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

Right-click an annotation in the search results 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 search results by a value by clicking on its 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 of the search results to choose the columns to display. This includes ‘Date Time’, ‘Note’, ‘Errors and Warnings’, ‘Spine Info’, and ‘Canvas’.

Editing searches

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 good/bad or as a particular user type.

Individual annotations can also be set with the keyboard.

  • g: Set selected annotation to good.
  • b: Set selected annotation to bad.
  • 0 .. 9: Set selected annotation to a specific 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 search 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 overlapping/duplicate annotations.
  • User Bool.
  • User Type. Find annotations tagged with a user type 0, 1, 2, …

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. (Spine Annotations) Find added spines that have a previous subtraction (on a previous timepoint) that is within specified distance along the segment tracing.
  • Jumping. Advanced, not used.
  • Changing User Type. Find all annotations that are connected to other annotations with a different user type.

Spines Tab

  • 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.

  • 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. Find spines that have their intensity analysis parameters manually set. Individual spine annotation can have their intensity analysis parameters set in a stack window using the info panel (keyboard i).
  • Int Bad. Find spines marked as intensity 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.

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.

Batch editing search results

All annotations in the search results can be set to a particular user type. Use the ‘Results to user type’ button in the lower right of the window.