Welcome to Image Processing with ImageJ. Whether you are new to the world of image processing or an advanced researcher, we hope you will enjoy reading this book and find it useful for your analytic tasks.
The ImageJ imaging analysis software is becoming increasingly used among a vast array of different disciplines. As its user interface is far from a spectacular’s view, a novel user may feel there are only a few things that this amazing program can add to its daily tasks. However, once the ImageJ basics are understood, it becomes a basic device in the toolbox of any scientist who needs to work with images on a daily basis.
This book covers briefly many basic image operations in ImageJ, and then proceeds to more complicated topics: advanced regions of interest delineation and management, filtering in spatial and frequency domains, or particle analysis.
One of the powers of ImageJ is the possibility of automating the different operations, so they can be replicated easily or applied to a large number of different images. This macro system is explained in detail through several exercises that help in showing the reader the potential of this system.
As ImageJ is a public domain software, many developers have contributed their own plugins in order to extend what ImageJ can do by itself. The last two chapters are dedicated to this topic from the perspective of the user who just wants to install new plugins, with a list consisting of our own selection, and also from the point of view of the developer who wants to use ImageJ as the platform to build powerful tools.
Independently of your background and objective, we hope this book has something for you.
Chapter 1, Getting Started with ImageJ, introduces the ImageJ image analysis platform and guides the reader through the installation process.
Chapter 2, Basic Image Processing with ImageJ, introduces the concept of digital image and the different types of data that ImageJ can handle, and then presents the intensity histogram and some basic image operations.
Chapter 3, Advanced Image Processing with ImageJ, describes more advanced imaging analysis techniques, such as modifying the pixel values of different images and performing local measurements. It also covers image filtering in the spatial and frequency domains.
Chapter 4, ImageJ Macros, presents one of the most powerful features of ImageJ: its macro system. Here we introduce this concept and show the reader how different operations can be automatized by giving several examples.
Chapter 5, ImageJ Plugins for Users, is used to explain how ImageJ can be extended very easily. There are literally hundreds of different plugins that extend its native features. In this chapter, we explain the ImageJ plugin system from the point of view of a user who does not necessarily need to know how to program. We perform a sample installation and list some plugins that we have found useful.
Chapter 6, ImageJ Plugins for Developers, is addressed for you if you are a developer. You might not just want to stop at using whatever plugins others have coded for you, but might want to try and implement your own algorithms. We explain briefly the ImageJ plugin architecture, the main classes that you will have to deal with, and how to integrate ImageJ with Eclipse, a very powerful Java IDE.
There is not much material needed in order to follow this book. As ImageJ is a multi-platform public domain software package coded in Java, you just need a desktop computer or a laptop, optionally with the latest Java version installed. And if you don’t have it, don’t worry too much, as ImageJ can provide it for you.
In order to follow the last sections of the sixth chapter, you will also need the Eclipse IDE installed on your system. Please remember that this chapter is aimed at people with prior programming experience, so if that is not your case, you will not need it.
Also, you will probably need some images to keep practicing, apart from the ones we already provided, but that is up to you.
This book is intended for everyone who does scientific work with images and is interested in knowing what can be achieved with ImageJ. The introductory part is a very broad introduction to the field of digital image processing, while the latter chapters are devoted to more complex analysis techniques in addition to an introduction to the macro and plugin system, that we hope will clarify these concepts to everyone interested in automating their analysis procedures or implementing their own image analysis algorithms. We have tried to accomplish a good balance between a step-by-step guide for non-advanced users and a nice introduction for developers who might want to use ImageJ as the development platform of their choice.
In this book, you will find a number of styles of text that distinguish between different kinds of information. Here are some examples of these styles, and an explanation of their meaning.
Code words in text are shown as follows:
You can also send the .class files that will be placed in your plugins directory.
A block of code is set as follows:
run(“Split Channels”); selectWindow(“tuberculosis_full.tif (blue)”); close(); selectWindow(“tuberculosis_full.tif (red)”); close(); selectWindow(“tuberculosis_full.tif (green)”); run(“Subtract Background...”, “rolling=30”);
New terms and important words are shown in bold. Words that you see on the screen, in menus or dialog boxes for example, appear in the text like this: “It can be done, as the error message states, by navigating to the Options | Memory & Threads command from the menu”.
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