General information

SmartScope comes with a few protocols that essentially dictate which steps are going to be performed during the imaging process and which algorithms are going to be used.

Some protocols come with a -precise variant. The main differences with their regular counterpart are:

• Eucentric height performed at the medium mag rather than the square mag. This is more precise as the hole pattern from the square mag can lead to erroneous cross-correlation.
• Hole re-centering should be more precise. This allows to start beam-image shift imaging with less initial image-shift.

When setting up a grid, all the protocols are availble via a dropdown menu with a additional default auto choice. This option follows a set of rule to select the best protocol for the grid and imaging type. Here's a breakdown of these rules:

Note

The auto will never select the -precise variant of a protocol. It has to be manually selected.

• SPA-Ptolemy -> Selected for all holey grids if tilt angle is 0 in the imaging parameters.
• SPA -> Selected for holey grid if tilt angle is not 0.
• NegativeStain -> Selected if the grid type is Negative Stain or Lacey

Advanced - Changing the rules for auto

These rules can be modified in a settings file. More details here