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Image Processing with ImageJ

Chapter 1. Getting Started with ImageJ

Welcome to the first chapter of Image Processing with ImageJ. ImageJ is public domain multi-platform software for image analysis written in the Java programming language. It includes predefined functions for a great variety of common tasks and can be extended easily using macros, scripting in several programming languages (including JavaScript and Python), and Java plugins.

In this brief introduction, you will read what ImageJ is, and how to install it, along with some minor configuration tricks. By the end of this chapter, you will have a working ImageJ installation in your system. Contents of this chapter include:

A brief description of ImageJ and its main purpose
An installation and upgrade guide
How to tweak the amount of memory used by ImageJ, in case you are working with big images

Installing ImageJ

ImageJ is software written in the Java programming language. In order to run it, Java Runtime Environment (from now on, just Java) should be installed in your system (go to http://java.com for more information). If you do not have it installed and cannot do it for any reason, you can download several ImageJ packages that include it, but the download size will be considerably larger. The current stable version of ImageJ (1.46r at the time of this writing, though the development is fast and new versions are released almost on a weekly basis) can be downloaded from: http://imagej.nih.gov/ij/download.html. The exact package to be downloaded depends on your particular situation (what operating system are you using, whether you have administrator privileges to perform a system-wide installation, and so on).

Depending on your particular needs, you may want to download the platform-specific installer package, or simply the platform-independent version that consists of a ZIP file, that can be uncompressed and run from your user directory, or even from a USB stick. The platform-specific packages are straightforward to use and behave just like a regular application for the operating systems they are built for; there is extensive documentation regarding the particular details of the installation process for each system in the main ImageJ webpage (Windows: http://imagej.nih.gov/ij/docs/install/windows.html; Linux: http://imagej.nih.gov/ij/docs/install/linux.html; Mac OS: http://imagej.nih.gov/ij/docs/install/osx.html). In the next subsections, we will talk a bit about performing a local installation with the platform-independent file. Depending on your particular configuration, you might want to use these files, as they do not require you to have administrative privileges, and allow you to install ImageJ in any folder in your user directory.

Windows

Download the file ij146.zip (or the one currently being offered) from the download page and unzip it to the folder where ImageJ will be installed. Inside the ImageJ/ folder, double-click on ImageJ.exe. The following dialog will pop up:

The auto-configuration process is pretty straightforward, and consists basically of detecting the path to your Java installation. If the path cannot be automatically found, you will be asked to provide the location of the javaw.exe file. Once this has been done, a new ImageJ.cfg file will be created in the directory where you have unzipped the file, and ImageJ will start. This file is created only in Windows. From that point on, double clicking on ImageJ.exe runs ImageJ, and a direct shortcut can be created on the desktop or where it is useful for your purposes.

Linux / Mac OS

Just like with the Windows version, download the ij146.zip (or the most current) file. Unzip it to the desired folder and execute the run script (on Mac systems, you can also double-click on the application icon). This file just contains a call to the Java virtual machine with the necessary parameters, so the java command needs to be in the system path; in this case, there is no Java autodetection or ImageJ.cfg generation. You can safely delete ImageJ.exe, as it is a Windows-only file.

Configuration options

Once you have a working ImageJ installation, you might want to tweak some configuration options, such as the appearance, font size, and proxy settings. These options are easily modified using the menus Edit | Options | Fonts…, Edit | Options | Appearance…, and Edit | Options | Proxy Settings….

The next section is dedicated to explain how to tweak the one configuration parameter that might be vital during your analysis tasks: the amount of system memory available to ImageJ.

Memory limit increase

If you run Help | About ImageJ... you will get this nice image:

Along with the version (note the upgrade!), the information of ImageJ's main author, and some other data that resembles those previously commented, you can see that 4095 KB of RAM memory is used, from a total of 640 MB (less than 1 percent). Every time you open a new image, the amount of memory being used increases, until the limit is reached. Once you get to this point, an error will pop up, as ImageJ will not have the necessary resources. The error will be something like this:

If you are going to work with big images, or you need to keep open a great number of them, it is wise to increase the memory limit for your system. It can be done, as the error message states, by navigating to the Options | Memory & Threads command from the menu. This will open the following dialog:

Here, you can select the total amount of memory you want ImageJ to use. For example, we change the Maximum memory field to a value of 2048, and click on OK. A new window will inform us that ImageJ will use the new limit upon restart.

