IsoNet

Dear Somaye, You can try to make RELION tomograms less blurry by tweaking the --SNR option in

Thanks Yuntao! Best Euan Am 13.01.2026 um 16:54 schrieb Yuntao Liu <procy...@gmail.com>:

Hi Yuntao, Yes, my initial tomogram was named Position_7_2_9.76Apx.mrc . Thank you very much for

Hi Micah, First of all, what you propose is, as far as I understand, exactly what is shown in panels

Hi Yuntao, Thanks for the reply. We just tested IMOD WBP reconstructions recently. Another issue

Hi all, I have following error in the refine step. F tensorflow/stream_executor/cuda/cuda_driver.cc:

Dear Katie, This issue can usually be alleviated by increasing the crop_size during prediction or

Hi Yuntao, Thank you for your answer, that was very helpful! Looking forward to your (or the

Hi Jan, I do not have experience processing soft X-ray data. I believe that the masking does not need

Hi Reza, This is the total of all tomograms. I guess more than 100 subtomos in total might be the

Hi everyone, Context: I am trying to train IsoNet on 5 out of 25 tomgrams on our HPC infrastructure.

Ah wonderful - many thanks Yuntao for alerting me to this - look forward to reading the preprint and

Hi, I recently had a very similar issue. It was Tensorflow not communicating with CUDA. To test this

Hi Bram, Whether this error happens only when you using hamming filter? How about continuing from

Hi Rangana, I have not tested the Tensorflow-2.16.1 with CUDA/12.1. This is probably because the some

Dear all. We found the fix. Thank you. Oleksiy On Wednesday, February 28, 2024 at 11:37:34 AM UTC+1

Thanks for the clarification. On Tue, 20 Feb 2024 at 17:46, YUNTAO LIU <yun...@g.ucla.edu>

Hi Reza, I think what you can do is to check the final alignment file ".aln" or ".tlt

Dear Yuntao, Thanks a lot for the reply! Yes, the corrected tomograms were still generated. Sorry I

Hi Hui, Yes, the parameter is present. Cheers, Stefan On Thursday, November 16, 2023 at 1:49:58 PM

Hi Huaxin, I recently learned from a user that a tomogram with some noise free regions will lead to

Hi Simon, You are correct, crop_size>cube_size is not important in refine step. There are two

Hi Felix, I previously had a desktop computer with 3080 running on a windows subsystem Ubuntu. I used

Dear Scott, I have not encountered this problem before. I wonder whether your tomogram star file has

Got it. Thanks for the advice. On Wed, Jun 28, 2023 at 2:12 AM YUNTAO LIU <yun...@g.ucla.edu>

Hi Yunfao, Cloning git did not fix the problem -perhaps I did this incorrectly. The version I

Hi Manjunath, I think you are referring to chunk_size in the deconvolution step. And yes, it

Hi Tanvir, Thank you for your information. If other people also have this issue, we may write this

Dear Chris, The answer is yes, it's okay to treat your data with multiple software before Isonet.

Hi Qing, IMOD is required to view in 3dmod. IsoNet could still run without IMOD, but you can not