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Image Processing with ImageJ

Book Description

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.

  • 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

  • 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.

    Table of Contents

    1. Image Processing with ImageJ
      1. Table of Contents
      2. Image Processing with ImageJ
      3. Credits
      4. About the Authors
      5. About the Reviewers
        1. Support files, eBooks, discount offers and more
          1. Why Subscribe?
          2. Free Access for Packt account holders
      7. Preface
        1. What this book covers
        2. What you need for this book
        3. Who this book is for
        4. Conventions
        5. Reader feedback
        6. Customer support
          1. Downloading the example code
          2. Errata
          3. Piracy
          4. Questions
      8. 1. Getting Started with ImageJ
        1. ImageJ – history and motivation
        2. What ImageJ is for (and what it is not for)
        3. Installing ImageJ
          1. Windows
          2. Linux / Mac OS
        4. First run
        5. Updating the installation
        6. Configuration options
          1. Memory limit increase
        7. Summary
      9. 2. Basic Image Processing with ImageJ
        1. Image reading/writing
          1. Opening images with a certain format
          2. Reading raw data
          3. Online sample images
          4. Saving images
        2. Zooming on the image and pixel values
        3. Color and multichannel images
        4. 3D and 4D images – stacks and hyperstacks
        5. Image adjust tools
          1. Image histogram and window/level parameters
          2. Thresholding
          3. Image resizing
        6. Summary
      10. 3. Advanced Image Processing with ImageJ
        1. Selecting regions of your image
          1. Basic selections – lines, length, and profiles
          2. Drawing regions of interest over an area
          3. The ROI manager and the image overlay
        2. Filters
          1. Image filtering in the spatial domain
            1. Edge detection
          2. The Fourier transform
          3. Image filtering in the frequency domain
        3. Particle analysis
        4. Summary
      11. 4. ImageJ Macros
        1. What is an ImageJ macro
        2. The macro recorder
        3. Running macros
        4. Modifying a recorded macro
        5. More about the macro language – basic syntax and operators
          1. Variables
          2. A brief note on debugging a macro
          3. Control structures
            1. The for loop
            2. The while loop
            3. The if (condition) and if (condition) … else statements
        6. Defining functions
        7. Some useful procedures
          1. Opening an image from a macro
          2. Finding out how many images are open
          3. Obtaining the dimensions of an image
            1. A note on slices, frames, and channels
          4. Selecting a specific image
          5. Speeding up a macro
        8. Adding a GUI to your macro
        9. The batch mode
        10. Installing macros for easy access
        11. Shared macros – the ImageJ macro directory
        12. Summary
      12. 5. ImageJ Plugins for Users
        1. ImageJ plugins
        2. Installing a plugin
        3. Some useful plugins
          1. LOCI Bio-Formats
          2. Image segmentation
            1. Auto Threshold and Auto Local Threshold
            2. The trainable Weka segmentation
            3. SIOX (Simple Interactive Object Extraction)
            4. Clustering
            5. Image registration
            6. Stackreg
          3. 3D volume rendering
            1. Volume Viewer
          4. Other utilities
            1. MosaicJ
            2. FigureJ
            3. Study anonymization
        4. FIJI (Fiji Is Not ImageJ)
        5. Summary
      13. 6. ImageJ Plugins for Developers
        1. A sample plugin
        2. The PlugInFilter interface
        3. Adding a GUI to your plugin
        4. The ImageJ plugin API
        5. Setting up ImageJ under the Eclipse IDE
          1. Our first Eclipse ImageJ plugin
        6. Sharing your plugin
        7. Using external libraries
        8. Summary
      14. Index