I have 2D classification results that show some unexpected intensity on the outside of my particles and when I try to use the enforce non-negativity and clamp-solvent parameters, the intensity is still there. I’m wondering what exactly these two parameters do? Is it possible that the intensity is still an artifact even if it appears with the non-negativity and clamp-solvent parameters active?
Welcome to the forum and thank you for your questions @mseidler. Hav you already read the parameter descriptions in the guide?
Hello, yes I have read those descriptions. I’ve included the results of my 2D classification here where the left image is the result without clamp-solvent and non-negativity and the right is with those two parameters activated. When non-negativity and clamp-solvent are deactivated there appears to be a bright strip on either side of the fiber before it fades into the background noise, and when those are activated there is still a bright strip on either side that doesn’t go away. If that bright strip was just a processing artifact would it go away with clamp-solvent and non-negativity?
Using clamp-solvent along with non-negativity forces 2D class to generate classes with positive density on top of zero background. This might help prevent the particles from aligning to noisy artefacts in the background, but the strips you showed in the images look more like something systematic with the dataset, thus not the type of artifact clamp-solvent and non-negativity were designed for.
This is great to know Serena, thank you for your response!