Re: access R from ImageJ macro

Posted by Marcel on Nov 20, 2014; 8:23am
URL: http://imagej.273.s1.nabble.com/access-R-from-ImageJ-macro-tp5010490p5010567.html

Hello Neil,

you have to download the Rserve libs:

http://rforge.net/Rserve/files/

(REngine.jar, RserveEngine.jar)

Put them in the plugins folder of ImageJ. The you have to start R and install and start the Rserve package:

> install.packages ("Rserve")

The start Rserve:

> library (Rserve)
> Rserve()

Now execute the example and everything should work.


Apropos: if you are looking for some advance ImageJ R functionality you can try out Bio7:

http://bio7.org

which has implemented ImageJ and an R GUI as an Eclipse plugin.

In this app i already implemented several methods to transfer image and selection data to R and vice versa, see the documentation here:

http://bio7.org/documentation/Main.html#toc-Subsubsection-4.3.3.1

Since version 1.7 R plots are opened in the ImageJ canvas (as a R plot device) and from multiple plots an ImageJ stack is created - see the video presentation on this website:

http://bio7.org/?p=2353

In the next weeks i will release a new version which adds e.g. the possibility to transfer ImageJ stack to a RasterStack in R or to transfer the Results Table as an R dataframe.

Best regards

Marcel