Micrograph denoiser

Particle Picking
1

Hello everyone,

I am trying to use the new Micrograph Denoiser and see these circles in the middle of my micrograph (with default setting). I am puzzled what are these, they are not present in my original micrograph after patch motion correction. I was wondering if I can change some parameters in input settings to fix these.

Anamika

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2

Were the micrographs you posted produced with Micrograph Denoiser default settings?

3

Yes they were produced with default settings.

4

@Anamika1 If you push the Show from top button under Event Log, you should be able to scroll down to a section with learning progress plot and two (split) panels of micrographs like

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Please can you post a screenshot of that for your example.

5

Here it is .

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6

I think in my case the training set does not match the validation set. Any suggestions to fix this issue.

7

Please can you provide details that make you think so?

8

I was just saying that based on comparing the plot you posted vs what my data plot look like in the post above.

9

Hi @Anamika1!

Did your collection facility provide you with a defect file? If so, did you provide it during motion correction?

Also, I wonder if you could share with us an example of your motion correction results (like those below):

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Thank you!

10

Hi, Please see below the example of motion correction file for this data and also I did not use the Detector defect file. By the way this data was collected on falconIV detector.

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11

Hi @Anamika1! Thanks for that info!

Do all of the diagnostic plots have this region of patches with little or no movement?

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12

Yes, that is the case.

13

Hi @Anamika1!

I believe this problem results from a hot pixel. When we apply the CTF to the micrograph before denoising it, a hot pixel will essentially recapitulate the CTF, resulting in the rings you can see there. I believe the easiest way to fix this is to reach out to your collection facility with this information and ask them for a defect file.

This hot pixel also seems to be affecting your motion correction results (note that the stationary patches are in the same place as the rings). I would therefore recommend getting a defect file even if you decide not to move forward with denoising.

I wish I had an easier fix for you, but I hope that is helpful!

14

Thanks, this make sense. I will try to process with defect file and see if that resolve the issue.

Anamika