Part 5—Animate NEO Data with ImageJ

Step 1 Create a Stack from a Sequence of Monthly NDVI Images for 2010

  1. Launch ImageJ by double-clicking its icon ImageJ Icon Small on your desktop (Mac or PC) or by clicking the icon in the dock (Mac) or the Start menu (PC).
  2. Choose File > Import > Image Sequence... and navigate to the NDVI 2010 folder where you stored the monthly images. Select the first image in the sequence and then click Open. Specify the Sequence Options and click OK.
    1. Choose File > Import > Image Sequence... and navigate to the NDVI 2010 folder.

    2. Select the folder with the images and then click Choose.

    3. In the pop-up box, 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.


      All twelve images will be imported into a stack. 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.
  3. Choose File > Save to save the stack as NDVI 2010.tif.
  4. Keep the stack open in ImageJ for use in Step 2.

If you had difficulty creating or saving the stack, right-click (PC) or control-click (Mac) here (TIFF 8.9MB Aug20 11) and download the NDVI 2010 stack to your computer. Then launch ImageJ and choose File > Open to load the NDVI 2010.tif file into ImageJ.

Step 2 Animate the NDVI 2010 Stack

  1. 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.
  2. Click and drag the scroll bar at the bottom of the stack window to move forward and backward through the stack. As you scroll through the stack, notice the changing slice counter and image label at the top of the stack window. Slice 1 is labeled 1/12, slice 2 is 2/12, and so on. The image below shows slice 8 of 12 of the NDVI 2010 stack. The scroll bar is at the bottom.


  3. You can also use the Next Slice (>) and Previous Slice (<) keyboard shortcuts to move forward and backward through the stack. Try each method of scrolling before going on.
  4. Choose Image > Stacks > Tools > Animation Options... to set the speed of the animation to five frames per second.
    1. Choose Image > Stacks > Tools > Animation Options...

    2. Set the Speed of the animation to 5 frames per second. Animate all the frames by setting the First Frame to 1 and the Last Frame to 12. Check Start Animation and click OK. The stack will start moving through the slices.

Step 3 Explore How Vegetation Changes During the Year

Keeling curve of CO2 concentrations. The red curve shows average monthly concentrations since March of 1958, and the blue curve shows the 12-month average. Click the graph for a larger view.
While viewing the images in the stack, consider the following questions:



The graph is known as the Keeling curve, named after Charles David Keeling, the scientist who supervised the long-term effort to collect the data. The regular changes in the red line are caused by seasonal variations. Averaging the monthly data with the six months before and the six months after it produces the blue curve. The curve indicates that CO2 levels have risen substantially over the past 50 years.
The figure was produced by Robert Rohde; it is a part of the Global Warming Art collection.


Step 4 Consider other Carbon Patterns to Animate

Now that you are familiar with the data available in NEO, and the animation tools in ImageJ, consider other relationships and patterns that you might want to illustrate using this method. You can animate two sets of data to show spatial patterns, or you can animate several months of data showing temporal patterns, as was demonstrated in this part of the chapter.

NEO Carbon related datasets

Ocean
  • Chlorophyll concentration

Atmosphere
  • Aerosol Optical Depth
  • Carbon Monoxide
  • Total Rainfall

Land
  • Active Fires (1 month - Terra/MODIS)
  • Leaf Area Index (1 month - Terra/MODIS)
  • Net Primary Productivity
  • Permafrost
  • Vegetation Index [NDVI]
  • Water Equivalent Anomaly (an indicator of drought)

Life
  • Chlorophyll Concentration
  • Leaf Area Index
  • Net Primary Productivity
  • Vegetation Index [NDVI]

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