Image Processing with ImageJ电子书

Image Processing with ImageJ

Table of Contents

Image Processing with ImageJ

Credits

About the Authors

About the Reviewers

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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 – 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

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

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

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

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

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

Index