Part 2: Stack and Animate Time-Series Images1 2
Introduction to ImageJ 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.
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.
Time-series images represent data collected for the same region but at different times. Stacking these images helps you to visualize change over time. 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.
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.)
loading the player
Create a Time-Series Stack with ImageJ
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.
Explore Basic Stack Functions
The albedo images from January 2009 through December 2009 are now assembled into a stack.
Animate the stack
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.
Add and delete slices
What if you need to add or remove a slice from a stack?
Unstack and restack slices
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?
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.
Create a Montage from a Stack
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.
Create a Stack from a Montage
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.
Your Assignment: Create Your Own Time-Series Stack
- Use the set of images that you downloaded in Part 1 to create a stack.
- If you prefer, you an also create a stack from other images, such as the Earth Observatory, Worlds of Change collection.
- To share your stack with your colleagues, make a montage from your stack and save it as a Jpeg to post. In addition, save the stack as an Animated Gif to post. Depending upon browser capability, some course participants may be able to see the animated gif playing when they click on the link to the file in your post. Do not be concerned if your animated gif shows up as a still image. The SERC CMS does not always handle these file correctly. As long as you have attached the montage, others will be able to view what you created.
- 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.)
- To open a stack in ImageJ that has been saved as an animated gif, choose File > Import > Animated GIF.
- Then go to the Part 2: Share and Discuss page and post both the jpeg montage of the stack you created plus the animated gif along with a description of what you created. You should also share ideas about how you might use it or similar animations to teach change-related concepts or other processes to your students, engaging in an online discussion with colleagues.
Adapted from Earth Exploration Toolbook chapter instructions, "Using NASA NEO and ImageJ to Explore the Role of Snow Cover in Shaping Climate" under Creative Commons license Attribution-NonCommercial-ShareAlike 1.0.
Adapted from Eyes in the Sky II online course materials, Copyright 2010, TERC. All rights reserved.
New material developed for Earth Analysis Techniques, Copyright 2011, TERC. All rights reserved.