Export aligned micrographs

Import and Export
1

We love using cryoSPARC Live, and have some instances where we would like to use the Patch aligned micrographs for import into other programs. I can see how to ‘export exposures’ from Live into my usual cryoSPARC instance. From there however, I am unclear on how to export the aligned, average micrographs.

Thanks!

2

Hi @simonbrown,

When you select “Export Exposures” in the cryoSPARC Live configuration tab, you should see this:

Live Export Result, 50%
Live Export Result, 50%868×148 53 KB

This means that Live created an “Import Movies” job in the cryoSPARC Project Workspace:

cryoSPARC imported movies, 50%
cryoSPARC imported movies, 50%1008×416 10 KB

This input group includes references to all data that Live computed for every imported movie, including raw movie frames, motion-corrected micrograph and CTF.

imported_movies output group, 75%
imported_movies output group, 75%2074×1152 256 KB

You can use this output by dragging it into the input slot of any other job that supports it as you normally would in regular cryoSPARC.

imported_movies output, 75%
imported_movies output, 75%1098×650 63 KB

3

G’day Nick,

Thanks for the reply. I think my question wasn’t entirely clear. I want to be able to output the aligned movies for use in other packages.

What I do currently is dig into the cryosparc database and copy out the aligned .mrc files from the ‘S1’ motion corrected directory. It would be nice to have a GUI option to access these files for export.

Thanks!

4

Hi @simonbrown, gotcha, thank you for clarifying. If I understand correctly, but this:

You mean a function to download the files from the browser running the cryoSPARC web interface to your local machine? Or do you need a way to copy the MRC files from the S1 directory to a different location on the machine running cryoSPARC?

We wouldn’t be able to do first case due to how large the MRC files are; it would be much slower than the process you’re already using (I’m assuming something like the scp and rsync tools).

5

This seems the more useful approach. Now I know where the files are it isn’t as pressing of an issue, but for a new user of cryoSPARC live this would be helpful. I can imagine a function under the configuration tab in Live, where as well as the current ‘export’ buttons, (that export into cryoSPARC), another set of buttons that can create a new export directory in the relevant Pxx directory, and place the aligned micrographs here.