Set-up Before Running¶

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.

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.

Calibrations¶

This application has the same calibration requirement as MSI applications, no additional calibration is needed if the same magnification and camera configuration 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 uses and at the magnification of "tomo" preset is required. Since we normally perform image-shift calibration for all magnifications, it should already be included.

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

Preferences and Settings¶

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

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