/*
  * Instructions-
  * Download this macro script, and go to plugins to install the "segmentation" macro script onto ImageJ
  * Once installed right click the "segmentation" icon to set the scale factor (0-10), and click ok
  * Click the icon again and set your desired Gaussian Blur radius, and for the outliers set your wanted radius and threshold, as a starting point I recommend trying out the radius=14 and threshold=50 
  * If you are not happy with the segmentation, modify the scale factor (incresae/decrease acordingly) before making adjustments to the outlier radius
*
* Segmentation script written by Eden Tamrat
*/


var SCALE_FACTOR = 2;

macro "segmentation" 
  {segmentN();
}

macro "segmentation Action Tool - CfffCfc9D25D26D27D28D29D2aD2bD34D36D37D38D39D3aD3bD3cD44D46D47D48D49D4aD4bD4cD53D54D55D57D58D59D5aD5bD5cD5dD63D64D65D67D68D69D6aD6bD6cD6dD73D74D75D76D83D84D85D93D94D95Da4Db4C000D15D16D17D18D19D1aD1bD24D2cD33D35D3dD43D45D4dD52D56D5eD62D66D6eD72D77D78D79D7aD7bD7cD7dD7eD82D86D8eD92D96D9eDa3Da5DadDb3Db5DbdDc4DccDd5Dd6Dd7Dd8Dd9DdaDdbCc96D87D88D89D8aD8bD8cD8dD97D98D99D9aD9bD9cD9dDa6Da7Da8Da9DaaDabDacDb6Db7Db8Db9DbaDbbDbcDc5Dc6Dc7Dc8Dc9DcaDcbCbbbDaeDbeDcdDceDdcDddDdeDebDecDedDeeDfcDfd"
  {segmentN();
}

macro "segmentation Action Tool Options" {
         Dialog.create("Nuclei segmentation Options");
	 Dialog.addNumber("scale factor:", SCALE_FACTOR);
     	 Dialog.show();
	SCALE_FACTOR = Dialog.getNumber();
}

function segmentN() 
        {setBatchMode(true);
        run("Scale...", "x="+(1.0/SCALE_FACTOR)+" y="+(1.0/SCALE_FACTOR)+" interpolation=Bilinear create title=small_tmp");
        run("8-bit")
        run("Gaussian Blur...");
	setAutoThreshold("Huang dark");
	run("Convert to Mask");
        run("Despeckle");
        run("Remove Outliers...");
	run("Fill Holes");
	run("Watershed");
	run("Scale...", "x="+SCALE_FACTOR+" y="+SCALE_FACTOR+" interpolation=Bilinear create title=big_tmp");
	setAutoThreshold("Huang dark");
	roiManager("Reset");
	run("Analyze Particles...", "size=0-Infinity circularity=0.40-1.00 show=Nothing exclude add");
	selectWindow("small_tmp");
	close();
	selectWindow("big_tmp");
	close();
	roiManager("Show All");
	setBatchMode(false);
}

EXTRA
//
// argument 0..4: (optional) display inputs
//		0 for object/background binary image
//		1 for watershed lines
//		2 for red overlaid dams
//		3 for labelized basins
//		4 for colorized basins

// Description of the arguments
//
// argument 1: (mandatory)
//		0 for dark objects on bright background, 1 otherwise
//
// argument 2: (mandatory)
//		0 a neighborhood of 4 pixels, 1 a neighborhood of 8 pixels (radius in pixels) 
//
// argument 3: (mandatory) 
//		minimum level [0..255]		
//
// argument 4: (mandatory) 
//		maximum level [0..255]		
//