Exporting accepted/rejected micrographs list?

Import and Export
1

I’m attempting to use cryoSPARC to curate micrographs before importing the acceptable original movies into Relion, but I can’t seem to find an easy way to access the list of accepted or rejected micrographs in a useful format. Is there a clean way to do this? Either just the list of micrographs or ideally a star file I can use to import the movies directly into Relion.

I’ve tried using csparc2star, but if I convert micrographs_rejected.cs I just get a list of the magnification value repeated and if I use the passthrough_micrographs_rejected.cs file I get the list of parameters corresponding to each micrograph but no micrograph name column. Is there an argument I can add to grab the names as well?

Thanks,
Nick.

EDIT: I found links to the accepted micrographs by using the export function and looking at the imported micrographs inside the exports directory. Is there a better way?

2

Hi @nkirk Did you find a solution to your problem? If so would you mind sharing.

Thanks

Abhilash.

3

Hi @Abhilash, no not really. I found a hacky way to achieve it though. I exported the rejected micrographs, that gives you a directory in exports with links to all the rejected micrographs. I then copied that list into a file ‘reject.txt’. I could then use that to remove links to bad micrographs in the original folder by using: xargs rm <reject.txt

Hope that helps.

4

Thank you @nkirk. I will try your method.

Abhilash