Image Processing with ImageJ: Get familiar with one of the world's most highly regarded Digital Image processors, ImageJ. This tutorial takes you through every aspect of viewing, processing, and analysing 2D, 3D, and 4D images, clearly and comprehensively.

In this section, we learn how to open and write different images.

Opening images with a certain format

First of all, we will need an image to open. For this first exercise, we are going to use one of the several public domain images showing the "happy face" on Mars. Go to http://www.msss.com/msss_images/2008/01/31/index.html and download the image you see (happy_face.jpg, image credit to NASA / JPL / Malin Space Science Systems). Store it on your hard disk in a place that is easy to access, as you shall need it right away.

Now run ImageJ, execute File | Open..., and select the file you just downloaded. ImageJ will load the image contents into a new window and you should see something like this:

You just opened your first image using ImageJ. Smile!

We have scaled the image to fit in the page (note the (50%) on the title bar; more on this later), so your window will be bigger. In any case, you can check some common elements to all images opened in ImageJ.

• Image title: In this...

Let's stick with the image we just opened for a while, as it will be a good template for the next exercise. If we want to zoom in or out of a given image, we can run the Image | Zoom | In [+] and Image | Zoom | Out [-] menu options. It is much easier to use the shortcuts, (+) and (-). The current zoom level is added to the image title bar if it is different from 100 percent (recheck the figure shown when we opened happy_face.jpg, and you will find the zoom level set to 50%). Now we can try zooming in and out of the tuberculosis_sample.tif file; the position of the mouse pointer on the image helps guiding the zoom in operation, since it is used to center the scaling. When the zoom level is too big, the main window stops getting bigger and the image is cropped. Two purple squares help the user keep track of the location inside the image. When this zoom level has been reached, you can keep the space bar pressed and drag the image around.

Zoomed image displayed...

Color images can be manipulated in different ways in ImageJ. The most basic option would be to use a pseudo color image, which is an 8-bit image in which every intensity value has a corresponding RGB color, resulting in 256 colors. This color mode is called pseudo color or false color because the color correspondence can be manually changed, depending on the color palette (or the Lookup Table) that we select. The GIF image format stores 8-bit images with the color palette included, so when we open a file in this format it will be displayed in color, although values for every pixel will be limited to 256 possibilities. Open the tuberculosis_sample.gif file again using the File | Open menu option. Now navigate to Image | Lookup Tables. In this menu, many LUTs are offered to be selected. Choose the one named Fire and the result will be:

16-bit image with a Lookup Table applied (Fire LUT) in order to display it with pseudo color

Digital images are not only bidimensional (2D) or multichannel (2D with several channels). We may have several 2D images with spatial, temporal, or any kind of relationship between them. These kinds of images are managed by ImageJ as stacks and hyperstacks. Stacks have three spatial dimensions: x, y, and z. Hyperstacks have four dimensions (x, y, z, and time) and both may also have several channels. As you may be thinking, these two kinds of images are really powerful, since almost any kind of single experiment that provides image results which are somehow related can be handled with them. Now, every image position is not a pixel but a voxel (it has volume), and has three or more dimensions. There is no need that all the dimensions are different from one, and consequently stacks are a subgroup of hyperstacks.

Let's open one sample stack to start familiarizing with this concept. Open the sample image described as T1 head (file t1-head.zip). This stack...

In this section, we will explore different tools that can be used for basic image processing.

In this chapter, you have seen how to perform basic image operations using ImageJ on a variety of image formats with special emphasis on adjusting different image parameters such as window/level and size. Now that you are familiarized with these simple operations, you are ready to go on to the next chapter, where we will show you how to perform more complex operations, such as local measurements or filtering.