Image Processing with ImageJ - Second Edition电子书

Image Processing with ImageJ Second Edition

Table of Contents

Image Processing with ImageJ Second Edition

Credits

About the Authors

About the Reviewer

www.PacktPub.com

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Preface

What this book covers

What you need for this book

Who this book is for

Conventions

Reader feedback

Customer support

Downloading the example code

Errata

Piracy

Questions

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

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

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

Maximum projection

Volume viewing and rendering

Processing time series

Normalizing time series data

Summary

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

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

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

7. Explanation of ImageJ Constructs

Frameworks for macros and plugins

Macros and scripting languages

BeanShell scripting

ImageJ main class

Functions to process images

Functions for selections

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

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

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

10. Where to Go from Here?

Basic development

Additional tools

Project management and feedback

Other resources

Summary

Index