Query Regarding Micrograph Flipping and Topaz Training

Import and Export
1

Dear CryoSPARC Community,

I have a question regarding the flipping of micrographs and their impact on particle picking and training in Topaz. Here’s the context of my workflow and the issue I’m encountering:

  1. Particle Picking in Warp 1.0
    -I picked particles in Warp 1.0, which successfully identified some rare views.
    -These particles were imported into CryoSPARC and linked to micrographs after performing patch motion correction and CTF estimation in CryoSPARC.
  2. Re-extraction in CryoSPARC:
    -During re-extraction, I enabled the Flip Micrographs Y option, which allowed the particles to be correctly re-extracted.
    -I verified that the particle locations were accurate by inspecting the 2D classes, which looked good.
    -Additionally, I forced re-extraction of CTF from the micrographs during the extraction job.
  3. Training Topaz:
    -I now want to train a Topaz model using the re-extracted particles and micrographs (from patch motion correction and patch CTF).
    However, the Flip Y option is not available in the Topaz training input micrographs. As a result, the particle coordinates are incorrect, and I cannot proceed with training.

I would greatly appreciate any advice or suggestions on resolving this issue. Specifically, I’m looking for a way to ensure that the particle coordinates align correctly with the micrographs during Topaz training.

Thank you in advance for your help!

Best regards,
HD

2

Hi CryoSPARC Community,

I resolved the issue by exporting the particles using cs2star with the --inverty option, then reimporting them into CryoSPARC and linking them to the corresponding micrographs. After this, the extraction job ran successfully without needing the flip y option.

Hope this helps anyone facing a similar issue!

Best

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