Part 3—Animate NEO's AOT Data with ImageJ

Step 1 Create a Stack from a Sequence of Monthly AOT Images for 2008

  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 AOT2008 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 AOT2008 folder.

    2. Select the first image in the sequence and then click Open.

    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.
      Sequence Options  Box
      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 AOT2008.tif.
  4. Keep the stack open in ImageJ for use in Step 2.

If you had difficulty creating or saving the stack, right-click (Win) or control-click (Mac) here (TIFF 8.9MB Jun16 10) and download the AOT2008 stack to your computer. Then launch ImageJ and choose File > Open to load the AOT2008.tif file into ImageJ.

Step 2 Animate the AOT 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.


    This image shows slice 2 of 12 of the AOT2008 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 > Animation Options... to set the speed of the animation to five frames per second.
    1. Choose Image > Stacks > 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 Aerosol Concentrations Change During the Year


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