Re: access R from ImageJ macro

Posted by CARL Philippe (LBP) on Nov 18, 2014; 10:09am
URL: http://imagej.273.s1.nabble.com/access-R-from-ImageJ-macro-tp5010490p5010516.html

Dear all,
In the case you want to combine ImageJ / Fiji with R (or even other
software) an alternative option may be to use knime
(https://www.knime.org/).
My best regards,
Philippe

Philippe CARL
Laboratoire de Biophotonique et Pharmacologie
UMR 7213 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : [phone]

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de
Richard Mort
Envoyé : mardi 18 novembre 2014 10:55
À : [hidden email]
Objet : Re: access R from ImageJ macro

Sorry I'm sending this again because there was a problem with my previous
post. Apologies if you get the following twice:

I've looked into this myself - Reserve seems like the most pragmatic
approach as you have access to all the functions in R. Calling ImageJ from R
is much more limited - I don't think you can use every command available
from within ImageJ.

You can use Reserve to execute an R script. I would imagine you could save
you results to a CSV file. Then use an R script to import them, run the
tests and write the results to another file or to ij.prefs and then open
with ImageJ.

There are lovely plotting tools for R so this could be a very useful
approach. Let me know if you'd like me to dig out an example.

Good luck!
R



On 17/11/14 21:37, Bio7 wrote:
> Here is an example how to call ImageJ from within R (library rJava
required):

>
> https://github.com/Bio7/Bio7/blob/master/ImageJ_Conference_2012/ImageJ
> _FromR/ImageJ_Example.R
>
> This is essentially what RImageJ in a similar way did (load ImageJ and
> then call the methods).
>
> Maybe this example can help you to create your own script.
>
> Another way would be to use Rserve or JRI from ImageJ, see here:
>
> https://github.com/Bio7/Bio7/tree/master/ImageJ_Conference_2012
>
>
> There are several other options.
>
> Another interesting approach would be to use Renjin (R as a JVM
> language) as an ImageJ lib:
>
> http://www.renjin.org/
>
> It is in an early stage but i guess some statistical test are already
> available:
>
> http://renjindemo.appspot.com/
>
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/access-R-from-ImageJ-macro-tp5010490p
> 5010497.html Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Dr Richard Mort
MRC Human Genetics Unit
MRC IGMM
University of Edinburgh
Western General Hospital
Crewe Road
Edinburgh.
EH4 2XU, UK

Tel: [phone]
Fax: [phone]


The University of Edinburgh is a charitable body, registered in Scotland,
with registration number SC005336.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html