thank you for your prompt reply and to develop Topaz.
Yes, I installed Topaz separately from cryosparc. With the terminal command “which topaz” I got the path (I can’t explain why it has been installed inside eman2 folder, by the way. Could be the error relies on the installation folder (eman2)?
Any suggestion is more than welcome.
yes, the terminal is the same for both cryoSPARC and Topaz, and Topaz has been activated as explain both in cryosparc guide and your github page.
Even Topaz Denoise give me the same error.
Did I install Topaz in the wrong way?
thank you for your support.
Apparently, now Topaz is working. I had to downgrade to version 0.2.3. Topaz Train (beta) worked, but Topaz Denoise (beta) didn’t, it gave me a " ValueError: min() arg is an empty sequence". I’m working on that.
Another thing, I cannot find Topaz Inference to observe the particles picked with Topaz Train. Is it present only in the last Topaz version?
Thank you again.
thank you again. Yes, I used Inspect picks and it works perfectly.
I would like to ask you some details about Topaz Train, I tried to check on the web but I couldn’t find anything. Are these UserWarning normal or there is some error?
both Topaz Train and Topaz Cross Validation gave me the same warning, but then both of them finished without any problem.
I noticed that Topaz extract, after Topaz cross validation, recognized the same particle multiple times. I think that I have to remove duplicate.
Is it normal?
Sorry to loop back to the original issue, but it seems I’m having a similar issue with “command “/home/exx/anaconda3/envs/topaz/bin/topaz --version” did not produce valid output:”, despite having 0.2.3 installed. If i just execute > /home/exx/anaconda3/envs/topaz/bin/topaz --version from this terminal it seems to provide the version just fine. Any suggestions here? For reference I’m on CS version 3.1.0
sorry to come to you so late.
No, there isn’t any reason, I just thought that it was the correct way to use Topaz with new micrographs and particles.
Good to know that the pre-trained model works as well!
Sorry for the misunderstanding.
Thank you for your support.