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 ‘View - Contrast Bar’.
  • Pixel intensity values below ‘min’ will be displayed as black
  • Pixel intensity values above ‘max’ will be displayed as white

Global image contrast

The global contrast panel provides an interface to set display parameters for all stacks. The values specified in this panel will be used each time a new stack window is opened.

Open the contrast panel with the main Map Manager menu ‘MapManager - Contrast’

The check boxes next to each channel specify if the value are to be used when a stack is opened.

The values can be saved from the Options Panel or the main Map Manager menu ‘MapManager - Save Options…’.


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 buttons panel and right-click menu.

Sliding z-projection and frame averaging

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. For frame averaging, each image is replaced by the average of itself with a number of frames after it.

Switch channels or to a sliding z-projection (frame average) using the following table. This is also available in the buttons panel which might be easier.

Switch to the sliding z-projection with shift to choose the number of slices and the type, either a sliding z-projection or a frame-average.

# Ch / Keyboard 1 2 3 4 5 6
1 Channel Ch 1 Sliding-Z N/A N/A N/A N/A
2 Channels Ch 1 Ch 2 Sliding-Z Ch1 Sliding-Z Ch2 N/A N/A
3 Channels Ch 1 Ch 2 Ch3 Sliding-Z Ch1 Sliding-Z Ch2 Sliding-Z Ch3
Sliding Z-Projection

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. Cycle different window candies with keyboard shift+c.

  1. None
  2. Scale Bar
  3. Scale Bar + Top Left Label
  4. Scale Bar + Top Left Label + Axis
  5. Scale Bar + Top Left Label + Axis + Slider

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).

Stack annotations

To manage annotations in a stack window, open the left control bar with keyboard [ or use the point list panel.

See stack annotations for details on creating and editing annotations.

  • Create an 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.
  • Select an annotation. Single-click to select an annotation. Selected annotations are yellow. Cancel the selection with keyboard esc.
  • Move an annotation. Right-click and select ‘move’ menu.
  • Delete an annotation. Keyboard del or right-click and select ‘delete’.
  • Setting an annotation tag. Use the right-click menu. Tags include: bad, intensity bad, and user type.
  • Setting an annotation note. Select the annotation and press keyboard n.

Right click

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

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.

Buttons panel

The buttons panel provides a quick interface to perform actions on stack and map plot windows.

Open the buttons panel from the main menu ‘MapManager - Buttons’.

The buttons panel will adjust its interface depending on the front most Map Manager window.

The actions provided in the buttons panel are also available from individual map manager windows using a right mouse-click. The purpose of the buttons panel is to make these actions more accessible.

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.

Animating a stack or frame scan

Keyboard / to start/stop an animation through all slices or frames. Use shift+/ to set the frame rate and if the animation will loop. Use keyboard / or keyboard . to stop the animation.

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

In most cases the voxel size will be set automatically. 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. Most of these functions are available in the right-click menu which also lists the corresponding keyboard shortcut. The buttons panel provides the same functions and may be easier to use.

Topic Keyboard/Mouse Action
  mouse-wheel Scroll images in a stack or time-series
  arrow-keys Pan image
  click-drag Pan image
  +/- Zoom image. Zooming follows the mouse cursor!
  ctrl + mouse wheel Zoom image. Zooming follows the mouse cursor!
  Enter/Return Full zoom image
  ] Toggle between 2 different window sizes
Window Candy    
  shift + c Toggle 4 different window candy options. Use this to display/hide stack scale and copy/paste to other programs.
  c Toggle contrast toolbar (top)
  [ Toggle annotation toolbar (left)
New Windows    
  h Histogram
  z Maximal Z-Projection
  i Object info panel
  shift+i Stack info panel
  t Toggle annotations on and off
  n Edit selected annotation note
  b Toggle selected annotation bad/good
  g Toggle grid on/off
  control + left arrow Go to previous annotation
  control + right arrow Go to next annotation
  / Start and stop movie of slices/frames
  shift + / Start and stop movie with options
  . Stop movie of slices/frames
Time Series    
  l Link window (lower case ‘l’ as in link)
  a Make selected annotation addition
  s Make selected annotation subtraction
  p Make selected annotation persistent (requires selection in previous timepoint)

# Ch / Keyboard 1 2 3 4 5 6
1 Channel Ch 1 Sliding-Z N/A N/A N/A N/A
2 Channels Ch 1 Ch 2 Sliding-Z Ch1 Sliding-Z Ch2 N/A N/A
3 Channels Ch 1 Ch 2 Ch3 Sliding-Z Ch1 Sliding-Z Ch2 Sliding-Z Ch3