We will use a large sigma value of 3 for this task. Run a Gaussian Blur filter on the image to blur out the “speckle”, actually Poisson distributed, statistical “photon shot noise”, and also to smooth out the inhomogeneity of the nuclear staining. Open the sample image of touching DAPI stained cell nuclei from a confocal laser scanning microscope.
Okay, so how can we denoise, segment, watershed (separate touching objects) and then count / measure the objects in Fiji? Read on…. Luckily, there is a method for doing exactly that. So, we are faced with the problem of being able to separate apparently touching, noisy, objects :-(. That gives objects fuzzy edges and adds uncertainty to the intensity values of each pixel, making it harder to segment properly. The PSF is much bigger than the width of a membrane! Just to make matters even worse the image is quite noisy, because it was made with a fast scan on a confocal laser scanning microscope, which inherently has a low signal/noise ratio. There is a membrane or two at least between them, but an optical microscope cannot resolve that. The nuclei often seem to touch each other, which in reality, of course, they can not. Worse still, in many tissues that are interesting for developmental biology, the cells are tightly packed, and are composed mostly of nucleus with very little cytoplasm separating them. however, the staining is not homogenous, as there are areas of more or less condensation of the chromosomes. The staining delineates the nuclei pretty well, since in a metaphase cell there is DNA all over the nucleus. A very common biological sample for microscopy is DAPI stained DNA in cell nuclei. Watershed Separation of touching DAPI stained nuclei images -Tutorial Introduction to the problem 
It is often useful on blob-like structures such as cell nuclei. Watershed separation is a technique for cutting apart connected components into
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