A problem with denoising.

[yushuv]

Hi all,
I have an odd problem with denosing. Not all the time I get the pictures of the denoised micrograph. It says it's done but I can't see anything even when I try to look at all of them and not just the ones in the cryosparc gui.

In the picture I added here I can see the that in the big dataset (J10) I can see them and in the small one (J14 and J16) I can't see any of them. I want to use these to see if the picking is right and since I can't see the denoise ones I can't see much if the picking is well enough for me.

I run them the same.

Thanks,
Yehuda

[tbepler]

This looks like a cryoSPARC problem rather than a Topaz problem, per se, so you may get better help on the cryoSPARC forums (https://discuss.cryosparc.com/).

@alexjnoble Have you ever run into this issue with the cryoSPARC integration before?

[alexjnoble]

Hi Yehuda,

I'm not sure what the error is from. Could you share the job output for both working and non-working denoise jobs?

Thanks,
-Alex

[yushuv]

Hi Alex,
Here are the two files of the outpout.
Sorry it toke so long we had power testing over the weekend so no computers.

Yehuda

fail.docx
worked.docx

[alexjnoble]

Hi Yehuda,

The job runs out of RAM. To solve this, decrease the size of the 'Shape of split micrographs' parameter.

Best,
-Alex

[yushuv]

Hi Alex,

I lowered it until 256 and it's still only doing a part of the micrographs. Is there anything else I could try?

[alexjnoble]

Hi Yehuda,

Could you try running it on CPU instead of GPU? There's an option in Cryosparc, I think.

Thanks,
-Alex

[yushuv]

Ok on CPU it works.
Maybe we have a deep GPU problem then we thought.

Thanks,
Yehuda