Figure 3b

image thresholded by Matlab threshold, using the level calculated by imageJ (0.006027, equivalent to an gray intensity of 395.

 

This image is identical to that produced by imagej, other than the image is inverted.

 

This shows that the problem isn't in the im2bw function, but rather in the way graythresh is calculating the cutoff level.

 

Matlab code is:

RedJ = im2bw(Red,0.0060273136);

 

Where:

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

RedJ = thresholded image, using level calculated by Imagej

0.0060273136 = threshold calculated by imageJ (=395/65535)

Done