The SerialEM Script Repository

Serial Section Maps

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Name Serial Section Maps
Category Other Data Acquisition
Language SerialEM Scripting
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

Version History

Version 2018.12


Upload date December 19, 2018
Download count 400
SerialEM version ≥ 3.7



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..."


This code can be shared and adapted under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) License (