our standard workflow for pre-processing is based on MC2 alignment + gctf during data acquisition on-the-fly.
Recently I re-processed some data with patch-motion correction and patch ctf in cryosparc with surprisingly great improvements in resolution.
I therefore think about switching to cryosparc-based pre-processing right away.
Is there a way to start these processes bash/script-based?
Cryosparc live unfortunately seems not to read bz2 compressed movies, in contrast to the “normal” import function. In addition, manual bookkeeping, file transfer, clean-up etc. is essential.