Micrographs are empty after motion correction

Motion Correction
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Hi all,
I’m currently processing a dataset with approximately 1275 micrographs, and I’ve noticed that after motion correction, at least 100 of them appear empty. Interestingly, when I hover over these micrographs during the “Curate Exposures” job, I can see a preview that shows the image and particles. However, when I click on the micrograph, it appears black and empty.
I checked the raw files using EMAN2, and they look fine, so I’m trying to understand what might be causing this issue. Could it be related to frame misalignment during motion correction, leading to failure in generating usable outputs? If that’s the case, is there a way to recover or reprocess these micrographs so they can still be included in the analysis?

Any insights or suggestions would be greatly appreciated.

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Did you also check the motion-corrected mrc files (dose-weighted and non-dose-weighted) outside CryoSPARC and confirm they are (or are not) black?

Please can you also email us:

  • the Curate Exposures job log (available under Metadata|Log)
  • browser console log and (compressed) HAR (see instructions). The recording of these files should include a page reload and an instance of a micrograph appearing black.
1 Like
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Thnk you @wtempel. I am new to cryosparc. Do I have to perform motion correction with a standalone motioncor2 in order to view DW and non DW files or is it possible to get these with cryosparc?

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@boise You can find these files in the motioncorrected/ subdirectory of the Patch Motion Correction job’s job directory.