Image Processing on Linux

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Linux Journal: 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,…MORE (Linux Journal)

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