Image Processing with ImageJ

Image Processing with ImageJ
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Table of Contents
Sample Chapters
  • 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

Book Details

Language : English
Paperback : 140 pages [ 235mm x 191mm ]
Release Date : September 2013
ISBN : 1783283955
ISBN 13 : 9781783283958
Author(s) : Javier Pascau, José María Mateos Pérez
Topics and Technologies : All Books, Other, Open Source

Table of Contents

Chapter 1: Getting Started with ImageJ
Chapter 2: Basic Image Processing with ImageJ
Chapter 3: Advanced Image Processing with ImageJ
Chapter 4: ImageJ Macros
Chapter 5: ImageJ Plugins for Users
Chapter 6: ImageJ Plugins for Developers
  • Chapter 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
    • Chapter 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
      • Chapter 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
        • 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
            • 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
          • Chapter 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
            • 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
                • Our first Eclipse ImageJ plugin
              • Sharing your plugin
              • Using external libraries
              • Summary

              Javier Pascau

              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, ( 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.

              José María Mateos Pérez

              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 (, 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.
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              What you will learn from this book

              • 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.


              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.

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