Using results from plugins in scripts

Posted by Marcello DiStasio on Oct 30, 2013; 10:17pm
URL: http://imagej.273.s1.nabble.com/Using-results-from-plugins-in-scripts-tp5005391.html

Hello ImageJ list, and apologies if this isn't the appropriate venue for
this question, but I have been unable to come up with an obvious answer
elsewhere.

I want to use a plugin (one that is a standard plugin bundled with Fiji as
a *.jar in the ./Fiji.app/plugins directory -- specifically
'Colour_Deconvolution') as part of an image processing pipeline that I am
writing using Jython.  I am able to run the command as recorded by the
Macro Recorder using the IJ.run method:

IJ.run(imp, "Colour Deconvolution", "vectors=H&E")

The problem is that this method returns nothing to the calling script.  The
method runs the command in Fiji, and 3 result images are generated and
shown.  What I want is access to one (or all) of these result images in my
calling script.  Is there a way (in Jython) to 'drill down' into the plugin
in order to get the ImagePlus objects for these results?

Thanks!
-Marcello

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