18.03.2012
Bio7 can be extended in several different ways with Eclipse plugins, R packages, ImageJ plugins and custom scripts (scripts to extend a menu or executed at startup).
1. To install (suitable) Eclipse plugins the Update-Manager can be used to install plugins from a remote website. An How-To was already posted with the GIT plugin as an example, see: http://bio7.org/?p=1066
2. R packages can be added in two different ways. One way is to use the package installer GUI of Bio7:
http://www.uni-bielefeld.de/biologie/Oekosystembiologie/bio7app/flashtut/rpackagesinstall.htm
Additionally the command line in R can be used to install packages.
3. ImageJ plugins (*.class or *.jar files) have to be installed in the plugins folder of the ImageJ Eclipse plugin which is e.g.: Bio7/plugins/com.eco.bio7.image_1.45.1/plugins.
Note: In the ImageJ Eclipse plugin the typical ImageJ folder structure can be found!
4. Groovy, BeanShell and R scripts, as well as ImageJ macros can be dropped to special folders to extend the default Bio7 menu (startup) functionality. The folders which are scanned by default are:
Path to folders: Bio7/plugins/com.eco.bio7_1.5.0/
| Folder Default (see Preferences!) |
Script Type | Menu | Bio7 Component |
| export_scripts | BeanShell,Groovy | File->Export-Scripts | Main Menu |
| import_scripts | BeanShell,Groovy | File->Import-Scripts | Main Menu |
| image_scripts | ImageJ Macros | Scripts->ImageJ-Macros | Main Menu |
| scripts | BeanShell,Groovy | Scripts->General-Scripts | Main Menu |
| r_scripts | R scripts | Scripts->R-Scripts | Main Menu |
| spatial_scripts | BeanShell,Groovy | Scripts->Spatial-Scripts | Main Menu |
| grid_scripts | BeanShell,Groovy | Scripts | Table View Menu |
| startup_scripts | BeanShell,Groovy | Scripts executed at startup if folder available! | – |