MultiThresholder

Author: Kevin (Gali) Baler (gliblr(at)yahoo.com)
History: 2005/07/21: First version
2005/08/03: Works with 16-bit and 32-bit images; adds "Refresh" button
2007/01/25: Fixes bug that caused an exception when running the sample macro using the MBF ImageJ bundle
Source: In Multi_Thresholder.jar
Installation: Download Multi_Thresholder.jar to the plugins folder, or subfolder, restart ImageJ, and there will be a new MultiThresholder command in the Plugins menu.
Description: This plugin allows the user to apply four different thresholding algorithms. The four algorithms are ImageJ's built in IsoData algorithm, Maximum Entropy, Otsu, and Mixture Modeling. More information about thresholding and the algorithms employed here can be found at the Image Thresholding Tutorial.

The MultiThresholder is macro recordable. Here is an example macro that uses the "Cell Colony" sample image to demonstate the four thresholding methods supported by MultiThresholder: 

    run("Cell Colony (31K)");
    run("Subtract Background...", "rolling=50 white");
    run("MultiThresholder", "Isodata");
    getThreshold(lower, upper);
    print("IsoData Threshold: " + lower + "-" + upper);
    wait(2000);
    run("MultiThresholder", "Mixture");
    getThreshold(lower, upper);
    print("Mixture Threshold: " + lower + "-" + upper);
    wait(2000);
    run("MultiThresholder", "Otsu");
    getThreshold(lower, upper);
    print("Otsu Threshold: " + lower + "-" + upper);
    wait(2000);
    run("MultiThresholder", "Entropy");
    getThreshold(lower, upper);
    print("Entropy Threshold: " + lower + "-" + upper);
    wait(2000);
    run("MultiThresholder", "Entropy apply");
To run this macro, select it and copy it to the clipboard (ctrl-c), switch to ImageJ, use Plugins/New (shift-n) to open a macro window, paste in the macro (ctrl-v), then run it using the macro editor's File/Run Macro command (ctrl-r).

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