Extract particles from new patch-motion job

We have processed a dataset to a high-resolution structure, from movies that were motion-corrected with MotionCor2. We wanted to try to improve the final map by re-doing the motion-correction, but this time with the Patch-Motion job from cryosparc. As it uses more "“patches”, we thought it might increase the quality of the data.
We’d like to extract the exact same particles that went into our current final map, from the new Patch-Motion and patch-CTF micrographs, both to see exactly what difference the Patch-Motion makes, and so we didn’t have to pick particles again.

However, when we tried to Extract, by dragging the particles from the final reconstruction to the Extract job, the jobs runs to completion, but no particles are extracted:
(1 of 4559) Finished processing micrograph 0. It had no particles in it
[CPU: 668.5 MB] – 0.1: processing J329/motioncorrected/2308680735959865002_100_00003_Nov25_patch_aligned_doseweighted.mrc
[CPU: 668.5 MB] – 0.0: processing J329/motioncorrected/9754716463340657858_101_00000_Nov25_patch_aligned_doseweighted.mrc

We first thought the problems were related to version-issues (3.0 and 3.1) with the patch-CTF jobs, but now we think the problem is actually that the micrographs are named differently:
9987682397164883840_118-9_00000_Nov25_patch_aligned.mrc (from patch-motion)
118-9_00000_Nov25.mrc (from MotionCor2)

In relion, we probably could have manipulated .star files to trick the software into combining the particles to the micrographs.
Is there a clever way to do this in cryosparc? I can’t make any sense of the .cs files.

One way I could envision is to copy over the patch-motion micrographs, and rename them to their “original” names, and then re-import in cryosparc, so the particles match the micrographs again? That would require me to find a clever way to batch-rename files whilst copying in the command line, though, and I’m not sure I can do this.

Is there an easier way to do this?
Many thanks


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Hi, I have encountered the very same problem.
I did see however that patch-motion correction within cryosparc live keeps the original file names.
So re-processing with cryosparc live is one option for overcoming that.

Hi, I have the same problem. Do you have any suggestions?

Hi Everyone,

If you imported the particles into cryoSPARC, you can connect the Patch Motion & CTF Estimated micrographs to the Import Particles job to reassociate the micrographs with the particles. The Import Particles job has parameters that allow you to fine-tune the query to match particle files with their corresponding micrographs.