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Updated: May 3, 2026

Focussed Ion Beam Milling and Scanning Electron Microscopy of Brain Tissue
Published on: July 6, 2011
Investigation of slice thickness and shape milled by a focused ion beam for three-dimensional reconstruction of
H G Jones1, K P Mingard1, D C Cox2
1National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, UK.
Abstract:
Three-dimensional reconstructions of microstructures produced by focused ion beam (FIB) milling usually assume a uniform slice thickness with flat and parallel surfaces. Measurement of the actual slice thickness and profile is difficult, and is often simply ignored. This paper reports the use of artificial 3D structures of known geometry to enable the full 3D profile of a sequence of slices produced by FIB to be measured for the first time. A transient period at the beginning of a milling process is observed in which the actual slice thickness varies by as much as ±50% from the target thickness (with significantly greater error near the base of the slice), before settling to a ±20% variation as the milling progresses. Although SEM images appear to show flat milled surfaces perpendicular to the top surface, the development of a curved, tapering milled surface is also observed. This profile is then maintained through the milling process with the bottom of the slice lagging the top by up to three slice thicknesses.
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