Week 3: Eyes on the Ice

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Intro to ImageJ Stacks

Intro to Stacks

What is a stack?

ImageJ can display two or more images in a single window, as a stack. The images or layers that make up a stack are called slices. Stack windows have a scroll bar across the bottom to cycle through the slices, and you can animate the images at a speeds from one frame every 10 seconds to over 1000 frames per second. Many operations, such as selecting, filtering, thresholding, and contrast enhancement can be applied to all slices in a stack.

To stack a set of images, they must all be the same width, height, and bit depth. The number and size of the images you can stack depend on the amount of memory in your computer.


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What are stacks used for?

Stacks are used to display and analyze images that are related to each other in some way, such as by time (temporal), space (spatial), or color (spectral). Stacking temporal images allows you to animate them to rapidly display them in sequence making changes over time easier to see and understand, and allowing you to precisely measure the same regions of the image over time. Stacks of spatial data can be animated and measured, but you can also use ImageJ to construct entirely new views of features in the images. Using spectral data, you can use ImageJ to create both natural and false color views of a scene.

The Lake Mead satellite images that you stacked and animated in Week 2 are an example of a time series data set. They represent data collected for the same region but at different times. Stacking these images helped you to visualize changes in the lake over time and to make measurements. An advantage of stacking images to make measurements is that when you select an area to measure on one slice of the stack, that selection automatically applies to all slices in the stack. This guarantees that you are measuring the exact same part of the image in every slice. Also, processes such as thresholding apply to all of the slices of the stack.

Stacks can be saved in several formats, including animated gif for web display and, with the appropriate software installed, QuickTime movie format.


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Create a Time-Series Stack with ImageJ

Download the data

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Create a stack from a sequence of images

  1. Choose File > Import > Image Sequence... and navigate to the Albedo folder.
  2. Open Image Sequence
  3. Select the first image in the sequence and then click the Open button.
    Open Image Sequence Box
  4. Specify the Sequence Options. Use all twelve slices, beginning with the first slice and incrementing by one. Do not scale the images. Check the Sort Names Numerically option and click OK.
    Sequence Options  Box

  • All twelve images will be imported into a stack named Albedo. The individual images in a stack are called "slices" in ImageJ. The window's status bar shows the number of the current slice and total slices (in this case, slice 1/12 or 1 of 12), the width and height of the image in pixels, and the memory occupied by the stack, in this case 12 MB.
  • Choose File > Save to save the stack as Albedo.tif.
  • If you had difficulty creating or saving the stack, right-click (Win) or control-click (Mac) here (TIFF 8.9MB Jan13 10) and download the Albedo stack.

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    Explore Basic Stack Functions

    The albedo images from January 2009 through December 2009 are now assembled into a stack.

    These images were downloaded from the NASA Earth Observations (NEO) site that you visited in Week 1. The images show how much sunlight Earth reflects (its albedo) during the course of a year. Albedo is derived from the Latin word "albus" for white. It is the percentage of solar (shortwave or ultraviolet) radiation reflected by a given surface on Earth. The range can be as little as 3% for water with light shining on it to as high as 95% for fresh snow cover. This reflected energy is measured in Watts per square meter (W/m^2 - the amount of energy per square meter). Higher values indicate more reflectance. Lower numbers represent areas of less reflectance.

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    Animate the stack

    Albedo Stack image

    You can step through a stack one slice at a time, or you can animate it like a repeating movie loop. ImageJ lets you control the speed of the animation, so you can show it at a speed that is best suited for viewing.

    1. Choose Image > Stacks > Start Animation to animate the stack.
    2. animation_speed_1
    3. The animation is probably going too fast to see what's going on. To slow it down, choose Image > Stacks > Animation Options....
      animation_speed_2
    4. The Animations Options window opens. Set the Speed to 5 frames per second, and click OK.
      animation_speed_3

    Movie Icon

    Experiment with changing the speed of the animation, carefully observing the albedo changes that occur during the year.


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    Add and delete slices

    What if you need to add or remove a slice from a stack?

