Spine Stack

A stack window displays a 3D image stack, one plane at a time (similar to ImageJ/Fiji).

A stack window zoomed in to a region of the image (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.

Stack Navigation

Arrow keys        Pan
+/-                      Zoom
Mouse Wheel   Scroll through image planes

Stack Contrast

It is critical to adjust the contrast of the displayed stack so details can be seen. See Histogram (keyboard-h). See Process panel and Advanced Topic: Stack Contrast.

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.

Spine Note. You can add a text note for a given spine by selecting the spine (yellow square) and then entering your note into the Spine Note field of the SpineInfo window.

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-C   :   Cycle trhough 4 different preset window candy options. Each candy preset turns different interface elements on/off.

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.

Candy Options (shift-C to cycle through these candy presets)

  1. Blank, just the stack image. Useful if you want to copy/paste what you see in stack window. When you cycle to Candy 1, scroll up/down one slice to remove stack text.
  2. Adds a scale bar
  3. Adds text describing the stack. Useful to know which map and session # the stack is coming from.
  4. Adds a scroll slider on the right of the stack. Useful to quickly scroll through large stacks.
  5. Add labels on the X/Y axis. Useful to see  the overall scale of the stack and the scale of elements within the stack.


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 Note. User entered note for a spine. To change the spine note, select a spine and enter text into the Spine Note text box.

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).

Spine Type. Calculated from the intensity profile of the 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 : Remaining spines not categoriazed as Stubby/Mushroom.
  • 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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