What is the definition of ice thickness in the hole finders¶

The ice thickness (t), as a first approximation, is proportional to the image contrast where image contrast is defined as the natural log of the ratio of the incident beam intensity (I0) to the transmitted beam intensity (I).

t = k * ln( I0 / I )

where k is known as mean free-mass thickness.

In various holefinders in Leginon, k is assumed to be 1 which makes t in an arbitrary unit. I0 is usually obtained from an empty hole under the same imaging condition, while I is that measured from the interested hole with ice. As demonstrated in our 2006 paper (J. Struct. Biol. v154,p303), k varies with defocus and can be affected by the presence of objective aperture. At high defocus, the relationship between image contrast and the ice thickness can also become non-linear. For practical purpose, it is important to maintain the same defocus when ice thickness of two experiment session is to be compared.

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