Pre-MSI Set-up¶

Design Presets¶

To start your own MSI experiment, you must decide what presets you want to use. Presets
are used to define scope and camera parameters with which images are acquired.

MSI presets can be customized to your need of data collection. By matching
nodes/subnodes in MSI with presets and move types, the behavior of the node is
defined.

For easy reference, preset names in MSI has been standardized at NRAMM although there
is no reason they have to be called in the way they are now. They are abbreviated to 2
letter codes to reduce the length of the filenames that contains every preset used in its
family history.

Preset name:	abbrev for:	in the context of:
gr	grid	em grid
sq	square	em grid square
hl	hole	quantifoil hole
fc	focus	focus image to be checked with fft
fa	focus-auto	automatic focusing
en	exposure-near	close-to-zero defocus exposure image in a focal pair
ef	exposure-far	far-from-zero defocus exposure image in a focal pair

Magnification:	Preset name:	Image Shift (x,y):	Dimension:	Binning:	Beam Coverage:	Exposure Time (ms):	Spot Size:	Defocus (m):
120	gr	Aligned	512	8	max	20	4	0.0
550	sq	Aligned	1024	4	1x CCD size	100	4	-2e-3
5000	hl	Aligned	512	8	1x CCD	20	4	-1.5e-4
50000	fc	0,0	512	1	<~ 1x CCD	300	4	-2e-6
50000	fa	0,0	1024	4	>2x CCD	50	4	-2e-6
50000	en	0,0	4096	1	2x CCD	170 (10e/A^2)	4	-1e-6
50000	ef	0,0	4096	1	2x CCD	170 (10e/A^2)	4	-2e-6

The preset parameters in this example are chosen to give the following
properties:

• en and ef is for final exposure and therefore has highest resolution and
  dimension.

• en stands for near focus exposure and therefore has lower defocus value than
  ef,the far-from-focus exposure.

• fa is for high resolution autofocus and therefore need to be high mag. The
  dimension and binning is a result of compromizing speed, S/N ratio and sensitivity to
  details.

• fc is for manual focus and ice melting and therfore more intense than fa. To get
  good FFT for checking Thon ring behavior, it is not binned. The small dimension is for
  increasing speed.

• hl is for intermediate targeting. It needs to cover the error range of modeled
  stage position to allow final targeting by image shift only, hence the magnification.
  The binning is for speed.

• sq is for grid square targeting. The image produced by the preset need to cover
  most if not all of the square but with enough resolution to evaluate the
  content.

• gr is for producing grid atlas. It is selected based on the size number of tiles
  needed to cover the whole grid in an acceptable time and the amount of distortion
  common to very low mag imaging.

In designing your own preset, follow the above properties using a mag that gives the
required coverage with your scope, camera, and grid mesh. If you have a 2k or 1k camera,
binning may not be as necessary as for a 4k camera whose data acquisition time is 10-30 sec
without binning.

Calibrations¶

If this is the first time calibrations have ever been completed for Leginon, complete
all the calibrations listed in <link linkend="calapp_chapter">the chapter on
calibrations</link>. Calibrations are extremely important to operate the TEM in a
consistent manner. As long as the calibrations are stable, later users do not need to
perform them. Most calibrations are HT and magnification dependent. Therefore, new
calibration may be required if your presets use different HT and/or magnification from all
previous users.