Gain correction using cisTEM

Hi,

Regarding gain correction using cisTEM's sum_all_mrc_files, is this done on the movie stacks (i.e mrcs). If so, what are the outputs and could they be applied to motion correction? I was trying to find some documentation on this.

Best wishes,

Noor

Hi Noor,

Yes, many of the command line files have no documentation.

sum_all_mrc_files (there is also a sum_all_tif_files). Will create a sum of all the mrc files (not mrcs) in the directory that it is run. If you set the option "Take reciprocal and scale" to yes, then it will produce a file that should be usable directly as a gain image. The idea is indeed that you put (or link) a set of movies that are consistent (i.e. they were all taken on the same day / session) into one directory and run one of these programs to get a gain reference for those movies.

Cheers,

Tim

Thank you Tim, I am doing

Thank you Tim, I am doing this right now.

Best wishes,

Noor

Hi Tim

I am using sum_all_tif. Does it also do some kind of normalization and outlier removal?

Thank you.

Hi,

In the released version it simply divides by the maxium value in the sum. You can perform outlier removal yourself using the "remove_outlier_pixels" program if you wish.

Cheers,

Tim