R scripts with imageJ functions

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R scripts with imageJ functions

Is it possible to use Bio7 to include imageJ operations within R scripts?
The equivalent to *.ijm macros but using R as syntax
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Re: R scripts with imageJ functions

This post was updated on .
It is possible to call ImageJ from within R with the rJava package.

I started a while ago with a R package to do that with rJava and the ImageJ API. Not finished yet, see:


However, you can easily and fast transfer ImageJ data (image pixels, image selection coordinates, Results table) to the R workspace with available available Bio7 functions (and Java API ) and then postprocess the data in R, see:


This has the advantage to use all ImageJ interface goodies and also create GUI elements (access to SWT and JavaFX to create interfaces, even within Bio7 with a custom GUI view or perspective).

All scripted languages (Groovy, JavaScript, Jython, BeanShell, Java) can access the new Bio7 API or Rserve R API directly (see the following scripts as an example):


By the way you an now also access selected R-Shell view variables from within R (a R character vector named '.r_shell_vars') when you want to create R plot scripts from selected variables in the R-Shell (e.g., to extend the scripts menu!)