SerialEM HowTo: Speed Up

Chen Xu

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For single particle data collection in automatic fashion, the speed becomes significant. If for each target position we can save a few seconds, total amount of time saved for 24 hours session is then not negligible. Efficiency is a real deal in this case.

For tomography data collection, efficiency is also in the consideration. One of the time consuming actions is to refine eucentricity for each target point before tilting series starts.

In this document, I discussed a few places where we might be able save some time.

You can also get pdf version of this document here.

Table of Contents
1 Recent Change related to K2 camera
2 Speed up using Modulo function
3 Rough positioning, but faster
4 Speed Up Eucentricity step for tilting series

1 Recent Change related to K2 camera

When it takes dose-fractionation series, or we call movie stacks, DM could take quite some time from start of exposure to the finish of writing data onto disk. The most time consuming part is the step of "preparing stack" by DM. Basically, the frames are first saved to SSD drive temporarily, and then are loaded back to memory and applied any action like aligning etc., before final prepared stack being saved to disk. At least this was the case for DM pre 2.30. Since 2.31, the preparing step is slightly different. But the total time for taking a movie stack is still significant.

However, in either case above, DM could be available to take single shot soon after exposure finishes and BEFORE total stack is done written. This provides a comfortable time window for SerialEM to perform some tasks, which saves quite some time. For example, we can ask SerialEM to move to the next target of stage position, fix Eucentricity, center the beam, autofocus and so on. Thus, we can take another movie stack as soon as previous one is finished, since everything else is ready.

The change on SerialEM side is that it doesn't have to wait to have total sum of the stacks return to SerialEM interface. Therefore, SerialEM can be freed up for some preparing tasks for next movie stack exposure. This is done by a new macro command

EarlyReturnNextShot #

This only works for K2 camera with dose-fractionation acquisition. The argument can be:

EarlyReturnNextShot 0