Blurry output in IsoNet2

[Somaye Badieyan]

Hello all,

I am running IsoNet2 with network-based CTF correction in the Denoise module (the isonet2-n2n method). The even/odd paired tomograms were generated in RelionTomo through the cryoCARE denoising workflow. I used mostly the default IsoNet2 parameters, except for those specific to my dataset, such as defocus and tilt angles, etc.

At the final prediction step, however, the output tomograms appear blurry. I checked the masks, and they seem fine. I have attached images of the original odd tomogram, the mask, and the final IsoNet2 prediction for reference.

Do you have any suggestions about what might be causing this blurriness?

Best,
Somaye

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Somaye Badieyan 
Research Scientist 
Life Sciences Institute 
University of Michigan - Ann Arbor 

[YUNTAO LIU]

Hi Somaye,

We found that the Relion reconstructed tomograms seem more blurry compared to WBP tomograms reconstructed from IMOD or Aretomo. You can also try to make the mask larger. 

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Best Regards,

Yuntao Liu,  Postdoc.

California NanoSystem Institute

University of California Los Angeles

[Ricardo Righetto]

Dear Somaye,

You can try to make RELION tomograms less blurry by tweaking the --SNR option in relion_tomo_reconstruct_tomogram (you can give it as an additional argument in the GUI). The default value is 10, you could try something like 100, which preserves more high-resolution information.

It's true though that the WBP reconstruction from IMOD or AreTomo3 tend to be of much higher quality due to the specific filtering choices involved.

Hope this helps,

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Ricardo Diogo Righetto

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