Cryosparc live data corruption

I have a problem with data processed by cryosparc live. It ran ok in the live session, and when I use the ab initio result (live) and start a refinement job (regular) or when I use the exported particles from live and run a new 2D classification (regular) I get errors like below. A ‘Check particles’ task does not complain about anything, so I guess something got confused with the metadata. During the live session I realized that the ‘total number of particles’ was about 500k higher than the ‘seen number of particles’. After exporting, I ran another live analysis with a different box size and everything seems ok with that workflow (also same number of total and seen number of particles).

How can I recover my first results (error below) and use the data for further analysis?


RuntimeError: Error ocurred (Invalid argument) at line 562 in mrc_readmic (1)

The requested frame/particle cannot be accessed. The file may be corrupt, or there may be a mismatch between the file and its associated metadata (i.e. cryosparc .cs file).

IO request details:
filename: /scratch/instance_cryosparc[…]/projects/P4/S9/extract/blob/384/20230606_data_08017_patch_aligned_doseweighted_particles.mrc
filetype: 0
header_only: 0
idx_start: 171
idx_limit: 172
eer_upsampfactor: 2
eer_numfractions: 40
num_threads: 6
buffer: (nil)
nx, ny, nz: 0 0 0
dtype: 0
total_time: -1.000000

Has the other Live analysis was performed in the same Live session as the earlier analysis?
In that case, processing output of the earlier session to which exported particles (metadata) refer may have been overwritten.
Please see Live Picking overwrite for a discussion and possible workarounds.

I exported exposures and particles before starting a new picking/extraction.

Thanks for the pointer to Live Picking overwrite, I will try to re-extract particles (Job: Extract from Micrographs - CryoSPARC Guide).

I was able to re-extract particles from my corrupted live results (ab initio) and continue with refinement. I have a related question: Is there a way to create a particle selection from my corrupted 2D selection referencing the newly re-extracted particle set instead of re-extracting the corrupted set and creating large amount of extra data?

What kind of selection criteria would you like to apply; what CryoSPARC job type are you thinking of running to select the particles?