Hi Maya,

CellProfiler scales images from 0-to-1, but otherwise leaves them untouched. Your image is a prime example of why we do this, in addition to standardize images regardless of the camera or image format bit-depth. I suspect that the histograms you display are in fact equivalent, however the Matlab histogram is so compressed toward the 0 end, it is obscuring the information that is obvious in the CP histogram. Your camera may be 14-bit, but almost surely the image is written in a 16-bit format. Thus the Matlab hist has a max of 2^16 = 65536, when in fact you camera is only using a tiny fraction of this dynamic range, compressed toward zero. You can confirm this easily by changing your x-axis in Matlab to the max intensity in your image, e.g.

and you will likely see that the two histograms look the more similar.

If you’re still unconvinced, post the image and we’ll take a look.

Cheers,

Dave