ice thickness estimates
Added by Anonymous over 19 years ago
Is it possible to carry out a calibration so that holes with a desired ice thickness in nm can be targeted? While setting up in MSI, in the Hole Targeting node, the zero thickness is entered into Lattice settings. Also, in the Acquisition settings, minimum and maximum mean thicknesses are entered for the targeted holes (and a maximum standard deviation). The recommended values in the Leginon manual are about 0.0 for minimum mean thickness and about 0.2 for maximum mean thickness (and about 0.2 for the standard deviation). Presumably these are relative thicknesses and are not in nm or any other unit? Is there any way to convert to an absolute thickness in nm? John Trinick says it is desirable to target holes between 40 and 70nm,
William
Replies (1)
ice thickness - Added by Anchi Cheng over 19 years ago
I have done some tests trying to convert absorbance to physical ice thickness. It is not as easy as it seems. The only method I know for calibration the conversion is by burning ice off an area and then tilt the stage to get the thickness by comparing the location of the footprint of the top and bottom extreme of the burned hole. The uncertainty is high in such measurement. To complicate the matter, at lower mag such as that of sq preset, the image intensity within a hole of a given ice thickness changes with defocus, for example. It appears that the edge of the holes act in a way similar to an aperture and created interference that sometimes increases the intensity within the hole relative to an unobstructed grid square. You may have better consistency at higher magnification but I have not tried it across defocus etc. I am working on these and will let you all know if I find a solution.