For data analysis and visualization, I predominantly use the R computing language. Here are some links to get started with R and see some applications to oceanographic data analysis. Most image processing code I have written in ImageJ, a freeware developed by the U.S. National Institutes of Health. I am in the process of converting code from my research into R packages and creating a GitHub page. In the meantime, some of the image processing code I have written is available on ResearchGate.

My favorite R packages: ggplot2, plyr, reshape2, and Hmisc.

New and useful R packages: dplyr and tidyr

ImageJ is implemented in Java, but it has a built-in macro language that is extremely useful for automating image processing tasks.