Stack

A stack displays either a 3D volume or a time-series, one image at a time. You can zoom with +/-, pan with the arrow keys, and scroll through images with the mouse wheel.

It is critical that you adjust the contrast of what you are viewing, you can do this in three ways:

  • With the contrast toolbar (keyboard ‘c’).
  • With the histogram (keyboard ‘h’).
  • With the global display options of the Process Window.
stack_basicA default stack window. The white text in the upper left tells you the slice you are viewing, the total number of slices, the bit depth of your stack, wether you are viewing a sliding z-projection (zs), and if your stacks are linked (L). The white bar at the bottom-right is a scale bar. stack_control_bar
A stack window with the contrast bar open. As you adjust the sliders, the image automatically updates. Open the contrast bar with keyboard ‘c’.
histogramA histogram for a stack. The histogram is calculated for the image plane you are viewing. Scroll the visible image plane in the stack window (mouse wheel) and the histogram will automatically update. The histogram window also allows you to set the contrast. Open the histogram window for a stack with keyboard ‘h’. process_imageThe process image window allows you to set global display defaults for contrast, color palettes, etc. It also gives you quick access to the histogram and maximal z-projection of the frontmost stack. Open the ‘process image’ window with the menu ‘bStack->Process Panel’.

Keyboard Shortcuts

Keystroke Action
Arrow Keys Pan
Mouse Wheel Set slice up/down
+/- Zoom in/out
Shift + / Shift – Zoom in/out (smaller steps)
Enter Full Zoom
1/2 Channel 1 / Channel 2
3/4 Channel 1 sliding Z-projection / Channel 2 sliding Z-projection
Shift + 3 / Shift + 4 Options for sliding Z-projection (set the number of planes)

 

Shift + H Print help in command window (prints this table)
c Contrast Toolbar
Shift + C Cycle through 4 Candy presets
h Histogram
z Maximal Z-projection
Shift + Z Maximal Z-projection Options
p Set pixel/voxel size
/  Play stack as a movie
s Toggle between 2 default window sizes, defined in stack browser options
r Create an RGB stack from a 2-channel stack
shift + I Open ‘Stack Info’ window to view detection parameters.
 Shift + ? Open ‘Spine Info’ Window

 Additional Features

stack_navigation_1
A stack zoomed in. Use the stack navigation window for a global view. Right-click and select ‘Navigation Window’.
stack_navigation_2
A navigation window for the stack on the left. The blue square shows you where you are zoomed in and will update as you pan and zoom the stack. Open the navigation window for a stack with right-click and select ‘Navigation Window’.
stack_options_panel
Open the stack options panel with a right-click and select ‘Stack Options Panel…’. In the stack options panel you can turn visual elements on and off: Scale Bar, Legend, Movie Bar, etc.
stack_util_2
The stack util 2 window allows you to manage a database of points to annotate your stacks. Open this window with a right-click and select ‘Stack Util 2 panel’.
stack_all_windows
This screenshot shows a stack window with all its accessory windows: Navigation, Histogram, Stack Util 2, and the global Process Image window.
stack_browser_windowThe stack browser allows you to manage multiple stacks and to display all stacks from an imaging session in a Canvas.
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