I was reading Steve on Image Processing blog (image analysis with MATLAB) - two consecutive posts Gray scale pixel values in labeled regions and Intensity-weighted centroids, with goals totally unrelated. Yet, both implementations begin the same way – thresholding of the image. I started to remember that this is very typical in image analysis. In all the MATLAB tutorials I’ve seen, especially tutorial intended for beginners, whatever you do, you have to start with thresholding. It seems strange because there are many sophisticated algorithms for grayscale and color images. Except, those are about image processing, while almost all image analysis algorithms are for binary images. ImageJ is another good example. Among a hundred of image manipulation/processing commands, there are a few image analysis tasks tucked in. And of those, what they call image analysis is either all manual or isn’t about analysis of the content of the image in the first place (like the color histogram). A couple of commands left are only for binary images. Once again, if you try to “Analyze Particles”, you get the message “Threshold first!”… I actually find this very encouraging because it means that what I am working on has some value… [A smiley face used to be here but apparently it messes up WordPress…]