// Initial Ridge Detection Macro
// 	  Make sure the RidgeDetection.jar is installed (Update -> Manage Sites -> check Biomedgroup Update Site)

// input data matrix from matlab using:
	//	(Data-min(Data(:)))./(max(Data(:)-min(Data(:))))*30000;
	//	imwrite(uint16(ans),'TestData.tif')

// Once data is opened in ImageJ, select data window and run script

data = getTitle();		// Data Variable
selectWindow("TestData.tif");
getDimensions(width, height, channels, slices, frames)	// Data variable dimensions
w2 = width/5;		// resize parameter for aspect ratio, 20% wide, 1000% long
h2 = height*10;		
run("Duplicate...", " ");
rename("Data_resize")
big = getTitle();		// Resized Data Window Variable, 16-bit
run("Size...", "width=&w2 height=&h2 average interpolation=Bicubic");
//run("Brightness/Contrast...");
run("Enhance Contrast", "saturated=0");
run("Duplicate...", " ");
rename("Data_resize_8bit")
comp = getTitle();
run("8-bit");	// Need to rescale for analysis
//run("Ridge Detection")
run("Ridge Detection", "line_width=8 high_contrast=23 low_contrast=0 estimate_width extend_line displayresults add_to_manager make_binary method_for_overlap_resolution=NONE sigma=2.81 lower_threshold=0 upper_threshold=0.17 minimum_line_length=0 maximum=0");