Patch Motion Cor for gain normalized movies

Motion Correction
1

Some data in our facility were accidentally collected as gain normalized mrc movies. We are able to import these movies with no gain reference. We can run full frame motion corr without a gain applied. But if we try to use patch motion correction we get the error below.

Is there a way to force Patch Motion Corr to run without a gain?

[CPU: 248.1 MB]
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 115, in cryosparc_master.cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/motioncorrection/run_patch.py”, line 45, in cryosparc_master.cryosparc_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi
File “/apps/cryosparc/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 700, in load_input_group
dsets = [load_input_connection_slots(input_group_name, keep_slot_names[idx], idx, allow_passthrough=allow_passthrough, memoize=memoize, force_innerjoin=force_innerjoin) for idx in range(num_connections)]
File “/apps/cryosparc/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 700, in
dsets = [load_input_connection_slots(input_group_name, keep_slot_names[idx], idx, allow_passthrough=allow_passthrough, memoize=memoize, force_innerjoin=force_innerjoin) for idx in range(num_connections)]
File “/apps/cryosparc/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 648, in load_input_connection_slots
dset = load_input_connection_single_slot(input_group_name, slot_name, connection_idx, allow_passthrough=allow_passthrough, memoize=memoize)
File “/apps/cryosparc/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 636, in load_input_connection_single_slot
assert output_result is not None, ‘No output result match for %s.%s in job %s’ % (slotconnection[‘group_name’], slotconnection[‘result_name’], job[‘uid’])
AssertionError: No output result match for imported_movies.gain_ref_blob in job J135

2

you can provide an empty gain file.

3

How do you make an empty gain file? like
touch emptygain.mrc ?

Update: don’t do this, it will complain your mrc file doesn’t have a header. :sweat_smile:

thanks!

4

should be named .gain, but yes I think completely empty is fine.

5

haven’t thought about this in years though, let me know if it works.

6

hmmm it’s still complaining:

[CPU:  308.0 MB  Avail:  46.52 GB]
Traceback (most recent call last):
  File "cryosparc_master/cryosparc_compute/run.py", line 115, in cryosparc_master.cryosparc_compute.run.main
  File "/apps/cryosparc/cryosparc_master/cryosparc_compute/jobs/imports/run.py", line 1061, in run_import_movies_or_micrographs
    gshapey, gshapex = read_gain_reference(gainref_abs_path, shape_only=True, data_format=data_format)
  File "/apps/cryosparc/cryosparc_master/cryosparc_compute/jobs/imports/run.py", line 1031, in read_gain_reference
    shape = tiff.read_tiff_shape(gainref_abs_path)
  File "/apps/cryosparc/cryosparc_master/cryosparc_compute/blobio/tiff.py", line 70, in read_tiff_shape
    tif = libtiff.TIFF.open(path)
  File "/apps/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/libtiff/libtiff_ctypes.py", line 503, in open
    raise TypeError('Failed to open file ' + repr(filename))
TypeError: Failed to open file b'/<redacted>/gain_references/empty_gain.gain'

Thanks for trying.

7

sorry! in the above, I definitely got it to work in cryosparc live routinely (because it won’t accept nothing for an answer), but hopefully experts can help sort it for this use case.

8

I recently had a new lab member experimenting/learning with EMPIAR 10551, which is pre-gain-corrected. Movies were imported without setting the gain reference location and all of them processed with Patch Motion Correction without issue.

CryoSPARC Live also works fine without setting a gain reference.

v4.6.2, although I’ve run pre-corrected movies on earlier versions without issue.

9

@s_cryoEM Please can you post the outputs of this command

cryosparcm cli "get_job('P99', 'J199', 'job_type', 'version', 'status',  'params_spec', 'errors_run', 'input_slot_groups')"

for these jobs (replacing P99, J199 with the actual project and job IDs):

  • movie import
  • full frame motion correction (successful)
  • patch motion correction (that failed with AssertionError)