Introduction

The smallest units which compose your image are the pixel. A pixel in your image is just a number that represents the amount of light emitted by your sample. When the image is displayed, the values of the pixels are usually converted into squares of particular colors, which are defined by the Look Up Table (LUT, more on that later). Although the colored square is nice to look at, for quantitative measurement, only the numbers matter. Here is an example of what we see (1. & 2.) and what the computer sees (3.):

ImageJ & Fiji

ImageJ was developed at the National Institutes of Health by Wayne Rasband and came to life in 1997.

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It can be readily extended by adding extra features in the form of plugins, macros or scripts. Unfortunately, it can be hard to know which optional features are really good and where to find them all. Fiji, which stands for Fiji Is Just ImageJ, goes some way to addressing this. It is a distribution of ImageJ that comes bundled with a range of add-ons intended primarily for life scientists. It also includes its own additional features, such as an integrated system for automatically installing updates and bug fixes and extra open-source libraries that enable programmers to more easily implement sophisticated algorithms. Therefore, everything ImageJ can do can also be accomplished in Fiji, but the converse is not true. Therefore, we strongly advise using Fiji.

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The user interface

Tips

• Shortcuts are present in the toolbar; for example, Stk will give you access to the stack menu. The toolbar can also be customized; click on the double arrow ">>" for more options.
• Files can be opened quickly by dragging them onto the Status bar. Most plugins you might download can also be installed this way.
• If you know the name of a command (including plugins) but forget where it is hidden amidst the menus, type Ctrl + L (or perhaps just L) to bring up the Command Finder.
• Should you ever lose this main window behind a morass of different images, you can bring it back to the front by pressing the Enter key.