Hi,
I have picked some particles using blob picker and filtered in 2D classificaiton. Now, I am running topaz train and it shows straight line on the ave. precisoin vs epoch plot.
Is it normal? How to interpret this?
Also, when I am running Topaz Extract I am getting an error “AssertionError: No particles extracted. Possible causes include ‘Particle threshold’ parameter being too high or a version discrepancy between the Topaz or PyTorch instance that trained the model and the one that is being used for extraction.”
I have a similar problem. I am trying to train Topaz on a small particle (~50*80 Å). The training set is 118 micrographs and 1800 particles. When running the Topaz train job , it finishes, but the test average is flat and the training precision is empty (see attached images). The output of your command is:
The grid seems a bit overcrowded if anything. The original picking was not well centered, resulting in the majority of 2D classes aligning to 2 or 3 particles, and I only included well centered picks in the training set, hence the very low particle number.
After giving it a second thought, this Topaz training job would probably not have yielded good results even if it finished properly, I will take a step back and optimize template picking.