Image Processing with ImageJ - Second Edition

Author: Jurjen Broeke;José María Mateos Pérez;Javier Pascau  

Publisher: Packt Publishing‎

Publication year: 2015

E-ISBN: 9781785881589

P-ISBN(Paperback): 9781785889837

Subject: TN911.73 Image signal processing

Keyword: 程序语言、算法语言,自动化技术、计算机技术,图像处理软件,计算机的应用,多媒体技术与多媒体计算机,电子出版物编辑出版

Language: ENG

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Description

Extract and analyze data from complex images with ImageJ, the world’s leading image processing tool About This Book • 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 Who This Book Is 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 In Detail 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

Chapter

Chapter 1: Getting Started with ImageJ

ImageJ distributions

The uses of ImageJ

The current state of ImageJ

ImageJ2

SciFIO and OME-XML

Bio-formats

Integrated environment for acquisition and processing

Obtaining and installing ImageJ

Installation of ImageJ

Installing on Windows

Installing on Mac OS X

Installing on Linux

The ImageJ folder structure

Plugins folder

Macros folder

Configuring a fresh ImageJ installation

Summary

Chapter 2: Basic Image Processing with ImageJ

Images in ImageJ

Image types

Grayscale images

Color images

Stacks and hyperstacks

Color images and multichannel stacks

Z-stack images and volumes

Time series

Multidimensional images

Extracting image and pixel information

Loading and saving images

Loading images and sequences

Saving images

Image calibration

Viewing images in ImageJ

Viewing multichannel images

Viewing time series

Summary

Chapter 3: Advanced Image Processing with ImageJ

Correcting images

Technical background

Correcting Shot noise

Correcting dark noise

Uneven illumination – background subtraction

Image normalization

Bleach correction

Stack processing

Processing Z-stacks

Stack projections

Volume viewing and rendering

Processing time series

Normalizing time series data

Summary

Chapter 4: Image Segmentation and Feature Extraction with ImageJ

Image segmentation

Image thresholding

Thresholding grayscale images

Thresholding color images

Morphological processing

Morphological operators

Erode and dilate

Skeletonize and watershed

Image filtering

Filtering in the frequency domain

Image filtering in the spatial domain

Feature extraction

Edge detection

Summary

Chapter 5: Basic Measurements with ImageJ

Selections and regions in ImageJ

Area selections

Line selections

Point selections

Basic measurements

Area selections and measurements

Oval selections

Polygon selections

Line selections and measurements

Kymographs

Line profiles

Colocalization

Semiquantitative colocalization

Particle analysis

Preprocessing and preparations

Summary

Chapter 6: Developing Macros in ImageJ

Recording macros

Recording a macro for conversion

Modifying macros

User input in macros

Opening a specific file

Saving an image to a folder

Adding choices

Performing input checking

Showing progress in macros

Processing the time series

Running macros in batch process mode

Installing macros

Summary

Chapter 7: Explanation of ImageJ Constructs

Frameworks for macros and plugins

Macros and scripting languages

BeanShell scripting

Saving and running your scripts

Plugins for ImageJ

ImageJ main class

WindowManager

ImagePlus

ImageProcessor

RoiManager

The Roi class

The Application Programming Interface

Setting up NetBeans IDE

Gathering all components

Setting up a project

Building ImageJ

Creating a plugin

Creating documentation

ImageJ Javadoc

Plugin Javadoc

Developing plugins using Maven

Construction of the POM

Creating a Maven plugin project

Creating an ImageJ2 plugin

Pros and cons of using an IDE

Summary

Chapter 8: Anatomy of ImageJ Plugins

The basic anatomy of a plugin

Legacy plugins

The PlugIn type

The PlugInFilter type

The PlugInFrame type

Implementing a legacy plugin

Combining macros and legacy plugins

SciJava plugins

The @Plugin annotation

Services

Commands

Running and debugging plugins

Compiling plugins

Compiling SciJava plugins

Debugging plugins

Examples of available plugins

Example plugins available in ImageJ and Fiji

MultipleKymograph

ColorTransformer2

MtrackJ

Coloc2

Goutte_pendante

Summary

Chapter 9: Creating ImageJ Plugins for Analysis

Plugin background and goal

Basic project setup

Creating a basic PlugInFilter

Testing our current implementation

Implementing the setup method

The return type and autocomplete

Javadoc for methods

Finishing the setup method

Implementing the run method

Detecting an object

Refining the detection

Detecting multiple objects

Implementing the measurements

Adding user interaction and preferences

Settings and options dialog

Adding external libraries

Adding the dependency for Apache POI

Creating an Excel file

Sharing your plugin

Creating a site

Uploading your plugin

Summary

Chapter 10: Where to Go from Here?

Basic development

Additional tools

Project management and feedback

Other resources

Summary

Index

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