This describes a workflow for annotating 3D annotations in a single stack. To annotate a timeseries of stacks, please see making a map.

1. Open and initialize Map Manager

  • Open Map Manager in Igor Pro (double-click the MapManager.ipf file).
  • Click in the Igor Pro command window to compile (the command window is titled ‘Untitled’).
  • Open the Stack Browser window by selecting the main menu ‘MapManager - Stack Browser’.

2. Load a stack

Load a folder of .tif files in the Stack Browser using the ‘Load Tiff Folder’ button.

You need to set the proper X/Y/Z stack scale, in um, with keyboard shift+p. This is a critical step in Map Manager as many measurements are made using um. Once annotations are created the scale can not be changed.

3. Display a stack

Once a stack is loaded in the Stack Browser, double-click on its name in the list to display the stack in a stack window.

4. Add 3D annotations

  • In a stack window, open the annotation toolbar with keyboard [.
  • Add a new 3D annotation with shift+click.
  • Delete an annotation by selecting the point (single left-click) and hitting keyboard delete or backspace.
  • Each annotation can have a textual note, select the annotation and press keyboard n to enter a note. Notes can then be searched using the search panel.
  • See stack annotations for more information.

5. Saving and loading annotations

  • Save stack annotations using the ‘Save Stack’ button.
  • The next time a folder of .tif files is opened, the annotations for each stack will automatically be opened

6. Generating reports

Map Manager provides tabular reports for annotation density. See reports.

7. Searching annotations

Open the Search panel from the main menus ‘Map Manager - Search’.

The search panel will search all annotations in a stack and return a list of annotations. Once generated, clicking on an annotation in the search results will display the annotation in the stack window.

Different types of searches are performed with buttons:

  • All : Generate a list of all annotations in a stack.
  • Notes : Generate a list of all annotations with notes.
  • Close : Search for annotations that have other annotations within a 3D distance.

If you zoom the stack window (ctrl+mouse wheel or keyboard +) you can snap to different points while maintaining the zoom using the search panel ‘Snap’ checkbox.

The search results are a static output report. Once a search is performed, if annotations in the stack window are modified (added, deleted, moved, etc.) the search results will not be automatically updated. If the annotations are modified in the stack window, simply regnerate the search results by perform the search again.