Figure 3a

Thresholded image produced by matlab's graythresh command. Graythresh outputs a value of 0.0039 (producing an image in which everything above 257 is selected).

 

This threshold is significantly lower than that generated by ImageJ's Otsu thresholding plugin. The output of imageJ's 16bit Otsu plugin corrisponds to a Matlab level of 0.006027, about 1.5x that calculated by MatLab.

 

Code used to generate this image is:

 

T = graythresh(Red);

RedThresh = im2bw(Red,T);

 

Where:

Red = image, loaded into memory as a 16bit array of 512x672

T = threshold level as calculated by graythresh command

RedThresh = resulting thresholded image (shown above)

 

 

Done