Leginon

h1. Set-up Before Running

h2. Preset Design

Preset design includes the normal gr, sq, hl, fa, and fc presets as in MSI. "tomo" preset is the preset used to collect the final tomogram. "preview" is set at minimal dose to check the quality of the region before final acquisition. The table here is for FEI Tecnai F30. For F20, your may use standard MSI application presets with the addition of "tomo" and "preview" at the magnification apropriate to your specimen.

h3. Example Multiscale Tomography preset parameters (on FEI Tecnai F30)

|_.Magnification:	|_.Preset name:	|_.Image Shift (x,y):	|_.Dimension:	|_.Binning:	|_.Beam Coverage:	|_.Exposure Time (ms):	|_.Spot Size:	|_.Defocus (m):	|_.Skip when cycling:|

|220 	|gr	|Aligned*	|512	|8	|max	|25	|8	|-1e-3	|no**|

|480 	|sq	|Aligned*	|1024	|4	|1x CCD size	|125	|8	|-1.5e-3	|no**|

|4500 	|hl	|Aligned*	|1024	|4	|1x CCD	|125	|8	|-1.2e-5	|no|

|34000	|fc	|0,0	|1024	|1	|<~ 1x CCD	|500	|8	|-1e-5	|no|

|34000	|fa	|0,0	|1024	|4	|<~ 2x CCD	|100	|8	|-5e-6	|no|

|34000	|tomo	|0,0	|4096	|1	|>2x CCD	|160	|8	|-1e-5	|no|

|34000	|preview	|0,0	|1024	|4	|2x CCD	|12 (0.25e/A^2)	|8	|-1.2e-5	|no|

*The image shift for these presets need to be aligned against one of the high mag preset such as "fa" or "tomo".

**Protocol from Lu Gan suggest activate "Skip when cycling for these LM presets" after all tomography targets are selected in "Tomography Targeting" node so that these presets are not used any more. The newer protocol by Jian Shi does not do so.

h2. Calibrations

This application has the same calibration requirement as MSI applications, no additional calibration is needed if the same magnification and camera conficuration are used. The exception is that the Tomography node uses images acquired in the same node to make the off axis correction in the tilt axis. As the result, the calibration of the move type the Tomography node usees and at the magnification of "tomo" preset is required. Since we normally perform image-shift calibration for all magnifications, it should already be included.

h3. Additional calibration need for the Example MSI-Tomography

|_.Preset	|_.magnification	|_.calibration type	|_.optional calibration|

|tomo	|34000	|image shift matrix	|stage position matrix or rotation and scale-only modeled stage position (if using tilt-corrected correlation)|

|hl	|4500	|modeled stage position||	

Again the calirbation is required only once in most cases. See the chapter on calibration for more details.

h2. Preferences and Settings

The default settings loaded at installation should be reasonably good for the first trial. See the section on MIS-Tomography preference setttings in the chapter on initial MSI application preference setup.