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Image Processing with ImageJ
Image Processing with ImageJ

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.

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Book Sep 2013 140 pages 1st Edition
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Product Details


Publication date : Sep 23, 2013
Length 140 pages
Edition : 1st Edition
Language : English
ISBN-13 : 9781783283958
Category :
Concepts :
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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

ImageJ – history and motivation


Tip

Readers who wish to read a more in-depth text about ImageJ's history should obtain the paper "NIH Image to ImageJ: 25 years of image analysis", published in Nature Methods, 2012, 9:7, pages 671-675.

ImageJ's development started as long ago as 1987, when it was not even named ImageJ and Java was yet to be born. That year, Wayne Rasband started coding a piece of software named "NIH Image" (after the National Institute of Health (USA), which funded his efforts) in order to provide a way to perform image analysis on the old Apple Macintosh II, which lacked an image analysis platform, and was starting to be the desktop system of choice for many scientists. He started distributing his software for free to anyone who requested it.

This imaging software became increasingly popular, but at the time the market for Apple computers was being surpassed by the PC. NIH Image was developed specifically for Apple systems and didn't work on the Windows platform. In 1995, the Java programming language was created by Sun Microsystems. This allowed Wayne to start porting his software so it would work on PCs, and at the same time maintain a single, multi-platform version of the source code. ImageJ was born.

During the development process, a great deal of care was taken to allow users to extend ImageJ's native capabilities with the help of macros that can be developed even by users with no prior programming experience; and an open API allowed experienced programmers to code their own plugins. This is one of the reasons for ImageJ's success among scientists that work with images regularly, along with the huge amount of macros and plugins available from the web page. At the time of this writing, the ImageJ's user mailing list had more than 2000 subscribers and is a very active discussion meeting point for everything related to this software and related projects.

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


If you perform a search for "imagej" on some popular academic databases (such as PubMed (http://www.ncbi.nlm.nih.gov/pubmed), IEEE Xplore (http://ieeexplore.ieee.org/), or Google Scholar (http://scholar.google.com), you will find that this software has been successfully used in a huge number of scientific papers in fields that span several disciplines, from confocal microscopy to X-ray analysis, vehicle license plate detection, ultrasound diagnosis of breast cancer, development of automatic 4D segmentation algorithms or tomographic image reconstruction, to cite just a small sample.

ImageJ is not intended to serve as a replacement for Adobe Photoshop, GIMP, or any other graphics editing program. It is less centered on layers, transparencies, cloning, or blurring, and more on quantification, filtering, measuring, and mathematical processing. This does not mean that an image cannot be modified using ImageJ, but the type of modification that ImageJ is intended to do is of a different nature than that of the programs mentioned previously.

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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.

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

What do you get with eBook?

Product feature icon Instant access to your Digital eBook purchase
Product feature icon Download this book in EPUB and PDF formats
Product feature icon Access this title in our online reader with advanced features
Product feature icon DRM FREE - Read whenever, wherever and however you want
Buy Now

Product Details


Publication date : Sep 23, 2013
Length 140 pages
Edition : 1st Edition
Language : English
ISBN-13 : 9781783283958
Category :
Concepts :

Table of Contents

13 Chapters
Image Processing with ImageJ Chevron down icon Chevron up icon
Credits Chevron down icon Chevron up icon
About the Authors Chevron down icon Chevron up icon
About the Reviewers Chevron down icon Chevron up icon
www.PacktPub.com Chevron down icon Chevron up icon
Preface Chevron down icon Chevron up icon
1. Getting Started with ImageJ Chevron down icon Chevron up icon
2. Basic Image Processing with ImageJ Chevron down icon Chevron up icon
3. Advanced Image Processing with ImageJ Chevron down icon Chevron up icon
4. ImageJ Macros Chevron down icon Chevron up icon
5. ImageJ Plugins for Users Chevron down icon Chevron up icon
6. ImageJ Plugins for Developers Chevron down icon Chevron up icon
Index Chevron down icon Chevron up icon

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