Pixel binning refers to the combination of the information of adjacent detectors in a CCD camera sensor to create one single pixel in the recorded image.
For instance, a 2 times; 2 binning gathers the electrons from a square of four detectors to record them in just one of the image pixels. Thus, the intensity per pixel increases in a factor of (about) four.
Binning is used to increase the Signal To Noise Ratio at the cost of reducing the Sampling Density (and therefore resolution). It is an option in some microscope models, and should be properly registered in order to have the proper parameters describing the acquired images. In the example above, not noticing that binning is active causes an error in the Sampling Distances of 100% that is critical for Image Restoration.
When describing the image Microscopic Parameters the real physical size of each VoXel in the image must be entered as Sampling Distances. Binning will increase this size: it is just a technical way of making your voxels larger!!!
We have sometimes seen that the Microscopic Parameters recorded in .stk data files do not include binning, and that z-stepper does something else than what the user thinks. Careful attention to use the right parameters in DeConvolution is highly recommended.