Image Processing with ImageJ

Javier Pascau, Jose Maria Mateos-Perez

• Publisher: Packt Publishing
• Year: 2013
• ISBN:
  9781783283958
• Edition: 1
• Topic: Ciencia de la computación
• Subtopic: Programación en Java

In Detail

Digital image processing is an increasingly important field across a vast array of scientific disciplines. ImageJs 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.

Approach

The book will help readers discover the various facilities of ImageJ through a tutorial-based approach.

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.

Image Processing with ImageJ

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Table of Contents

Image Processing with ImageJ

Credits

About the Authors

About the Reviewers

www.PacktPub.com

Support files, eBooks, discount offers and more

Why Subscribe?

Free Access for Packt account holders

Preface

What this book covers

What you need for this book

Who this book is for

Conventions

Reader feedback

Customer support

Downloading the example code

Errata

Piracy

Questions

1. Getting Started with ImageJ

ImageJ – history and motivation

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

Installing ImageJ

Windows

Linux / Mac OS

First run

Updating the installation

Configuration options

Memory limit increase

Summary

2. Basic Image Processing with ImageJ

Image reading/writing

Opening images with a certain format

Reading raw data

Online sample images

Saving images

Zooming on the image and pixel values

Color and multichannel images

3D and 4D images – stacks and hyperstacks

Image adjust tools

Image histogram and window/level parameters

Thresholding

Image resizing

Summary

3. Advanced Image Processing with ImageJ

Selecting regions of your image

Basic selections – lines, length, and profiles

Drawing regions of interest over an area

The ROI manager and the image overlay

Filters

Image filtering in the spatial domain

Edge detection

The Fourier transform

Image filtering in the frequency domain

Particle analysis

Summary

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

Variables

A brief note on debugging a macro

Control structures

The for loop

The while loop

The if (condition) and if (condition) … else statements

Defining functions

Some useful procedures

Opening an image from a macro

Finding out how many images are open

Obtaining the dimensions of an image

A note on slices, frames, and channels

Selecting a specific image

Speeding up a macro

Adding a GUI to your macro

The batch mode

Installing macros for easy access

Shared macros – the ImageJ macro directory

Summary

5. ImageJ Plugins for Users

ImageJ plugins

Installing a plugin

Some useful plugins

LOCI Bio-Formats

Image segmentation

Auto Threshold and Auto Local Threshold

The trainable Weka segmentation

SIOX (Simple Interactive Object Extraction)

Clustering

Image registration

Stackreg

3D volume rendering

Volume Viewer

Other utilities

MosaicJ

FigureJ

Study anonymization

FIJI (Fiji Is Not ImageJ)

Summary

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

Our first Eclipse ImageJ plugin

Sharing your plugin

Using external libraries

Summary

Index

Image Processing with ImageJ

Copyright © 2013 Packt Publishing

All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, without the prior written permission of the publisher, except in the case of brief quotations embedded in critical articles or reviews.

Every effort has been made in the preparation of this book to ensure the accuracy of the information presented. However, the information contained in this book is sold without warranty, either express or implied. Neither the authors nor Packt Publishing, and its dealers and distributors will be held liable for any damages caused or alleged to be caused directly or indirectly by this book.

Packt Publishing has endeavored to provide trademark information about all of the companies and products mentioned in this book by the appropriate use of capitals. However, Packt Publishing cannot guarantee the accuracy of this information.

First published: September 2013

Production Reference: 1160913

Published by Packt Publishing Ltd.

Livery Place

35 Livery Street

Birmingham B3 2PB, UK..

ISBN 978-1-78328-395-8

www.packtpub.com

Cover Image by Aniket Sawant (<[email protected]>)

Credits

Authors

José María Mateos Pérez

Javier Pascau

Reviewers

Cristina Chavarrías

Ron DeSpain

Dr M Partridge

Acquisition Editor

Rubal Kaur

Commissioning Editor

Yogesh Dalvi

Technical Editor

Krishnaveni Haridas

Project Coordinator

Esha Thakker

Proofreader

Mario Cecere

Indexer

Monica Ajmera Mehta

Graphics

Abhinash Sahu

Production Coordinator

Shantanu Zagade

Cover Work

Shantanu Zagade

About the Authors

José María Mateos Pérez is a Spanish researcher and a Ph.D. student in the Medical Imaging Laboratory of the Hospital General Universitario Gregorio Marañón (http://image.hggm.es), in Madrid, where his main research lines deal with automatic segmentation and kinetic analysis modeling of dynamic nuclear imaging sequences. He has also been an experienced ImageJ user and has developed several macros and plugins. One of them, jClustering, has been published in PLOS ONE, a peer-reviewed journal. When he has enough time to procrastinate, he also likes to develop data analysis tools in Python and R.

I would like to thank María for her support during the writing of this book. Also, I feel the need to mention The Army of Small Animals that live or lived in our house. They are a force for good.

Javier Pascau received his Ph.D. from Polytechnic University in Madrid, in 2006, and is currently a visiting professor at Carlos III University in Madrid. He has been a part of the Biomedical Imaging and Instrumentation Group, a research laboratory with a multidisciplinary team of engineers, physicists, biologists, and physicians located both in the university and Hospital General Universitario Gregorio Marañón, (biig.uc3m.es). His research and teaching cover areas such as medical image processing, analysis, quantification, and multimodal registration, both in preclinical and clinical environments. He has been involved in the development of small animal PET and CT devices, and in the last few years he has led several projects on intraoperative radiation therapy and image guided surgery. He has authored more than 30 papers, published in peer-reviewed journals over the last 13 years.

I want to thank all my colleagues at the university and the hospital, since my knowledge on image processing is the result of multiple interactions in this multidisciplinary environment. Special thanks to my family and to my tireless coauthor, who has lead this common work.

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