Patch based CTF query




I have a query regarding the new patch-based CTF estimation algorithm. Based on the 3D-surface that is generated, it looks like the algorithm has some kind of local smoothing - assuming that nearby regions have similar defocus values.

This will be more or less true for particles in thin ice that is bent or tilted, but is unlikely to be true for large particles in thick ice, where often a lot of the variation in per particle defocus comes from the z-position of the particle in the ice (e.g. adhered to one interface vs the other), rather than the shape of the ice itself. In this case it is quite common that two particles adjacent in x-y will have very different z-positions, and hence different local defocus values.

Is there any plan to take account of this, e.g. by refining the patch based estimates at the extracted particle positions during the Patch CTF Extract job, or as another parameter to refine during homogeneous refinement?



@olibclarke I do think defocus refinement works pretty well, recovering the correct defocus even over hundreds of nm.

If that holds, shouldn’t the global defocus (or a simplistic local defocus for tilted micrographs) ought to be a sufficiently close initial guess?


Absolutely - but per particle defocus refinement is not implemented in cryoSPARC? Or has it been added in 2.8 and I missed it?


No, it’s not available in cryoSPARC, I meant this as a statement of principles/priorities based on how it’s working for me in Relion and cisTEM (I routinely move between all three programs for the same projects).


Oh yes - as do I (more relion than cisTEM) - but would be nice to have it integrated in cryoSPARC too


Agreed! Do you have an opinion about astigmatism refinement in Relion? I can’t tell if it’s helpful or not…usually the images don’t have much astigmatism so I worry about the angle “just spinning around” during optimization.