The search panel allows a stack or map to be searched for stack db objects.

Interacting with results

Performing a search will create a list of object matching the search criteria. Selecting an entry in the search results will select that object in any open stack and map plots. Likewise, selecting an object in a stack or map plot will select the object in the search list (if it is in the list).

  • Single-click or scroll with keyboard will select the object in existing stack windows (it will not open or pan/zoom the existing stack windows).
  • Double-click to open and select the object in its corresponding stack.
  • Option-click to zoom the object in an already open stack plot.
  • Right-click to open a run plot.

Types of searches

First select the type of object with ‘Object Type’ popup. Start by selecting ‘Spine’.


  • All. All objects of ‘Object Type’
  • Bad. Objects marked bad
  • Errors and Warning. Objects with Intensity Analysis errors and warnings. USe the Error and Warning checkboxes in the upper right of the panel to toggle these columns on and off.
  • Int Dirty. Returns spines with dirty intensity analysis. Spines with dirty intensity analysis can be analyzed in the main map manager panel, intensity tab.
  • Int User.
  • Int Bad.
  • Notes. Objects with notes matching the search criteria. Use ‘*’ as a wildcard. Use ‘*’ to return all objects with notes, use ‘thistext*’ to search for notes starting with ‘thistext’.
  • Closeness. Returns object that are within specified distance (um) of each other.
  • V Spines. Return spines where the z-plane of the spine head is farther (in z) from the connected backbone/dendrite line.
  • ROI Bounds. Return spines with background ROI within specified distance (um) from edges of image. This is useful if stack alignment has been run causing images to be shifted/rotated resulting in undefined regions on the edge of the image.
  • Segment Ends. Return objects within specified distance (um) of the end of their segment/backbone line.

Map Tab

  • Addition.
  • Subtraction.
  • Persistent.
  • Transient.
  • Bad Runs. Return a list of objects that have a mixture of good and bad within their respective run. This is used for debugging and will be removed.
  • Re Added. Return a list of added spines that have a previous subtraction (on a previous timepoint) that is within specified distance along the backbone/dendrite.

Manual Tab

Return a list of objects matching a user specified criterion.

Do this by selecting a statistic in the list, specify a value, and an operator (>, >=, <, <=, =, Not).

For example, to generate a search of all long spines, select sLen2d/IntCh1, enter a spine length (um) like 4, select ‘>’ operator and press the ‘Manual Search’ button.