Map grids (advanced)
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Name | Map grids (advanced) |
Permalink | https://serialemscripts.nexperion.net/script/78 |
Category | High-Level Functions |
Language | SerialEM Scripting |
Description | This script allows the user to choose between mapping single or multiple grids from the auto loader as well as just mapping the grid that is currently on the compustage. |
Author | Christian Dienemann |
Version History
Version 1.0
Upload date | October 26, 2022 |
Download count | 251 |
SerialEM version ≥ | 3.9 |
Documentation
Features
- Mapping grids from autoloader (defined by start/end slot) or what is on the compustage
- Skips empty autoloader slots
- Option to determine eucentricity of the grid before mapping
- Opens a new navigator and saves it to a user defined location if there is no navigator open (uses currently open navigator otherwise)
- Grid maps are saved in separate files per grid
- A jpg snapshot is saved after mapping a grid (for visual inspection during the mapping)
Configuration
At the top of there script there are a few variables to configure:
mag_check : checks whether this mag is set before starting (e.g. a mapping imaging state)
montage_x : number of pieces in X to acquire
montage_y : number of pieces in Y to acquire
overlap : overlap between tiles in pixels (!)
sd_threshold : image value standard deviation threshold that defines whether there is enough contrast in an image to be used for the rough eucentricity task
default_dir : the default directory to be set when there is no navigator open
It might be necessary to experiment a bit with montage_x/y and the overlap setting to adjust to your imaging conditions.
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/)