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Image Processing with ImageJ - Second Edition

Book Image

Image Processing with ImageJ - Second Edition

Overview of this book

Advances in image processing have been vital for the scientific and technological communities, making it possible to analyze images in greater detail than ever before. But as images become larger and more complex, advanced processing techniques are required. ImageJ is built for the modern challenges of image processing – it’s one of the key tools in its development, letting you automate basic tasks so you can focus on sophisticated, in depth analysis. This book demonstrates how to put ImageJ into practice. It outlines its key features and demonstrates how to create your own image processing applications using macros and ImageJ plugins. Once you’ve got to grips with the basics of ImageJ, you’ll then discover how to build a number of different image processing solutions. From simple tasks to advanced and automated image processing, you’ll gain confidence with this innovative and powerful tool – however and whatever you are using it for.

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Image Processing with ImageJ - Second Edition
Nov, 2015 | 256 pages
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Table of Contents (17 chapters)
Image Processing with ImageJ Second Edition
Image Processing with ImageJ Second Edition
Credits
Credits
About the Authors
About the Authors
About the Reviewer
About the Reviewer
www.PacktPub.com
www.PacktPub.com
Preface
Preface
Free Chapter
1
Getting Started with ImageJ
Getting Started with ImageJ
ImageJ distributions
The uses of ImageJ
The current state of ImageJ
Integrated environment for acquisition and processing
Obtaining and installing ImageJ
The ImageJ folder structure
Configuring a fresh ImageJ installation
Summary
2
Basic Image Processing with ImageJ
Basic Image Processing with ImageJ
Images in ImageJ
Summary
3
Advanced Image Processing with ImageJ
Advanced Image Processing with ImageJ
Correcting images
Stack processing
Summary
4
Image Segmentation and Feature Extraction with ImageJ
Image Segmentation and Feature Extraction with ImageJ
Image segmentation
Morphological processing
Image filtering
Feature extraction
Summary
5
Basic Measurements with ImageJ
Basic Measurements with ImageJ
Selections and regions in ImageJ
Basic measurements
Colocalization
Particle analysis
Summary
6
Developing Macros in ImageJ
Developing Macros in ImageJ
Recording macros
Modifying macros
Showing progress in macros
Running macros in batch process mode
Installing macros
Summary
7
Explanation of ImageJ Constructs
Explanation of ImageJ Constructs
Frameworks for macros and plugins
The Application Programming Interface
Setting up NetBeans IDE
Summary
8
Anatomy of ImageJ Plugins
Anatomy of ImageJ Plugins
The basic anatomy of a plugin
Running and debugging plugins
Examples of available plugins
Summary
9
Creating ImageJ Plugins for Analysis
Creating ImageJ Plugins for Analysis
Plugin background and goal
Basic project setup
Creating a basic PlugInFilter
Adding user interaction and preferences
Adding external libraries
Sharing your plugin
Summary
10
Where to Go from Here?
Where to Go from Here?
Basic development
Additional tools
Project management and feedback
Other resources
Summary
Index
Index

Setting up NetBeans IDE

We will now look at how to set up an Integrated Development Environment (IDE) that can be used to develop ImageJ as well as plugins for ImageJ. There are many IDEs available for Java. While this section will show you how to set up a specific IDE called NetBeans, many of these settings and configurations can be replicated in your preferred IDE.

The setup I will describe is for the NetBeans IDE, which is developed by the same company that manages the Java language. It can be downloaded in different variants, including a variant for Java development, webpage development, and C++ development. If you only wish to develop plugins for ImageJ, the Java SE (Standard Edition) or Java EE (Enterprise Edition) downloads should be fine. The enterprise edition is similar to the standard edition, but it has additional APIs for multilevel and scalable applications as well as secure network applications. It is possible to extend the basic Java edition and add modules for web development...

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