How can I do batch processing of images using ImageJ in Java or clojure?

Question

I want to use ImageJ to process several thousand images.

Is there a way to make any generic imageJ plugin and apply it to hundreds of images automatically?

For example, let's say I want to take a thousand images and apply polar conversion to each ---

The polar conversion plugin for ImageJ can be found here:

http://rsbweb.nih.gov/ij/plugins/polar-transformer.html

Fine! Let me use it. From:

http://albert.rierol.net/imagej_programming_tutorials.html#How%20to%20automate%20an%20ImageJ%20dialog

I find that I can apply the plugin using the following:

(defn x-polar 
  [imageP]
  (let [thread (Thread/currentThread)
        options ""]
    (.setName thread "Run$_polar-transform")
    (Macro/setOptions thread options)
    (IJ/runPlugIn imageP "Polar_Transformer" "")))

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(defn x-polar 
  [imageP]
  (let [thread (Thread/currentThread)
        options ""]
    (.setName thread "Run$_polar-transform")
    (Macro/setOptions thread options)
    (IJ/runPlugIn imageP "Polar_Transformer" "")
    (let [return-image (IJ/getImage)]
      (.hide return-image)
      return-image)))

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Answer 1

, ImageJ , . ( , :)) , Polar_Transformer.java :

http://gist.github.com/452826

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