Signal subtract, align, then revert to un-subtract particles

hi, is it possible to do subtraction, then align, then swap out the particles so that I have my unsubtracted particles using my alignments from the subtracted ones? The reason is that I have density that is messing up alignment. I want to remove it just to get the alignment of the core, then revert back so I can see how the subtracted areas look once I’ve aligned correctly on the core.


Hi @orangeboomerang,

Unfortunately there is no way to directly do this with the current functionality in cryoSPARC. Thank you for pointing this out, it would be a very useful tool and we’ll add it to a list of possible future improvements.


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Hi all,

Just an FYI for any future readers browsing: this functionality (i.e. using alignments from a subtracted stack of particles, but using the original un-subtracted images for a local refinement or otherwise) should be supported using the lower-level input functionality in the job builder, and Daniel Asarnow provided a brief description about how to do this here: Keep linked copies of original particles after signal subtraction



@mmclean - you should be able to do this now using the standalone reconstruction job with lower level inputs, right? change particle image inputs to unsubtracted, but use orientations from subtracted?