I am trying to import movies from a Krios SerialEM data collection run, and the defect.txt file is not recognized by the movie import job. Here is the defect file I have been trying to use:
The error message I get when importing the job says "defect file is in an unrecognized format.
I have already tried using the clip command ini mod to convert the .txt file to a defect_map.mrc as is suggested elsewhere on the internet. The commands I’ve used are:
Any pixels which have a value of zero in the gain reference will be treated as dead pixels. So yes, defects can be specified without an additional defect file, as long as those pixels in the gain reference is set to zero.
That having been said, we are interested in adding SerialEM defect file support to CryoSPARC. Are you able to make the full defect file (as output by SerialEM) available to us? It would be quite helpful in testing.