Eyes in the Sky II > GIT Web Course > Module 1 > Week 3 > Intro to ImageJ Stacks

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.


Image stack saved as animated gif.Nov Arctic Sea Ice Stack.gif


Image stack saved as QuickTime movie (QuickTime must be installed on your computer to view. This is just an example don't worry if your computer can't view it.)


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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

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.

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?


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Unstack and restack slices


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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?

showShow me an interpretation of how albedo changes during the year
Overall the intensity of the sunlight changes along with the seasons. In the late winter and early spring, the reflectance is at its maximum. Spring brings the return of the intense sunlight to the snow covered areas and before the snow melts, this combination of spring sunlight and snow cover creates a very bright period in March and April in the Northern Hemisphere. However, as the snow cover decreases from May through July, the albedo decreases, demonstrating that conifer trees are not especially reflective and are, in fact, absorbing summer sunlight. Conifers have extremely low albedo, 5-15%. In the late summer and fall the snow cover returns and as a result the albedo again increases in the Northern hemisphere.

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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.

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Create and Explore More Stacks

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.

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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