The SerialEM Script Repository

Check grid

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Name Check grid
Category Other Data Acquisition
Language SerialEM Scripting
Description Quick survey of TEM grid.
Author Jason de la Cruz

Version History

Version 1.0


Upload date June 30, 2017
Download count 592
SerialEM version ≥ 3.7



Modify settings in section below. Set "setIntensityCmd" to either "SetIlluminatedArea" for FEI Titan series or "SetPercentC2" for all other microscopes. Decide on condenser beam illumination (aperture, spot size); enter desired spot size in settings section. Then set "lowMag" to lowest mag with unobstructed view of TEM grid (i.e., the mag you use for whole-grid atlas), adjust intensity for optimum signal, center beam shift, then record intensity value in "lowMagIntensity".

When ready to start, open file to save autodoc metadata (with .mdoc or .idoc) then run the script. Close the file when done.

Please check that beam is centered in low mag before continuing.
Ensure all checkboxes in "Script > Controls..." dialog are unchecked to avoid "low counts" errors.


Copyright (c) 2017, Howard Hughes Medical Institute. License ISC: Internet Software Consortium license, This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.