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SPA multi-shot of changing custom patterns

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Details

Name SPA multi-shot of changing custom patterns
Permalink https://serialemscripts.nexperion.net/script/82
Category Single Particle
Language SerialEM Scripting
Description Multiple records of cherry-picked features. Suitable for certain in situ SPA.
Author shenping wu

Version History

Version 1

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This script requires additional scripts to be run – please refer to the Required Scripts section below.

Upload date February 26, 2025
Download count 19
SerialEM version ≥ 4.2 

            
	    	
	    		
	    

	     
			
Required Scripts

	    	    

				
The following scripts are required to run this script, either because the are called directly or they provide functions:

	    	    	
		    	
Documentation

                  
SerialEM  v4.2beta 3 (Feb.28 2024) or later is required.

It requires a grid with regular hole pattern as this is needed for defining the hole vectors. Instructions available at https://sphinx-emdocs.readthedocs.io/en/latest/SerialEM_note_define-IS-vectors.html

After the vectors are defined, any type of grids (lacey, lamella) may be used for data collection. 

Each custom multishot pattern is in its own group. Points in one group must be on the same tile of the square montage. If they are spread across multiple tiles, the calculated Image Shift vector can be very off.

The first point of each group is for positioning and autofocusing, preferably on carbon (Set Low dose - focus position on tilt axis = 0 um). The remaining points form a custom pattern. Each group must contain a minimum of two points. 

When cherry picking the points, the following factors need to be considered: 

1) spacing between points can't be too small to avoid overlapping of neighboring exposures.

2) the first point should be roughly in the middle of the custom pattern so that image shifts are minimized. 

3) the overall size of the pattern needs to be reasonable so that the maximum image shift is within the optimal performance of the instrument. 

4) one pattern (points within one group) must be on a single tile.   
        
	
License

        
This code can be shared and adapted under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) License (https://creativecommons.org/licenses/by-nc-sa/4.0/)