A stack window displays a 3D image stack, one image plane (slice) at a time.


Mouse-wheel to scroll up and down through images.


Click and drag will pan the image. Keyboard arrow-keys will also pan.


Ctrl+mouse wheel to zoom in and out. Keyboard +/- will also zoom in and out. All zooming is done by following the mouse pointer. Keyboard Enter will return image to full zoom.

Selecting annotations

Single mouse click will select an annotation. Selected annotations are highlighted in yellow. Keyboard n to edit the selected annotation note. Right-click will show context menu for selected annotation.

Canceling annotation selection

Keyboard esc will cancel all selections.

Image contrast

The contrast bar is used to set image contrast in a stack window. Image contrast is critical, if contrast is not set properly you may not see dim but otherwise important structures in your images. Setting the contrast does not modify the image, it is purely for display purposes.

  • Open the contrast bar with keyboard c or use the right-click menu
  • Pixel intensity values below ‘min’ will be displayed as black
  • Pixel intensity values above ‘max’ will be displayed as white


The histogram window show a histogram of pixel intensity values for each image in a stack.

  • Open the histogram window with keyboard h or use the right-click menu.
  • The histogram window shows a pixel intensity histogram for one image.
  • Scroll through the image in a stack (mouse-wheel) and the histogram for each image will be show.

Multiple color channels

Use keyboard 1, 2, and 3 to switch between channels one, two, and three. Channels can also be selected using the right-click menu.

Sliding z-projection

A sliding z-projection is a special stack where each image plane is replaced by a small maximal z-projection showing slices just above and below the current image plane. Here is an example:

Sliding Z-Project

Switch to a sliding z-projection for channel 1 with keyboard 3 and for channel 2 with keyboard 4. You can also use the right-click menu.

Switch to the sliding z-projection with shift+3 or shift+4 to set the number of slices in each maximal z-projection.

Tip. The keyboard keys used to switch to a sliding z-projection change depending on the number of color channels. For stacks with one color channel, they become '2'. For stacks with two color channels, they become '3' and '4'. For stacks with three color channels, they become '4', '5', and '6'.

Maximal Z-Projections

Open a maximal Z-Projection with keyboard z or use the right-click menu. This allows you to set the top and bottom slice that goes into the Z-Projection.

Once the Z-Projection window is open, it behaves just like a stack window (with only one slice). For example, you can zoom with +/-, pan with arrow keys, open the contrast bar with keyboard c, view a histogram with keyboard h, and copy/paste the image to another program, etc., etc.

Scale bar

Each stack will display a white scale bar in µm. Control the length of the scale bar in Options.

Window Candy

  • There are five different window decorations or candy options: (i) all, (ii) none, (iii) scale, (iv) scale + scroll, and (v) something else.
  • Cycle different window candies with keyboard shift+c.
  • Set the default window candy in Options.
  • Note: The grid will only display when window candy is set to ‘All’ (when the stack axis are visible).

The navigation window opens a new window with a maximal z-projection of the stack and shows the current zoomed view as a blue square.

  • Right click and select ‘Navigation Window’ menu. A navigation window will be opened and your current zoomed view of the stack will be shown as a blue square.
  • Zoom with +/- or pan with arrow keys and the blue-square tracks what you are looking at.
  • The navigation window is, by default, a maximal z-projection of the entire stack.

Zoom window

Right click and select ‘Zoom Window’. The zoom window will follow the mouse pointer and show a zoomed in region of the current image.

Right click

Right-click on the image and you will get a contextual menu to activate the features described on this page.

Copy/Paste image into other programs

Igor Pro is very good at copying images to the clipboard so they can be pasted into other programs. From a stack window, copying will copy the image with all the annotations, it does not copy the contrast (top) and scoring (left) toolbars. Annotations can be hidden with t.

Voxel size

The x/y/z voxel size of each stack is set with keyboard shift+p. Setting the correct voxel size in µm is critical as MapManager performs many calculations in µm (NOT IN PIXELS). The voxel size must be set before annotations are created. Once annotations are created, you should not change the voxel size.

Keyboard commands

Map Manager makes heavy use of keyboard shortcuts. Use the right click menu to see the mapping between the function and the key. Here is a list of keyboard shortcuts. In a stack window, use keyboard shift+h to print this table.

Topic Keyboard Action
  arrow-keys Pan image
  +/- Zoom image
  Enter Full zoom image
  ] Toggle between 2 different window sizes
Image Display    
  1 Channel 1
  2 Channel 2
  3 Sliding Z-Project - Channel 1
  4 Sliding Z-Project - Channel 2
  c Toggle contrast toolbar (top)
  [ Toggle scoring toolbar (left)
New Windows    
  h Histogram
  z Maximal Z-Projection
  shift+z Maximal Z-Projection - Options
  i Object info panel
  shift+i Stack info panel
Voxel Size    
  shift+p Set voxel size
  / Start and stop movie of slices
  shift+c Toggle 4 different window candy options
  shift+h Print this help
Object Scoring    
  t Toggle annotations (tracing) on and off
  b Toggle selected object bad
  control + left arrow Go to previous object
  control + right arrow Go to next object
Map Run    
  l Link window (lower case ‘l’ as in link)
  a Make selected object addition
  s Make selected object subtraction
  p Make selected object persistent (requires selection in previous timepoint)

Stack annotations

See stack annotations for details on creating and editing annotations. To easily manage annotations, open the left stack db panel with keyboard [ or use the point list panel.

Selecting an annotation

single-click, selected annotations are yellow. Cancel the selection with keyboard esc

New annotation

shift+click to create a new annotation. All annotations are 3D, the x/y coordinate is given by the position of the mouse cursor and the z coordinate is the currently viewed image slice.

Move annotation

right-click and select ‘move’ menu

Delete annotation

Keyboard del or right-click and select ‘delete’

Point info

The Point Info window shows information about the currently selected object.

  • Open the Point Info window from any stack window using keyboard i.
  • Use the point info window to annotate objects with text notes.