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Showing posts from December, 2009

Research systems with free software

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I want to share with you research systems I have built using free and open-source software. My research is in analyzing magnetic resonance imaging (MRI) brain images. Your research will be different than mine but I think many of you can benefit from the same tools and systems. My main research system is composed of the image processing tool ImageJ ( http://rsbweb.nih.gov/ij/ ), the relational database management system MySQL ( http://www.mysql.com/ ), and the statistics and plotting tool R ( http://www.r-project.org/ ). Additional software connects these tools into a system. The MySQL JDBC Connector ( http://dev.mysql.com/downloads/connector/j/3.1.html ) allows ImageJ to store and retrieve data from MySQL. RMySQL ( http://cran.r-project.org/web/packages/RMySQL/ ) allows R to access and display data stored in MySQL. Next I will demonstrate how this system works in my research and hopefully how they can help in yours. ImageJ is an image processing graphical user interface (GUI) w