Benefits of Topaz denoise

Tips
1

Dear colleagues,
could anybody objectively comment, perhaps by just mentioning a personal experience, on the benefits of denoising micrographs with topaz, vs non-denoised? I really want to try it but with a very limited computational power. It feels like my pc will melt as soon as I start the denoising job.
Thank you in advance,

2

Hi @ALBA,

I tried using both original and denoised images to train topaz. In my case with a rod-shape 280 kDa protein, that most of my images have defocus -(1.2~2.8)um and CTF-fit 2.8~3.2 Å, I didn’t see denoised images helped, sometime even worse.

Best,
Feng10

3

Hi ALBA,

Are you asking whether denoising images is useful for visualization, or if denoising images is useful for subsequent Topaz picking? If it’s the former, you can make a small subset of images and denoised them. If it’s the latter, in our various tests we have not seen any particular advantage of using denoised images for Topaz picking.

I hope that helps.
Best,
-Alex

4

Dear Feng, Alex, many thanks for this and sorry for not asking a clearer question. I was indeed thinking about Topaz picking, on denoised vs non-denoised micrographs. As I heard from a colleague at my university, denoised images did not help him as well, although Topaz picking has been great in general.
Thanks for sharing! Best wishes

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5

Hi,
Does performing denoise on entire dataset with movies helps improve overall map reconstruction or density ? Is there any benefit with regard to the map except just for visualization?

Thanks

6

@diffracteD We tried to look at that in this paper:

The algorithm is also noise2noise, the architecture is a little different and there is per-dataset training. IMO it may be possible that this approach can eventually help 3D classification, but software would have to account for the change in the shape of the signal.

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