MultiThresholder

Authors: Kevin (Gali) Baler
Gabrial Landini
Wayne Rasband (wsr at nih.gov)
Source: In Multi_Thresholder.jar
Installation: This plugin is built into ImageJ 1.45j and later as the Image>Adjust>Threshold command.
Description: This plugin allows the user to segment the current image using any of the 15 thresholding methods from Gabriel Landini's Auto Threshold plugin. More information about each of the methods is available as comments in the source code.

[screen shot]

The MultiThresholder is macro recordable. Here is an example macro that uses the "Cell Colony" sample image to demonstate the 15 thresholding methods supported by MultiThresholder: 

  run("Cell Colony (31K)");
  run("Subtract Background...", "rolling=25 white");
  threshold("Huang");
  threshold("Intermodes");
  threshold("IsoData");
  threshold("Li");
  threshold("Mean");
  threshold("MinError(I)");
  threshold("MaxEntropy");
  threshold("Minimum");
  threshold("Moments");
  threshold("Otsu");
  threshold("Percentile");
  threshold("RenyiEntropy");
  threshold("Shanbhag");
  threshold("Triangle");
  threshold("Yen");
  threshold("Yen (apply)");

  function threshold(method) {
     run("MultiThresholder", method);
     getThreshold(lower, upper);
     print(method+": "+lower+"-"+upper);
     wait(2000);
  }
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).
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
2009/04/12: Uses the 13 thresholding methods from Gabriel Landini's Auto Threshold plugin; adds "Dark Background" checkbox
2009/04/14: Adds "Mean" and "MinError(I)" methods; adds "Stack Histogram" checkbox

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