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Image Processing with ImageJ - Second Edition
Image Processing with ImageJ - Second Edition

Image Processing with ImageJ - Second Edition: Extract and analyze data from complex images with ImageJ, the world's leading image processing tool

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Image Processing with ImageJ - Second Edition

Chapter 2. Basic Image Processing with ImageJ

After following the instructions in the previous chapter, you should have a working and running installation of ImageJ. This chapter will deal with the following topics:

  • Supported image types in ImageJ
  • Multidimensional images
  • Loading and saving images
  • Viewing and obtaining pixel values
  • Calibrating images for measurements

Images in ImageJ

ImageJ has a wide support for multiple common image formats such as JPEG, PNG, and TIFF. With the help of the Bio-Formats plugin, a wide range of proprietary image formats can also be loaded (for example, STK files [Metamorph], and LSM files [Zeiss]) as well as certain medical image formats (Dicom) and astronomy formats (FITS). The most recent version of Fiji comes with the Bio-Formats plugin and supports the files of almost all the major image formats.

This chapter will use some of the image files that are available from the sample images item in the File menu. These files are accessible from the Internet, so they require a functional Internet connection. The whole suite of images is also available as a single download from the ImageJ website. When using the Fiji distribution, the image set can be cached locally by going to File | Open Samples | Cache Sample Images from the menu.

We will start by opening one of these sample images to demonstrate some of the features in...

Summary

In this chapter, we discussed the different image types that are supported by ImageJ. You also saw how to load images from a disk or from a URL. We looked at the anatomy of an image window in ImageJ and the information that can be viewed. We applied a calibration to images in order to prepare for length and area measurements. Finally, we looked at different ways of viewing different image types. You learned how to adjust the brightness and contrast of the images.

In the next chapter, we will look at ways to perform basic processing steps using the ImageJ interface.

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Key benefits

  • Design automated image-processing solutions and speed up image-processing tasks with ImageJ
  • Create quality and intuitive interfaces for image processing by developing a basic framework for ImageJ plugins.
  • Tackle even the most sophisticated datasets and complex images

Description

Advances in image processing have been vital for the scientific and technological communities, making it possible to analyze images in greater detail than ever before. But as images become larger and more complex, advanced processing techniques are required. ImageJ is built for the modern challenges of image processing – it’s one of the key tools in its development, letting you automate basic tasks so you can focus on sophisticated, in depth analysis. This book demonstrates how to put ImageJ into practice. It outlines its key features and demonstrates how to create your own image processing applications using macros and ImageJ plugins. Once you’ve got to grips with the basics of ImageJ, you’ll then discover how to build a number of different image processing solutions. From simple tasks to advanced and automated image processing, you’ll gain confidence with this innovative and powerful tool – however and whatever you are using it for.

Who is this book for?

The book has been created for engineers, scientists, and developers eager to tackle image processing with one of the leading tools available. No prior knowledge of ImageJ is needed. Familiarity with Java programming will be required for readers to code their own routines using ImageJ.

What you will learn

  • Install and set up ImageJ for image processing.
  • Process images using ImageJ's built-in tools
  • Create macros to perform repetitive processing tasks
  • Set up and use an integrated development environment for ImageJ plugins
  • Create plugins with a user-friendly interface for processing
  • Use established ImageJ plugins for processing and quantification
  • Generate a simple interface based on a real world example and create other interfaces for other projects
  • Speed up interface development by setting multiple parameters interactively
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Publication date, Length, Edition, Language, ISBN-13
Publication date : Nov 30, 2015
Length: 256 pages
Edition : 1st
Language : English
ISBN-13 : 9781785889837
Languages :
Concepts :
Tools :

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Product Details

Publication date : Nov 30, 2015
Length: 256 pages
Edition : 1st
Language : English
ISBN-13 : 9781785889837
Languages :
Concepts :
Tools :

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Table of Contents

11 Chapters
1. Getting Started with ImageJ Chevron down icon Chevron up icon
2. Basic Image Processing with ImageJ Chevron down icon Chevron up icon
3. Advanced Image Processing with ImageJ Chevron down icon Chevron up icon
4. Image Segmentation and Feature Extraction with ImageJ Chevron down icon Chevron up icon
5. Basic Measurements with ImageJ Chevron down icon Chevron up icon
6. Developing Macros in ImageJ Chevron down icon Chevron up icon
7. Explanation of ImageJ Constructs Chevron down icon Chevron up icon
8. Anatomy of ImageJ Plugins Chevron down icon Chevron up icon
9. Creating ImageJ Plugins for Analysis Chevron down icon Chevron up icon
10. Where to Go from Here? Chevron down icon Chevron up icon
Index Chevron down icon Chevron up icon

Customer reviews

Rating distribution
Full star icon Full star icon Full star icon Half star icon Empty star icon 3.4
(5 Ratings)
5 star 40%
4 star 20%
3 star 0%
2 star 20%
1 star 20%
Bruce Comber Jul 02, 2024
Full star icon Full star icon Full star icon Full star icon Full star icon 5
it answered specific questions that I ahd
Feefo Verified review Feefo
Marcos de A. Souza Sep 27, 2017
Full star icon Full star icon Full star icon Full star icon Full star icon 5
This book is excelent to beginners with me. I lik'd!!!
Amazon Verified review Amazon
D. J. Stupple Feb 17, 2016
Full star icon Full star icon Full star icon Full star icon Empty star icon 4
Four stars, because the book is very informative on ImageJ and basic principles of image processing (I am up to page 55, so far). It is let down by the images being all in greyscale, while the captions repeatedly refer to colour features in the images. One image so far appears to be not printed at all.Some of the images for the processes described do not seem to be available from the Packt website(I will edit if this changes), but the samples provided by ImageJ are so far all available. Useful book, poor publishing and support.
Amazon Verified review Amazon
JB1650 Jun 07, 2019
Full star icon Full star icon Empty star icon Empty star icon Empty star icon 2
Somebody needs to write a tutorial book on ImageJ. These authors tried, but this is not a good book. Seriously - black and white photos are used to explain color gamut. Where was the editor? The book has the feeling of being thin, especially for $40. I don't know what else to recommend - there are some PDF tutorials up on the web, perhaps those would be better.
Amazon Verified review Amazon
Marcia F. Stornetta Sep 30, 2017
Full star icon Empty star icon Empty star icon Empty star icon Empty star icon 1
Either the publisher has a cruel sense of humor, or I was shipped a defective copy. All of the images are grayscale in this book, which seems like a significant oversight given 1) the nature of the subject matter and 2) that the authors make explicit mention to the colors in sample images multiple times.Perhaps the most egregious example of this mismatch is an image on page 81, with the following description on page 82: "The shapes with a circularity of 1.00 are colored orange (ellipse) and light green (oval). The red ellipse has a very low circularity (0.28), while the cyan oval has an intermediate circularity (0.48)." To reiterate, the image in question is in grayscale.Adding insult to injury, the images are of a uniformly poor quality. This is highlighted on page 23, where the authors compare a photo of Lenna that they attempt to deliberately reduce in quality by repeated JPEG compressions. However, the photos are indistinguishable! This is something that the authors or editor should have noticed.Concerning the didactic content of the book, it tries to strike a nice balance between material for the absolute beginner (chapters 1-5), intermediate users (chapter 6), and advanced users/developers (chapter 7-9). But, depth is definitely not its strong suit.Were the book not plagued by image quality issues, it would be easier to view this as just a mediocre book (2 stars), but given these reasons, it is impossible to rate anything but 1 star.Attached are the two images referenced from the book.
Amazon Verified review Amazon
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