Denoising imported micrographs

Troubleshooting
1

I am trying to denoise some micrographs that were motion corrected in cryosparc but the associated connected data is no longer linked to the micrographs.

I had to reimport the micrographs with an import job.

I then ran patch motion/ctf on 200 micrographs and then denoise training on this subset.

I then took these into a denoise job and got this error:

Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 129, in cryosparc_master.cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/micrograph_analysis/run_denoise.py”, line 80, in cryosparc_master.cryosparc_compute.jobs.micrograph_analysis.run_denoise.run_train
AssertionError: Input micrographs must be background-subtracted. Use Patch Motion.

I thought that I may be able to borrow the background subtraction from the small subset, so I connected that to the job and reran it. That produced this error:

Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 129, in cryosparc_master.cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/micrograph_analysis/run_denoise.py”, line 79, in cryosparc_master.cryosparc_compute.jobs.micrograph_analysis.run_denoise.run_train
TypeError: object of type ‘NoneType’ has no len()

Does anyone know how to get past this without rerunning patch motion on all of the micrographs?

Thank you!

2

Do you mean no longer linked to the movies?

3

Yes that is correct.

4

In this case, I understand that the movies are available, but no longer at the same path as they were when you ran patch motion correction? If this is the case, you may need to update the symbolic links of the Import Movies job upstream from that old patch motion correction job.
If you want to train a denoising model, patch motion correction in a recent CryoSPARC version is required.

5

Hi unfortunately this isn’t quite the case, it’s more complicated. But this is useful to know in the future. Thanks.

The movies were corrected in a live session. At some point 90% of the data was lost from the live session due to moving the session. The actual underlying data (corrected mics etc) was still in the session folder but not associated with the cryosparc live session. We decided to just rerun patch motion and CTF.

6

Thanks for providing the additional background info.

Did this resolve the issue for which you opened this forum topic?