MeasureIce: accessible on-the-fly measurement of ice thickness in cryo-electron microscopy

MeasureIce is an ice thickness measurement tool for screening and selecting acquisition areas of cryo-EM grids. Ice thickness is arguably one of the most important factors limiting the resolution of protein structures determined by cryo-electron microscopy (cryo-EM). The amorphous atomic structure of the ice that stabilizes and protects biological samples in cryo-EM grids also imprints some additional noise in cryo-EM images. Ice that is too thick jeopardizes the success of particle picking and reconstruction of the biomolecule in the worst case and, at best, deteriorates eventual map resolution. Minimizing the thickness of the ice layer and thus the magnitude of its noise contribution is thus imperative in cryo-EM grid preparation. In this paper we introduce MeasureIce, a simple, easy to use ice thickness measurement tool for screening and selecting acquisition areas of cryo-EM grids. We show that it is possible to simulate thickness-image intensity look-up tables, also usable in SerialEM and Leginon, using elementary scattering physics and thereby adapt the tool to any microscope without time consuming experimental calibration. We benchmark our approach using two alternative techniques: the ice channel technique and tilt-series tomography. We also demonstrate the utility of ice thickness measurement for selecting holes in gold grids containing an Equine apoferritin sample, achieving a 1.88 angstrom ngstrom resolution in subsequent refinement of the atomic map.

Automated summary

MeasureIce is a simple and easy-to-use ice thickness measurement tool for screening and selecting acquisition areas of cryo-EM grids. It allows simulating thickness-image intensity look-up tables using scattering physics, making it adaptable to different microscopes without the need for experimental calibration. The utility of ice thickness measurement in selecting suitable grid holes is demonstrated, achieving high resolution in subsequent refinement of the atomic map.