The SerialEM Script Repository

Serial Section Maps

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Details

Name Serial Section Maps
Permalink https://serialemscripts.nexperion.net/script/43
Category Other Data Acquisition
Description Script to acquire updated maps for items that have been transferred from a previous section. It will mainly take care of keeping the Navigator labels consistent.
Author Martin Schorb
Literature reference https://doi.org/10.1101/389502

Version History

Version 2018.12

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Upload date December 19, 2018
Download count 23
SerialEM version ≥ 3.7.0-beta

            
	    	
	    		
	    

Documentation

Serial Section maps



This is the procedure to transfer a large number of Navigator Items from one section to the next:


- save navigator
- open in text editor
- copy the desired map items into a new text editor window
- Find and replace the registration with a higher number
- copy these items back at the end of the navigator
- remove all items with Color = 5 (NoRealign) and the registration points
- save navigator
- load new navigator in SerialEM
- change active registration back to the original one
- iterate across a few points or use the Realign with Rotation strategy for finding a single map location.
- select a map with an easily recognizable feature from the duplicates
- change to low mag and move to this feature on the next section
- mark obvious landmark points in both the live image and the map

- transform items and save navigator
- realign to first map on the new section
- run eucentric rough
- open a new image file for the maps of this section
- increase the section index
- run the script for the inital map
- save map into the file
- select the new map for anchor state
- set all other maps to acquire
- run "Acquire at points" with RealigntoItem, choose the serialsections script and tick "Skip Z moves..."

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/)