    1. Click on the stack to stop the animation. Flip through the stack to where you want to add the new slice. Choose Image > Stacks > Add Slice.
      add_delete_1
    2. A new slice is added. Notice how the slice counter displays 5/13, indicating you are now on slice 5 of 13 slices.
      add_delete_2
  • To delete a slice, flip to the slice you want to get rid of and choose Image > Stacks > Delete Slice.
  • Movie Icon

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    Unstack and restack slices

    1. To unstack the slices into separate image windows, choose Image > Stacks > Stack to Images.
      unstack_stack_1
    2. Each slice of the stack is now in its own window.
      unstack_stack_2
  • To restack the images, choose Image > Stacks > Images to Stack.
  • Movie Icon

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    Interpret Your Results

    As you and your students explore time-series images, think about the patterns that you are observing. What do they mean? What do the data show?


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    Create a Montage from a Stack

    ImageJ Montage

    Stacks are great on your computer screen, but how do you represent the image series in a printed report? The solution is to create a montage rows and columns of thumbnail images on a single page to save and import into your report.

    1. Choose Image > Stacks > Make Montage... make_montage_1
    2. The Make Montage window opens. Enter 3 for the number of Columns, 4 for rows, and .50 for the Scale Factor. Make the First Slice 1 and the Last Slice 2. Increment the montage by 1. Use 2 for the Border Width and 10 for the font size. Check Label Slices and click OK. make_montage_2
    3. Here is what the montage should look like. make_montage_3


    Movie Icon
  • Close all of the open image and stack windows before continuing.
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    Create and Explore More Stacks

    1. To save a stack as an animated gif, choose File > Save As > Animated GIF (Near the bottom of the menu - don't use GIF near the top of the menu.)
    2. save_as_animated_gif
    3. To open a stack in ImageJ that has been saved as an animated gif, choose File > Import > Animated GIF.
    4. import_animated_gif
    5. Posting either a jpeg montage of a stack you created or an animated gif along with a description is the required Tuesday posting for this week. You should also post ideas about how you might use it or similar animations to teach change-related concepts or other processes to your students.
    6. This weekly activity is required and is due on Tuesday, February 16, 2010.







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      Explore More if You Have Time: Create a Stack from a Montage

      glacial_retreat

      What if you download a montage of two or more images combined in a single window, and want to turn them into a stack to animate them? The important thing to keep in mind is that all of the images need to be the same width and height to stack them.
    1. Choose File > Open..., navigate to your Week 3 folder, and open the glacial_retreat.jpg image.
      montage_to_stack_1
    2. Use the Rectangular selection tool Rectangular Selection Tool to carefully select a rectangle around the 2001 glacier image. Then choose Image > Duplicate to create a new image window from your selection.
      montage_to_stack_2
  • Click the Window menu and choose the original glacier image from the list of open windows at the bottom of the menu. (Be careful not to click on the image outside the rectangular selection. If you do, and accidentally cancel the rectangular selection, choose Edit > Selection > Restore Selection to bring it back.)
  • Drag the selection rectangle up to the second glacier image and carefully align it with the edges of the 2003 image. You can nudge the selection rectangle a pixel at a time in any direction using the arrow keys on your keyboard.
  • Choose Image > Duplicate to create a new image window from your selection. Then continue this process until you have duplicated all three glacier images.
  • Close the original window containing the three glacier images.
  • Choose Image > Stacks > Images to Stack. Flip through or animate your stack.


  • Movie Icon
  • Save your completed stack to your Week 3 folder.
  • Close all of the open image and stack windows before continuing.
  • If you had difficulty creating or saving the stack, right-click (Win) or control-click (Mac) here (TIFF 1.3MB Feb13 10) and download the Glacial Retreat stack.




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    Resources



  • Refer to the ImageJ documentation on stacks.
  • Learn more about satellite remote sensing.



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    Movies on this Page





    How to download movies


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    Flash video versions

    Download these versions to play on your computer. You'll need an appropriate movie player to view the file, such as Flash Player, Real Player (Mac / Win), or Adobe Media Player.

    Movie Icon Scrolling Through a Stack

    Movie Icon Changing Animation Speed

    Movie Icon Adding and Deleting Slices

    Movie Icon Unstacking and Restacking

    Movie Icon Montage to Stack

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    iPod versions

    Download these version to play on your iPod or iPhone.

    Movie Icon Scrolling Through a Stack

    Movie Icon Changing Animation Speed

    Movie Icon Adding and Deleting Slices

    Movie Icon Unstacking and Restacking

    Movie Icon Montage to Stack


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