Thanks for providing these micrographs, I’ll take a look at all the details here and let you know exactly what fields are required in the .star file to allow particle locations to be imported from crYOLO into CryoSPARC v4.
Then connect the imported micrographs to this Import Particles job so that the job can find the correspondences between the particle locations and the micrographs. Try that out and let me know if it works.
Filament picks can be imported if, in the particle star file, each particle pick has an associated rlnHelicalTubeID field that maps the particle to an ID that specifies which filament it belongs to (unique for each filament). Is such a field generated by crYOLO during the tracing procedure? CryoSPARC also can read: rlnAnglePsiPrior (the in-plane rotation angle of the filament, which could be estimated during picking), rlnHelicalRise (the helical rise in Angstroms, if known), and rlnNrHelicalAsymUnits (the number of unique asymmetric units per particle, if known). These are mapped to data fields in the filament result in the Import Particles job. The imported micrographs and their star file shouldn’t need any modifications from the standard case.
It’s also possible to import filaments without any of these fields, but it is preferable to at least have the rlnHelicalTubeID because this can be used downstream in Helical Refinement for proper gold-standard particle splits.
Is there any other filament-related information generated by crYOLO that could be useful when importing filament picks into CryoSPARC?
Filament picks can be imported if, in the particle star file, each particle pick has an associated rlnHelicalTubeID field that maps the particle to an ID that specifies which filament it belongs to (unique for each filament).
So far, the IDs are only unique for one micrographs, not across all filaments on all micrographs. Is that a problem?
The filament star file looks valid, but right now we do assume rlnHelicalTubeID is unique across the entire dataset when converting it to CryoSPARC’s filament_uid. Do you know if in standard RELION helical datasets rlnHelicalTubeID is only guaranteed to be unique within a single micrograph? If so, we should probably update our import code…
Re: the confidence value – we could certainly read this into CryoSPARC. Currently for other particle picking software like Topaz, we read confidence values into our pick_stats results so that particles can be thresholded/subset by that confidence value in our Inspect Picks job (it overwrites the “normalized cross correlation” value that we normally compute in our in-house template/blob picking algorithms). Which rln field would this confidence value be written to?