Bioimage Data Analysis
An Open Access Textbook
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.
How to use Algorithms
As explained above many textbooks are available for image processing, even with words such as “Biological” or “Medical” included in their title. However these textbooks in most cases explain only image processing algorithms and how they work. To use these algorithms in biological research, more information on how to combine those algorithms to deal with protein / cell / tissue images for quantitative analysis is required: But this is largely missing. Let us take a metaphor of preparing sushi. For good sushi to be prepared, a series of various types of knives are required. A sushi cook selects appropriate knife at each step starting from a fish to convert it to a piece of beautiful sushi on table. Current image processing textbooks are as if only listing various knives and their purposes, but not explaining the orders and steps it should be taken for using these knives. In addition, different knives are required for treating different types of fish, but this is also missing from the textbook as well.
Biological research papers published in academic journals using image analysis do provide how images were analyzed in their Materials and Methods section.
However, when it comes to practical steps, provided information mostly is not enough to reproduce their analysis. This has been hindering the propagation of image analysis techniques to wider scientific community. By providing detailed protocols for image analysis using realistic examples, this book intends to supplement such missing information to ease non-experts to do their own image analysis.