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A finite phase plate also intercepts diffracted light, altering low spatial frequencies. Halos and shade-off can therefore mimic borders or obscure interiors.^[ref] In the coherent zero-mode model of phase contrast, the separation is perfect by assumption, so that model cannot predict those artifacts.

Phase-contrast microscopy converts specimen-dependent phase differences into visible light intensity differences. It can reveal structures in living, unstained biological cells, allowing their changes to be followed without first making an absorbing preparation.^[ref] The key question is how an optical microscope can read a phase when an ordinary detector records light intensity.

Consider a transparent specimen with complex amplitude transmission $t(x,y)=e^{i\varphi (x,y)}$. In ideal in-focus coherent imaging with all relevant spatial frequencies transmitted, its image has $I=|t{|}^2=1$: varying $\varphi$ alone produces no brightness detail. This is a particular model, not a claim that all transparent specimens are invisible. Diffraction, defocus, absorption and a finite optical pupil can already change a real image.

A phase-contrast microscope images an illuminating annulus onto a phase plate ring near the objective's rear focal plane. The aligned ring attenuates and shifts direct light relative to most diffracted light; their interference changes image brightness.^[ref]

The method is beautiful because the bright direct beam becomes its own reference: a small specimen-dependent complex amplitude can interfere with it and change the image at first order. Merely magnifying an invisible phase pattern would leave $|t{|}^2$ unchanged.

A specimen whose leading optical effect is a spatially varying phase, rather than absorption. A thin specimen with refractive index $n_s$ in a medium of refractive index $n_m$ has, in a straight-path approximation,Here $\lambda$ is the vacuum wavelength; the integral is an optical path length difference. For the chosen values $\lambda =550\mathrm{nm}$, thickness $1\mu \mathrm{m}$ and $n_s-n_m=0.005$, the phase is $\pi /55\simeq 0.0571$ radians. This calculation does not identify thickness separately from refractive index contrast.^[ref]