Hello, after I updated the service from v4.2.1-230403 to v4.4, the following warning appeared when the user ran the 2D Classification task. I would like to ask whether this warning affects subsequent work, and is it a problem caused by the update?
Could not find micrograph pixel size in particle's locations. Will assume particle image pixel size is equal to micrograph pixel size! Note that if particles were downsampled, this will be false, and remove duplicates will use an incorrect distance scale.
Thanks for the report. This is indicative of a bug fix that was added in v4.4, fixed with a metadata addition. If you see this message, the behaviour has not changed since v4.3, however it means that the metadata added in v4.4 was not found. This is currently an issue that we’re investigating, and is being discussed in this thread: 2D-classification error of invalid values detected in location/micrographs_psize_A
If you notice obtaining the same AssertionError: Invalid values (zeroes) detected in location/micrograph_psize_A in 2D classification or in remove duplicate particles, please do let us know on that thread and we will contact you about obtaining cs files to help us find the fix.
could I ask you if this bug is still happening? I found also this warning today: Could not find micrograph pixel size in particle’s locations. Will assume particle image pixel size is equal to micrograph pixel size! Note that if particles were downsampled, this will be false, and remove duplicates will use an incorrect distance scale. What should I do in that case please?
Hi - We got that same message in a 2D classification task with v4.4.1. (
Could not find micrograph pixel size in particle's locations. [...]
) . Previously, particles were processed and extracted with v4.3.0
(Meanwhile, the project was also detached and re-attached to a new instance, but from your threads above, it may not be the reason of the warning for us. Note, it only happens on 2D classification. If we run a NU-refinement, there is no warning re the pixel not found.
may be triggered when the new Remove duplicate particles option in 2D classification is used with particles picked in older versions of CryoSPARC.
For particles picked in CryoSPARC versions older than 4.4.1, we recommend disabling the Remove duplicate particles option in 2D classification. The standalone Remove Duplicate Particles job type, for which one can specify a custom Micrograph pixel size, can instead be used after the 2D classification job.
If one anticipates extensive use of 2D classification in a project with pre-v4.4.1 particles, it may be preferable to re-pick particles in v4.4.1 for use in 2D classification.