Book Image

Image Processing with ImageJ

Book Image

Image Processing with ImageJ

Overview of this book

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.
Table of Contents (13 chapters)
Image Processing with ImageJ
Credits
About the Authors
About the Reviewers
www.PacktPub.com
Preface
Index

The batch mode


One common operation you will probably need to do at some point is to apply a macro to a large number of images. You have an option of using the setBatchMode(arg) function and code the logic for opening and closing each file. However, there is a simpler way of accomplishing this, which is just navigating to the Process | Batch | Macro... menu option. When you run it you will get a dialog similar to the following one:

This dialog will allow you to apply a macro to all the images contained inside a given folder (Input...) and will store the result into another one (Output...) with the image format selected in the Output Format option. If you leave the output folder field empty, nothing will be saved (you may want to do this if your macro consists of a list of measurements and does not involve any image modification). You can write your macro code in the textbox or in an open (Open...) one that you have coded previously. The Test button runs the macro on the first image of the...