Gain reference from falcon4 camera

Import and Export
#1

Hi,

I tried to do motion correction with .eer file collected from falcon 4 camera, and I received this error:

  Loading gain data from J7/imported/000263580115278685410_FoilHole_17683150_Data_17681946_17681948_20220118_195424_EER.eer ...

[CPU: 201.1 MB] Error occurred while processing J7/imported/000263580115278685410_FoilHole_17683150_Data_17681946_17681948_20220118_195424_EER.eer
Traceback (most recent call last):
File “/work/FAC/FBM/DMF/sgruber1/cryoem_gruber/cryosparc/cryosparc_worker/cryosparc_compute/jobs/pipeline.py”, line 53, in exec
return self.process(item)
File “cryosparc_master/cryosparc_compute/jobs/motioncorrection/run.py”, line 109, in cryosparc_compute.jobs.motioncorrection.run.run_rigid_motion_correction_multi.motionworker.process
File “cryosparc_master/cryosparc_compute/jobs/motioncorrection/run.py”, line 145, in cryosparc_compute.jobs.motioncorrection.run.run_rigid_motion_correction_multi.motionworker.process
File “/work/FAC/FBM/DMF/sgruber1/cryoem_gruber/cryosparc/cryosparc_worker/cryosparc_compute/blobio/mrc.py”, line 140, in read_mrc
data = read_mrc_data(file_obj, header, start_page, end_page, out)
File “/work/FAC/FBM/DMF/sgruber1/cryoem_gruber/cryosparc/cryosparc_worker/cryosparc_compute/blobio/mrc.py”, line 88, in read_mrc_data
dtype = mrc_datatype_to_dtype(datatype)
File “/work/FAC/FBM/DMF/sgruber1/cryoem_gruber/cryosparc/cryosparc_worker/cryosparc_compute/blobio/mrc.py”, line 65, in mrc_datatype_to_dtype
assert False,‘Unsupported MRC datatype: {0}’.format(datatype)
AssertionError: Unsupported MRC datatype: 1243414722

Marking J7/imported/000263580115278685410_FoilHole_17683150_Data_17681946_17681948_20220118_195424_EER.eer as incomplete and continuing…

i have a gain file that has .gain format, and i am using cluster with Slurm schedular, the version i have is v3.3.1+220315

#2

Hi @yli18 , maybe you need to update your cryosparc up to the latest patch so that it can support eer files properly… Local motion correction with EER file not working (resolved with patch) - #2 by sente

#3

Can you confirm that FoilHole_17683150_Data_17681946_17681948_20220118_195424_EER.eer is indeed the intended gain reference file? I would not have expected an EER file to provide the gain data.
Something might have gone wrong during the preceding eer file import (Job J7?). What was specified for

  • Movies data path
  • Gain reference path

You can find the information under the Inputs and Parameter tab of the import job (J7).

2 Likes
#4

Seeing a related issue with the following error in patch motion.

Error occurred while processing J298/imported/014569539110538124320_FoilHole_13005754_Data_12924297_12924299_20220613_194521_EER.eer
Traceback (most recent call last):
File “/home/cryosparc_user/V3.X/cryosparc_worker/cryosparc_compute/jobs/pipeline.py”, line 60, in exec
return self.process(item)
File “cryosparc_master/cryosparc_compute/jobs/motioncorrection/run_patch.py”, line 118, in cryosparc_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi.motionworker.process
File “cryosparc_master/cryosparc_compute/jobs/motioncorrection/run_patch.py”, line 139, in cryosparc_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi.motionworker.process
KeyError: ‘gain_ref_blob/path’

#5

May we have a look at the job.json files of this failed job and of job J298?

#6

emailed files to xxxxx@xxxxxx.xxx

#7

The json file for the upstream import job, which you emailed us, specifies a Gain reference path that may not be in MRC format. I wonder if this caused a problem during import, which in turn may have lead to the KeyError.
If the gain reference is indeed not already in MRC format, you may want to retry the upstream import and this motion correction job after converting the gain reference to MRC format. Your microscope facility may be able to help with the conversion.

#8

Tried that using both tif2mrc and newstack. Still have the same error.