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Image Processing with ImageJ

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Javier Pascau, José María Mateos Pérez

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 Details

ISBN 139781783283958
Paperback140 pages

About This Book

  • 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

Who This Book Is 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.

Table of Contents

Chapter 1: Getting Started with ImageJ
ImageJ – history and motivation
What ImageJ is for (and what it is not for)
Installing ImageJ
First run
Updating the installation
Configuration options
Summary
Chapter 2: Basic Image Processing with ImageJ
Image reading/writing
Zooming on the image and pixel values
Color and multichannel images
3D and 4D images – stacks and hyperstacks
Image adjust tools
Summary
Chapter 3: Advanced Image Processing with ImageJ
Selecting regions of your image
Filters
Particle analysis
Summary
Chapter 4: ImageJ Macros
What is an ImageJ macro
The macro recorder
Running macros
Modifying a recorded macro
More about the macro language – basic syntax and operators
Defining functions
Some useful procedures
Adding a GUI to your macro
The batch mode
Installing macros for easy access
Shared macros – the ImageJ macro directory
Summary
Chapter 5: ImageJ Plugins for Users
ImageJ plugins
Installing a plugin
Some useful plugins
FIJI (Fiji Is Not ImageJ)
Summary
Chapter 6: ImageJ Plugins for Developers
A sample plugin
The PlugInFilter interface
Adding a GUI to your plugin
The ImageJ plugin API
Setting up ImageJ under the Eclipse IDE
Sharing your plugin
Using external libraries
Summary

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

In Detail

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.

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