Researchers at the Arizona State University (ASU) are working on software tools to analyze databases of biological images, that’s called PASSaGE (Pattern Analysis, Spatial Statistics and Geographic Exegesis). One of these projects is using machine learning technology to compare the expression patterns captured in the images. So far, the software was used to explore a database of embryonic fruit flies images to see if the genes share the same spatial patterns. This would indicate that these genes also share similar functions. The goal of the developers is to build a tool able to search biological image databases as fast as Internet search engines are doing.
If you want more information about this project, you can read a paper presented last year at the Computational Systems Bioinformatics Conference (CSB), “Classification of Drosophila embryonic developmental stage range based on gene expression pattern images” (PDF format, 6 pages, 2.52 MB).
Overview of PASSaGE
Spatial analysis is a fundamental part of scientific inquiry, including ecological, evolutionary and environmental science, epidemiology, geology, geography, and mathematics. Recent technological advances in genome sequencing, global positioning systems, and remote sensing have led to a rapid expansion of the number and size of spatially explicit datasets available for analysis. These new data have advanced the scope of spatial analysis to an even braoder variety of human endeavors, but have also rapidly outpaced the capabilities of traditional spatial analytic software and methods.
The need to overcome data limitations inherent in much of the specialized spatial analysis programs commonly available led to the development of PASSaGE: Pattern Analysis, Spatial Statistics, and Geographic Exegesis, a free, easy-to-use program for general spatial analysis. With a fairly simple point-and-click, mouse- and menu-driven interface, but flexible and powerful analysis customization, PASSaGE has been a very popular system for analyzing data in spatial context in both the laboratory and the classroom. The first version of PASSaGE has been downloaded by thousands of users from over 57 countries and 145 U.S. universities.
The Software PASSaGe is free (Windows, Linux, and Macintosh) and could be download here
As an example, you can see on the left a collage of fruit fly gene expression images. “The proper development of each football-shaped fly embryo depends on the coordinated expression of thousands of genes. By studying the expression pattern of single genes, typically displayed in wide bands or narrow striped patterns, scientists can gain insight into the control and regulation of large genetic networks. Similar gene networks are found throughout biology, and break downs in these processes may result in birth defects, heart disease, cancer and aging. (Credit for image and caption: Biodesign News at ASU)
