Feb. 16, 2016

Now Available for Download: Open Access Textbook "Bioimage Data Analysis", Edited by Kota Miura

  • Bioimage Data Analysis - Download Now!Bioimage Data Analysis - Download Now!

Modern microscopes allow capturing of detailed images and movies of cells and proteins. These image data could be used for analysis and modeling of living systems by extracting numerical parameters out of images.

Although there are many textbooks covering theories and practices for image processing algorithms, textbook that explains practical aspects of how to use those algorithms for addressing biological questions is largely missing. This book will be a bridge for this gap: Specific topics in cell and developmental biology are selected as realistic examples of research scenes and step-by-step instructions will be provided for treating those images in quantitative manner. We use three software packages, ImageJ, R and Matlab in the textbook. These are the most commonly used image processing and analysis platforms. Programming using these platforms is becoming more and more important to analyze massive amount of image data. Beside the knowhow of algorithm usages, we will also explain the construction of the analysis pipeline by scripting.  

In the upcoming newsletters, I would like to present a short abstract for the chapters of the book, so that you can get an impression about the topics covered.

Chapter 2: Tools Overview
Many software packages are available for analyzing biological image data but it often is difficult to find information on differences in their capability especially from the user point-of-view. We provide a quick overview of selected software pacakges in this chapter.
Chapter 3: ImageJ
ImageJ macro is a scripting language convenient for automating bioimage analysis protocols. This chapter is a detailed step-by-step tutorial for beginners of macro coding, expecting those without any experience in computer programming. Techniques explained in this chapter are required skills for understanding other application chapters using ImageJ macro. By following small image analysis examples, you are introduced with programing notions such as variables, manipulation of strings and array, loops and conditional statements.
Chapter 4: Introduction to Matlab
This chapter is a brief introduction to Matlab covering the most important concepts for image analysis with this software.
You will learn matrix based operations to analyze images and to visualize the results with statistical plots. This includes introduction to the most important programming language control statements, basic calculus as well as all the necessary image analysis commands used in the following chapters.

For a step-by-step understanding of the software several small exercises are proposed. 

The electronic version of the book is now available at http://bit.ly/BIAS-book free of charge (a registration is, however, needed).


Imaging Data Analysis

Register now!

The latest information directly via newsletter.

To prevent automated spam submissions leave this field empty.