Processing phase plate data


We recently collected some test apoferritin images with phase plate. The Relion 2D classes with ~7k particles look reasonable. However I couldn’t get good results in cryosparc with either 2D classification or refinement.

Any tips on processing phase plate images in cryosparc?

The top is relion 2d classification and the bottom is cryosparc 2d classification.


1 Like

Hey there,

We are seeing similar results, however we have substantially more particles. I’m not sure exactly what the problem is either. Any response would be welcome.


matt B

Hi @Hui, @belousoff,

Thanks for reporting.
Phase plate data generally has not required any modifications, but this is something we’ll investigate.
@Hui would it be possible for you to share this data with us for testing? I will email you.


Hi @apunjani and @belousoff

Thank you for replying.

@apunjani sure I can share those images.


Happy to share the data. Perhaps shoot me an email and I can give you a google drive link.

Thanks @belousoff, I’ve emailed you about data transfer.

We have a similar case to this - phase plate date, 2D classes in relion look great, classes in cryosparc look lousy, lacking in high res features.

In relion, the classes with default parameters didn’t look great, but switching on the “Ignore CTF until first peak” parameter helped a lot.

There is no direct equivalent to this parameter in cryosparc, so in this case was there any parameter to tweak that helped?