SerialEM Note: Refine ZLP on Au Foil Grids


Chen Xu








This is to introduce new implemented “Custom Time” script commands to handle refining Zero Loss Peak (ZLP) over Au foil girds.

Background Information

SerialEM has one script command to handle the ZLP refinement over time. Very useful. For example, if we put a line at the end of script LD-group like this:

RefineZLP 30

It will refine ZLP position if longer than 30 minutes since last refinement. It works very well for us, on a typical carbon based holey grid. Unfortunately, it doesn’t run well on a gold foil based grid which it is very “black” between holes. This is mainly due to large pieces of gold crystals that form the film diffract electron beams away in relatively large angle so they don’t hit the camera. SerialEM’s refineZLP routine works by comparing camera counts at different energy shifts. If there is clear count drop, the slit edge is detected. When with a Au foil grid, if the area but not a hole is used for such refinement, the black nature of the film causes this procedure likely to fail. When we take multi-hole exposure for 4 holes, for example, the stage position is on such “black” area.

It is possible to move to one of the multi-holes after exposure is done, but we prefer not to it for every exposure because ZLP might have been refined recently. Otherwise, time is wasted.

Therefore, we need a timer to track time and then perform two tasks in this situation after certain period. 1) move to a nearby hole, and 2) refine ZLP.

Timer Function Commands

This timer function is now available.

The two script commands related to the timer functions are:

SetCustomTime name
ReportCustomInterval name

Below is how to use them.

Use the Timer Functions

1. set timer to start counting, for example, one can simply run one-line command like this:

SetCustomTime ZLP

ZLP is the name of this timer. You can set up multiple timers with different names so they won’t confuse.

  1. Add this section to the end of your LD-group:

#SetCustomTime ZLP
ReportCustomInterval ZLP
If $repVal1 >= 30
  MoveToLastMultiHole         # move to a hole (bright area)
  RefineZLP                   # refine ZLP now!
  SetCustomTime ZLP           # reset timer

You can use the timer function, similar to the above example, to perform various periodic tasks across the Acquire items conveniently.