I am learning how to do negative staining on cells for TEM, and I am seeing highly variable shapes/arrangement of nuclei. Is this normal, or did something go wrong with the processing?
I agree with Vladimir (positive staining) is indicated in the images you are displaying. Nuclei can be near circular in sectional view, but the more common shape is non-round. Many can be highly convoluted, almost Amebia-like. The same shapes can be detected with SEM (with the right protocol), but more importantly, cryo-sectioning of cryo-fixed tissue produces the same convoluted shapes. Cryo-TEM was, for many years, considered the go-to method for proofing chemical fixation methods. But, since we have perfected chemical fixation methods, cryo-techniques are now much less commonly done.
If your fixative pH is correct for the tissue, and your osmolarity is correct, you should get good chemical fixation results.
Your cells seem to be stained positively with probably Uranyl acetate and lead citrate and of course post-fixed by osmium. Negative staining is generally used to stain particulate samples like isolated proteins or cell organelles.
In the TEM you can visualize a 2D projection of your 3D object. The size and shape of the nucleus vary from cell types, growth phase, and the plane of the section.