In Windows systems, this value is stored in the Image.cfg file. Another option is to edit that file before running ImageJ. These are the contents of that file in a regular installation, though the exact path may vary:

C:\Program Files\Java\jre7\bin\javaw.exe
-Xmx640m -cp ij.jar ij.ImageJ

As you can see, this is just a call to the Java Runtime Environment with the appropriate parameters to run ImageJ. -Xmx640m defines the amount of memory available for the Java virtual machine. If we change that value to -Xmx2048m, we will accomplish the same result as before. This way of changing the total amount of memory can also be used in Linux; in this case, the value is stored in the run script as another argument for the Java virtual machine. These are the typical contents of the run script upon installation:

java –Xmx512m –jar ij.jar

This script just calls the java executable with the configured memory limits, and launches the application inside the ij.jar file. This memory limit can be changed directly in the script file.

Bear in mind that, for memory amounts bigger than 2 GB, a 64-bit system and appropriate Java version is needed.

Note

It is not a good idea to give ImageJ all the available memory. Your operating system and other programs need their share too.

Key benefits

Learn how to process digital images using ImageJ and deal with a variety of formats and dimensions, including 4D images

Understand what histograms, region of interest, or filtering means and how to analyze images easily with these tools

Packed with practical examples and real images, with step-by-step instructions and sample code

Description

Digital image processing is an increasingly important field across a vast array of scientific disciplines. ImageJ's long history and ever-growing user base makes it a perfect candidate for solving daily tasks involving all kinds of image analysis processes. Image Processing with ImageJ is a practical book that will guide you from the most basic analysis techniques to the fine details of implementing new functionalities through the ImageJ plugin system, all of it through the use of examples and practical cases. ImageJ is an excellent public domain imaging analysis platform that can be very easily used for almost all your image processing needs. Image Processing with ImageJ will start by showing you how to open a number of different images, become familiar with the different options, and perform simple analysis operations using the provided image samples. You will also learn how to make modifications through ImageJ filters and how to make local measurements using the selections system. You will also find the instructions necessary to record all the steps you perform so they can be saved and re-run on the same image to ensure analysis reproducibility. Finally, you will get to know some different ImageJ plugins and will learn how to implement your own.

Who is this book for?

This book is targeted at scientists, engineers, technicians, and managers, and anyone who wishes to master ImageJ for image viewing, processing, and analysis. If you are a developer, you will be able to code your own routines after you have finished reading this book. No prior knowledge of ImageJ is expected.

What you will learn

Install and configure ImageJ and its plugins

Open different image formats

Move around the image, zoom in and out, and obtain pixel values

Master the different selection tools

Plot the image profile and understand the histograms

Handle 3D and 4D images

Use the macro recording system

Create your own macros beyond the recorder

Build your own plugins using the ImageJ editor

Integrate ImageJ with the Eclipse IDE to improve the plugin development process

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Robin Cole Feb 18, 2016

A very basic introduction, pretty much what you will find on the introductory website.

Amazon Verified review

年寄りの冷や水 Jan 02, 2015

この本に従ってマクロの使い方などを習得することができました。

Michael W. Konrad Jun 04, 2014

ImageJ is a Goodsend for a scientist who need to analyze images. This book is a clear and comprehensive introduction to ImageJ and all the plugins that you can down load for it. Worth 10X the price.

Kindle Customer Mar 07, 2014

I am somewhat disappointed. The book does not go (much) beyond what is already available in the online documentation for imageJ. I was looking for more examples, tricks and tips illustrated by examples. The book might be a convinient way to find basic information otherwise scattered online, but doesn't really add to it. Considering the low cost of the Kindle version it may still be worth it for those who don't like to hunt and pick through online resources.

Michelle Cronin Dec 30, 2013

not enough detailed info on how to really quantitate fluorescent images which is what i was hoping for. Good for someone who has never even opened image J before.

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.

What do you get with Print?

Image Processing with ImageJ

Chapter 1. Getting Started with ImageJ

ImageJ – history and motivation

Tip

What ImageJ is for (and what it is not for)

Installing ImageJ

Windows

Linux / Mac OS

First run

Updating the installation

Note

Configuration options

Memory limit increase

Note

Summary

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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.

What do you get with Print?

Key benefits

Description

Who is this book for?

What you will learn

Product Details

What do you get with Print?

Product Details

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