• Mouse wheel to scroll up and down through images, arrow keys to pan, +/- to zoom
  • Image contrast is critical, open contrast bar with keyboard ‘c’, adjust min/max contrast with sliders.
  • View a histogram with keyboard ‘h’
  • Closing a stack window does not remove it from memory (the stack remains open)

Keyboard commands

Arrow keys : pan image left/right and up/down  
+ : zoom in (follows mouse pointer) 
- : zoom out (follows mouse pointer) 
Return/Enter : view entire image  

Esc : cancel selection

1 : view channel 1 
2 : view channel 2 

3 : view a sliding maximal z-projection of channel 1 
4 : view a sliding maximal z-projection of channel 2 

c : toggle contrast control bar
h : open histogram window
] : toggle between two different window sizes

sift+c : cycle through 4 different window 'candy' displays

shift+p : Set pixel/voxel size

shift+? : open the 'Point Info' window  
	Object notes can be set in the Point Info window.  

Contrast bar

  • Open the contrast bar with keyboard ‘c’
  • 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’.
  • 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.

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.

Point info

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

  • Open the Point Info window from any stack window using shift+?.
  • Use the point info window to annotate either nodes or edges with notes.
  • Use the point info window to annotate edges as ‘diving’, ‘surface’, ‘Has Pericyte’ and ‘Branch Order’.


  • Contrast is critical, if not set properly you will not see objects in your image that are actually there.
  • Closing a stack window does not remove the stack from memory.
  • Zooming with keyboard +/- follows the mouse pointer