java - ImageJ jar file plugin shortcut creation -

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i have been working on developmental biology project marking various nuclear markers along dapi stain determine percentage of marker expression. have found imagej plugin itcn (http://rsbweb.nih.gov/ij/plugins/itcn.html) works great each marker when using clahe program. problem have around 6000 images analyze , love able automate process. have recorded macro such following (which can looped individual image files) :

open("image"); run("8-bit"); run("clahe"); run("itcn "); close();

but itcn icon wont start analyzing automatically, nor there programmed short cut job. ignorant java programming , love know if there anyway around easy problem.

thanks in advance michael

the itcn plugin implemented pluginframe , settings not recordable, have discovered. however, looking @ source, seems plugin uses class called itcn_runner once has gathered options, should able call programmatically.

however, can't macro language. easiest alternative use imagej's built-in javascript scripting. example, start macro recorder usual, select "javascript" in top left. first couple of commands appear me (with reformatting clarity) as:

imp = ij.openimage("/home/mark/test.tif"); ij.run(imp, "8-bit", ""); ij.run(imp,        "enhance local contrast (clahe)",        "blocksize=127 histogram=256 maximum=3 mask=*none* fast_(less_accurate)");

then if @ source code of itcn plugin can see how create itcn_runner class , run - example:

runner = new itcn_runner( imp,                           1, /* width*/                           5.0, /* minimum distance */                           0, /* threshold */                           false, /* detect dark peaks */                           null /* mask imageplus */ ) runner.run()

that produces output in window, has same name "results " prefixed.


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