Image Processing on Linux

I've covered several scientific packages in this space that generate nice graphical representations of your data and work, but I've not gone in the other direction much. So in this article, I cover a popular image processing package called ImageJ. Specifically, I am looking at Fiji, an instance of ImageJ bundled with a set of plugins that are useful for scientific image processing.

The name Fiji is a recursive acronym, much like GNU. It stands for "Fiji Is Just ImageJ". ImageJ is a useful tool for analyzing images in scientific research—for example, you may use it for classifying tree types in a landscape from aerial photography. ImageJ can do that type categorization. It's built with a plugin architecture, and a very extensive collection of plugins is available to increase the available functionality.

The first step is to install ImageJ (or Fiji). Most distributions will have a package available for ImageJ. If you wish, you can install it that way and then install the individual plugins you need for your research. The other option is to install Fiji and get the most commonly used plugins at the same time. Unfortunately, most Linux distributions will not have a package available within their package repositories for Fiji. Luckily, however, an easy installation file is available from the main website. It's a simple zip file, containing a directory with all of the files required to run Fiji. When you first start it, you get only a small toolbar with a list of menu items (Figure 1).

Figure 1. You get a very minimal interface when you first start Fiji.

If you don't already have some images to use as you are learning to work with ImageJ, the Fiji installation includes several sample images. Click the File→Open Samples menu item for a dropdown list of sample images (Figure 2). These samples cover many of the potential tasks you might be interested in working on.

Figure 2. Several sample images are available that you can use as you learn how to work with ImageJ.

If you installed Fiji, rather than ImageJ alone, a large set of plugins already will be installed. The first one of note is the autoupdater plugin. This plugin checks the internet for updates to ImageJ, as well as the installed plugins, each time ImageJ is started.

All of the installed plugins are available under the Plugins menu item. Once you have installed a number of plugins, this list can become a bit unwieldy, so you may want to be judicious in your plugin selection. If you want to trigger the updates manually, click the Help→Update Fiji menu item to force the check and get a list of available updates (Figure 3).

Figure 3. You can force a manual check of what updates are available.


Joey Bernard has a background in both physics and computer science. This serves him well in his day job as a computational research consultant at the University of New Brunswick. He also teaches computational physics and parallel programming.