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Image Processing with ImageJ
Second Edition
Jurjen Broeke
José María Mateos Pérez
Javier Pascau
BIRMINGHAM - MUMBAI
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Image Processing with ImageJ
Second Edition
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.
ISBN 978-1-78588-983-7
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Credits
Reviewer
Jan Eglinger Indexer
Monica Ajmera Mehta
Commissioning Editor
Neil Alexander Graphics
Disha Haria
Acquisition Editor
Manish Nainani Production Coordinator
Conidon Miranda
Technical Editor
Parag Topre
Copy Editor
Karuna Narayanan
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About the Authors
Jurjen Broeke has a PhD in neuroscience from Vrije Universiteit (VU) Amsterdam
and uses live-cell imaging techniques to study the fundamental processes of
neuronal function. As a neuroscientist, he studies the processes involved in neural
communication. Besides acquiring images, Jurjen also develops software to analyze
dynamics in ImageJ, MATLAB, and R. When not enjoying the outdoors and taking
pictures, he develops technical hardware and software solutions in the Department
of Functional Genomics at VU.
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Javier Pascau received his PhD from Polytechnic University in Madrid in 2006
and is currently a visiting professor at Carlos III University, Madrid. He has been a
part of Biomedical Imaging and Instrumentation Group, a research laboratory with
a multidisciplinary team of engineers, physicists, biologists, and physicians located
both in the university as well as Hospital General Universitario Gregorio Marañón
(biig.uc3m.es). Javier's 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. In the last few years, Javier has led several projects on
intraoperative radiation therapy and image-guided surgery. He has authored more
than 40 papers published in peer-reviewed journals over the last 15 years.
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About the Reviewer
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Table of Contents
Preface vii
Chapter 1: Getting Started with ImageJ 1
ImageJ distributions 1
The uses of ImageJ 3
The current state of ImageJ 4
ImageJ2 4
SciFIO and OME-XML 5
Bio-formats 5
Integrated environment for acquisition and processing 5
Obtaining and installing ImageJ 6
Installation of ImageJ 6
Installing on Windows 6
Installing on Mac OS X 7
Installing on Linux 8
The ImageJ folder structure 8
Plugins folder 9
Macros folder 9
Configuring a fresh ImageJ installation 10
Summary 11
Chapter 2: Basic Image Processing with ImageJ 13
Images in ImageJ 13
Image types 15
Grayscale images 15
Color images 15
Stacks and hyperstacks 18
Color images and multichannel stacks 18
Z-stack images and volumes 20
Time series 20
Multidimensional images 20
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