbone radius by following the brightest path
  • Manual Connect. Allows you to edit the spine line. Drag the (red) spine line so that it follows the brightest path and accept the new connection by a single mouse click.
  • Move Spine. Allows you to move the spine head.
  • Delete spine. Delete the selected spine (This is only allowed in stack view, it is not allowed in a stack run. In a stack run you can mark spines as ‘Bad’).


When you create a spine (shift+click), the spine is connected to the backbone radius creating a spine line. This is done by finding the brightest path between the spine head and the dendritic backbone. If the spine line is not accepatable, you can use Manual Connect to change its connection point.

Spines within a stack are given sequential numbers as they are created (0, 1, 2, …). These numbers are displayed with an arrow pointing to the spine. [These are different from the numbers you see in a stack run.

Screen shot of a map, a stack, a spine selection, spine info, and the navigation window.

Keyboard shortcuts

ctrl-E   :   Bring up spreadsheets of spine and  line properties (see ‘spine properties’ below). Useful to export all the spine properties for one stack.

shift-T : Toggle spine markings and backbone lines on and off. This is useful when you want see fine details in an image that is obscured by spine and line overlays or to copy/paste the image you are viewing into another program.

shift-? : Open/close SpineInfo window. Each stack window has its own ‘SpineInfo’ window. The SpineInfo window will automatically update as spines are selected in the stack. The map window also has a SpineInfo window. Once a spine is selected, you can enter a text note in the SpineInfo window.


The spineinfo window shows properties of the user selected spine. Open and close the spineinfo window with shift-?. You can edit the ‘Spine Note’, all other fields are not editable.

Spine Index. The index of a selected spine. As spines are created (with shift-click) they are given an index 0, 1, 2, …

X Y Z. The 3D position of the spine head. This is set when you shift-click a spine and can be edited by right-clicking a spine and selecting ‘Move Spine’.

Length. The length of a spine line. This is the 2D euclidean distance between the spine head and the connection point.

SNR. A very basic signal to noise (SNR) ratio between the average pixel intensity around the spine head (signal) and a similar region in the background. [See Intensity Analysis]

Distance. The distance of a spines connection point along the backbone line. [See fudiciary point, backbone lines…]

Lifetime. The lifetime of a spine connected as a spine run through a map. Units here are map sessions (NOT real-time).

Type. Categorizes each spine into a spine type based on the intensity profile of its spine line. Travelling down the spine line from the connection point to the spine head.

  • Stubby : If the length of the spine line < stubby_thresh (0.5 um).
  • Mushroom : If the derivative of the intensity profile passes a threshold (xxx).
  • Filipodia : If the derivative of the intensity profile does NOT pass a threshold.
  • Other : User entered type.

Spine properties

roix : x stack position of spine head
roiy : y stack position of spine head
roiz : z stack position of spine head
type : Spine type (mushroom, filipodia, stubby, other)
note : User entered text note
spineLen : Distance between spine head and connection point on radius (length of spine line).
spineLen3d : Spine length in 3D. We have found that large z-steps can contaminate spine length measurements.
spineAngle : Different angles of spine line w.r.t. local dendritic backbone.
connDist : distance along backbone (away from fiduciary point)
signal : Very simplistic ROI around spine head. See Intensity Analysis for proper signal/noise measurements.

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