Leginon

h1. Pre-MSI Set-up

h2. 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.

h2. 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.