Image Processing with ImageJ. Get familiar with one of the world's most highly regarded Digital Image processors, ImageJ. This tutorial takes

Image Processing with ImageJ. Get familiar with one of the world's most highly regarded Digital Image processors, ImageJ. This tutorial takes - Opis

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. Spis treści:
Image Processing with ImageJ
Table of Contents
Image Processing with ImageJ
Credits
About the Authors
About the Reviewers
www.PacktPub.com
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Why Subscribe?
Free Access for Packt account holders
Preface
What this book (...) więcej 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 mniej