Nikon Ni-E is an advanced upright optical microscope operated for the study of nanoparticles and cells interaction, nanogels, lab-on-a-chip devices and other biological samples. The microscope has two camera ports for one colour camera (DS-Fi2, Nikon, Japan) for bright field imaging and a monochrome camera for low intensity fluorescence measurements (Orca R2, Hamamatsu, Japan), respectively. A large selection of objectives is available, including among others water-dipping objectives and high magnification long-working distance objectives. The camera supports both transmitted and reflected light image formation. Contrast mechanisms for image formation include phase contrast (100x) and polarization resolved imaging.