Eyes in the Sky II > GIT Web Course > Module 1 > Week 2 > Intro to ImageJ

Week 2: Analyzing Change Over Time

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Intro to ImageJ

Sample of images in ImageJ

ImageJ is free public domain image processing software developed at the National Institutes of Health. Its power and flexibility allow it to be used as a research tool by scientists in many disciplines, from medicine to astronomy. Installers are available for Windows, MacOS and OSX, and Linux.

You can use ImageJ to display, annotate, edit, calibrate, measure, analyze, process, print, and save raster (row and column) image data. It reads most common raster image formats as well as raw data files in text format, such as from spreadsheets. ImageJ also supports stacks - multiple images in a single window - for animation and analysis.

Movie Icon

Click on the movie to start playing.

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To help you become comfortable using geospatial technology, we have created a number of short videos that demonstrate basic operations and analysis techniques. These videos are embedded within the instructions throughout the pages of this course. You can quickly find them by looking for the movie camera Movie Icon icon. In addition, all the videos on a given page can be downloaded to your hard drive. You may find it useful to run these videos from your hard drive rather than the Internet, especially if your Internet connection is slow or unstable. The videos are available in flash video and iPod (mp4) formats. You may also use these videos in your teaching if you like. Download and access all the movies on a page from the Movies on this Page section at the bottom of the page.

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Download and Install ImageJ


Go to the ImageJ Download page, and download and install the application for your operating system.

    Click the ImageJ Download page and it will open in a new window. Click the link that appears directly below the name of your computer's operating system (e.g. Mac, Linux, Windows). This action will transfer a compressed file of the software to your computer. Your browser should automatically expand the file, creating an ImageJ folder on your computer's hard drive.

    ImageJ Download page

For more details, or if you have problems running the application, access ImageJ's Installation Instructions then select your operating system.


Note to Windows Users: It is recommended that you install ImageJ in the Documents directory, rather than in the Program Files directory. For security reasons, Windows 7 and Windows Vista do not allow programs to alter themselves by writing files to the Program Files directory. If ImageJ is installed in the Program Files directory, then the update function in Step 2 below will not work properly.
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Update ImageJ Software

ImageJ Updater Window

Double-click the ImageJ icon to launch the application and choose Help > Update ImageJ.... A window will appear, telling you the version you are currently running and a list of upgrade versions. Choose the version you want to upgrade to (usually the most recent, or default version) and click OK. After the update downloads, re-launch ImageJ to run the new version.


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Help with Updating ImageJ: Some users have reported problems updating ImageJ in certain versions of Windows. This is causing some of the tools and instructions (for example, setting the Threshold level for the Wand tool) to not function properly.

The quickest way to fix this is to reinstall ImageJ to the Documents directory. Alternately, you can manually update ImageJ with the instructions below:

  1. Right-click the link at right to download the ij.jar file. Be sure to save it as simply ij.jar. ij.jar (Jar Archive 1.4MB Feb8 10)
  2. When prompted where to save the file, navigate to the ImageJ folder and save the file there. Replace the existing ij.jar file.
  3. For most installations, the ImageJ folder will be in the Program Files directory on your hard drive. The path to the ImageJ folder is c:\Program Files\ImageJ.
  4. If you are still having difficulties, please email Larry Kendall directly at larrykendall@verizon.net.
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The ImageJ Toolbar

The ImageJ toolbar contains both built-in and customized tools for manipulating images. Most of the tools are similar to those used in other graphics programs. You will learn about the tools as you use them.

ImageJ Tool Bar

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Download Images

Download two images of Lake Mead to your Week 2 folder or directory.

  1. If you haven't already created a folder (directory) on your computer for your Week 2 files, make one now.
  2. Click the grayscale thumbnail image below to open a full-size version in a separate window. Then right-click (Win) or control-click (Mac) the full-size image to choose File > Save Image As... and save it to your Week 2 folder. Close the image window after you have downloaded its file.
    • Lake Mead 2004 grayscale small, with scale bar lake_mead_2004_grayscale.jpg
  3. Then repeat the procedure for the color image of Lake Mead.
    • Lake Mead 2004 color small, with scale bar lake_mead_2004_color.jpg

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Explore a Digital Image

In ImageJ, choose File > Open..., navigate to your Week 2 folder, and open the lake_mead_2004_grayscale.jpg file. This is a grayscale satellite image of the area around Lake Mead, Nevada, taken by one of the Landsat satellites.

Zoom in and out

The squares you see are the dots or pixels (short for picture elements) that make up the image. An important concept is that despite the impression given by those amazing FBI image processing techs you see in movies and television you can't zoom in to an image indefinitely. When you reach the point where you can distinguish the individual pixels, you won't see additional details by zooming in more.

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Scroll to move around

When you're zoomed in, how do you move around an image?


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Investigate Pixel Data

By the numbers - pixel values and coordinates

A digital image no matter where it comes from or how it is produced is really just a string of numbers. Most of the time when you're working with digital images, the software keeps the numbers hidden from you. What makes ImageJ so useful is that you always have access to the numbers. Understanding this will help you and your students unlock the power of ImageJ.

An important concept here is that storing all this information in an image file on your computer is much more efficient than it seems. The computer doesn't need to store x- and y-coordinates just the pixel values, in one long string, plus the width and height of the image. The coordinates are just information about the pixel under the cursor its column and row number that the software reports to the user.

To reconstruct the image correctly, the computer just needs to "know" the number of columns and rows in the image. This kind of grid of rows and columns is also called a raster, which is why this type of digital image is also called a raster image and why ImageJ is called a raster image processor.


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Play With Color

Lookup tables

So far, you know that a digital image is a string of numbers arranged in rows and columns. How does the computer know what each number should look like when it displays that pixel on your screen? It's pretty simple, really. In addition to a string of numbers, the computer has a "secret decoder ring" called a Lookup Table that it uses in paint-by-number fashion. In a very simple image with only four possible values, the lookup table might look like 0 = black, 1 = blue, 2 = red, 3 = white. In an 8-bit image, the 256 possible values correspond to 256 colors. (Okay, we know what you're thinking, but black, white and all those grays ARE colors!) The lookup table can be stored in the file with the data, or you can control it using the software that's displaying the data.

The key thing to remember about lookup tables is that they change the appearance of the image, not the pixel values themselves. The colors may change, but the numbers don't.
Now we can put it all together into a simple definition of a digital image:

A digital image is a series of numbers, arranged in a grid of rows and columns, and displayed according to a lookup table.

This image is an 8-bit image. Each pixel is represented in the computer's memory by an 8-bit binary number, representing 256 possible values from 0 to 254. Another term for the number of binary bits used to describe the value of a pixel is bit depth. You can think of the bit depth as the 3rd dimension of an image (width and height are the other two).


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Color images


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Explore More If You Have Time

When values represent something other than brightness

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Resources


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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 Quick Tour of ImageJ

Movie Icon Updating ImageJ

Movie Icon Zooming

Movie Icon Scrolling

Movie Icon Pixel Coordinates and Values

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iPod versions

Download these version to play on your iPod or iPhone.

Movie Icon Quick Tour of ImageJ

Movie Icon Updating ImageJ

Movie Icon Zooming

Movie Icon Scrolling

Movie Icon Pixel Coordinates and Values

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