White density around the denoised membrane

[YunjieChang]

Hi everyone,

This is not an issue, but more like a question here.

I tried cryocare11 to denoise my tomogram (size: 455455200, pixel size: 13.5 angstrom). I did motion corrections by MotionCor2, aligned tilt series by IMOD and did CTF correction by IMOD ctfphaseflip.

For the denoising, I used exact same parameters shown in the manual (https://github.com/juglab/cryoCARE_pip/blob/master/README.md). However, in the denoised tomogram, there are strong white densities around the cell membrane. First image is one section of the denoised tomogram, second image is the zoomed in view of the white framed region in the first image. Red arrows indicating the white densities around the membrane.

Is it normal to see the strong white contrast around the membrane? Or did I set something wrong?

Thanks! Yunjie

[tibuch]

Hi @YunjieChang,

This is normal and related to your defocus. Usually you can also find them in your raw data, but less visible due to the noise.

You could probably reduce them by reducing your defocus, but this would also affect your contrast overall.

Best wishes, Tim-Oliver

[YunjieChang]

OK. Thanks for the reply Tim. I may try a different focus later.

Best Yunjie

On Mon, Oct 3, 2022 at 3:46 PM Tim-Oliver Buchholz @.***> wrote:

Hi @YunjieChang https://github.com/YunjieChang,

This is normal and related to your defocus. Usually you can also find them in your raw data, but less visible due to the noise.

You could probably reduce them by reducing your defocus, but this would also affect your contrast overall.

Best wishes, Tim-Oliver

— Reply to this email directly, view it on GitHub https://github.com/juglab/cryoCARE_pip/issues/32#issuecomment-1265060144, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANADRR2O34B4BFKTZ7Y3LHLWBKFNRANCNFSM6AAAAAAQ2W4ZTQ . You are receiving this because you were mentioned.Message ID: @.***>

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Best Yunjie Chang