Reference based motion correction terminated with an error: fewer than 2 particles on image

[qianpu1605]

Hi

I got an error message when I run "reference based motion correction, (see attached image):

“Fatal error: Specified micrograph has less than two particles. Job process terminated abnormally”

However, a message from output showed that all movies that have less than two particles were removed before “Optimize Hyperparameters”.

It would be a great appreciated if you could let me know how to sort it out or give me advice.

Best regards

Pu Qian

[leetleyang]

Hi Pu,

Perhaps you can try disabling the recentering feature?

(4.5.1) RBMC crash (low particle count removal failed?)

Hi @rbs_sci, sorry for the delay getting back to you on this. I have a theory regarding a possible cause… In 4.5 we introduced particle recentering and it’s also on by default. Are you using it? If so, one possible cause is particle recentering followed by rejection of particles too close to a micrograph edge. Those steps are done after the initial screening for micrographs with less than 2 particles. That ordering is definitely a bug, but I don’t know if it’s your bug. Are you using particle re…

Cheers,
Yang

[DanielAsarnow]

You can also remove them before hand using the exposure curation job.

[hsnyder]

Hi @qianpu1605, as leetleyang said, this is probably a bug in CryoSPARC v4.5. The bug has now been fixed and the fix was released today as part of a CryoSPARC patch.

[sasi]

Hey! I updated cryosparc including the latest patch, however the error still persists

[hsnyder]

Hi @sasi,

This is a different error, actually - it’s saying that you have no movies with at least 2 particles. Is it possible that you connected movies and particles that don’t correspond to each other? Particles “remember” which movies they were extracted from, and this information is necessary for RBMC, local motion, extraction, etc, to work correctly. The “reassign particles to micrographs” job can be used to transfer particles from one set of movies to another.

Note that if you import one set of movies twice, even if they’re the same physical movies, they’re treated as different movies in cryosparc. So suppose you have a set of movies, if you import them twice (imports A and B), and extract particles from A, but then connect those particles and movie set B to RBMC, you would see this error.

–Harris