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. Author manuscript; available in PMC: 2010 Jan 1.
Published in final edited form as: J Struct Biol. 2009 Apr 8;167(1):11–18. doi: 10.1016/j.jsb.2009.03.019

Table 1.

Example presets typically used for ET data collection in Leginon (assumes a 4k × 4k camera)

Preset name Atlasa Grid Square Hole
Example image graphic file with name nihms-123659-t0005.jpg graphic file with name nihms-123659-t0006.jpg graphic file with name nihms-123659-t0007.jpg graphic file with name nihms-123659-t0008.jpg
Magnification - 100x 480x 3kx
Size (pixels/side) - 512 512 512
Defocus (μm) 0 0 0 -100
Pixel size after
binning (nm)		 - 840 170 28
Dose delivered to
specimen (e-/Å2)		 negligible negligible negligible <0.01
Field of view
(μm/side)		 ∼2000 430 90 14
Description/Use Selecting viable grid squares Building the atlas Selecting regions with good
holes		 Selecting potential targets and
corresponding focus positions
Preset name Tomography Preview Focus Tomography
Example image graphic file with name nihms-123659-t0009.jpg graphic file with name nihms-123659-t0010.jpg graphic file with name nihms-123659-t0011.jpg
Magnification 22.5kx 27.5kx 27.5x
Size (pixels/side) 1024 1024 2048
Defocus (μm) -20 - -10
Pixel size after
binning (nm)		 1.9 1.6 0.78
Dose delivered to
specimen (e-/Å2)		 <0.25 0b 1-3c
Field of view
(μm/side)		 2.0 1.6 1.6
Description/Use Highly defocused to enhance
contrast / Final selection and
prioritization of targets		 Adjusting defocus and stage
z-height		 Acquiring the tilt series
a

Atlas is not technically a preset but actually a montage of Grid images.

b

Focus targets are selected to be out of the specimen area.

c

Tomography preset dose depends on the tilt series dose and current tilt angle.