Cell change shape frequently as they move and divide but the measurement of the thickness is difficult. Current microscopy techniques can measure the dimensions in X and Y axis very accurately but cannot measure the cell thickness. Confocal microscopy, that is usually used with fluorescence dyes can measure the thickness of the cell but it requires fluorescent label. However, if you need to account for the thickness and enhance the image dependent on thickness then looking through a phase contrast microscope will serve the purpose.
However, it is still useful to get an exact number on the thickness and one company is creating an instrument that will allow the measurement of thickness in real time. Their link is below but they have used their prototype instrument to measure the movement of a paramecium in real time where the colors represent the thickness of the paramecium.
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