Use the search panel to find annotations in a single stack or map or all loaded stacks and maps.

Opening the search panel

  • From the main menu ‘MapManager - Search’
  • From the time-point window ‘Search’ button


Select the type of object to search with the ‘Object Type’ popup.

Select the scope of the search, either a stack or a map, and choose wether to ‘include bad’ annotations in the search.

Click any of the buttons down the left hand side of the panel to perform a search. The resulting annotations will be show as a list on the right.

Interacting with results

All searches will return a list of annotations. Right-click an annotation to open the annotation in a stack or run plot. Selecting an annotation (left-click) will select that annotation in any open stack and map plots. Likewise, selecting an annotation in a stack or map plot will select the annotation in the search result list (if it is in the list).

Sort the results by clicking on the column header. Additional ‘smart’ sorting is provided with the sort buttons:

  • Sort. Sort by idx, map, segmentID, sess, pnt
  • Sort Mod Time. Sort by mSeconds, idx
  • Sort Segments. Sort by map, sess, segmentID, pDist, idx

Right-click the columns to choose the columns to display. This includes ‘Date Time’, ‘Note’, ‘Errors and Warnings’, and ‘Spine Info’.

Editing searches

Once a search is performed, right click on an annotation in the results list to open a popup to either display or edit the annotation. Annotations can be tagged as bad or as a particular user type.

Types of searches


  • All. Find all annotations of ‘Object Type’.
  • Bad. Find annotations marked bad.
  • Notes. Find annotations with notes matching the search criteria. Use an asterix (*) as a wildcard. Use * to return all annotations with a note, use thistext* to find annotation with notes starting with ‘thistext’ or ending with ‘thistext’ using *thistext.
  • Closeness. Find annotations that are within specified distance (um) of each other. This is useful for finding erroneous/duplicate annotations.
  • User Bool.
  • User Type. Find annotations tagged with a user type 0, 1, 2, …


  • V Spines. Find spines where the z-plane of the spine head is farther (in z) from the connected backbone/dendrite line. This is useful for finding spines that project out of the imaging plane.
  • Segment Ends. Find spines within specified distance (um) of the end of their segment/backbone line. This is useful for finding problematic spines during spine intensity analysis.

Map Tab

  • Addition. Find annotations that are addition.
  • Subtraction. Find annotations that are subtraction.
  • Persistent. Find annotations that are persistent (not that usefull).
  • Transient. Find annotations that are transient. Transient annotations occur in only one time-point.
  • Bad Runs. Find annotations that have a mixture of good and bad within their respective run. This is used for debugging and will be removed.
  • Re Added. (Spines) Find added spines that have a previous subtraction (on a previous timepoint) that is within specified distance along the backbone/dendrite.
  • Jumping.
  • Changing User 1.
  • Changing User Type. Find all annotations that are connected to other annotations with a different user type. In general, user types (like bad) should be the same for all connected annotations.

Manual Tab

Find annotations matching a user specified criterion.

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

For example, to find all spines/filapodia longer than 3 um, select ‘Stat:sLen2d Type:IntCh1’, enter a value 3, select ‘>’ operator and press the ‘Manual Search’ button.

Intensity Tab

  • Int Dirty. Find 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.
  • ROI Bounds. Find 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.
  • Errors and Warning. Find annotations with Intensity Analysis errors and warnings. To display the Errors and Warnings columns, right-click the column headers and select ‘Errors and Warnings’. See intensity analysis.