Importing Reference Based Motion Correction Hyperparameters in different workspaces

Motion Correction
1

I recently tried some reference based motion correction which worked very nicely at bin2. However, when I moved to unbinned processing I tried to import the hyperparameters from the bin2 job and kept getting assertion errors (drag and drop). In the end I just recalculated the hyperparameters and this got around it. I’m not sure if this is a bug or if I’m doing something silly!

Error message:
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 129, in
cryosparc_master.cryosparc_compute.run.main
File
“cryosparc_master/cryosparc_compute/jobs/motioncorrection/run_reference_motion.py”,
line 548, in
cryosparc_master.cryosparc_compute.jobs.motioncorrection.run_reference_motion.run_refer
ence_motion_correction
File “cryosparc_master/cryosparc_compute/jobs/motioncorrection/refmotion.py”, line
1259, in
cryosparc_master.cryosparc_compute.jobs.motioncorrection.refmotion.mainfn_reconstruct
File “cryosparc_master/cryosparc_compute/jobs/motioncorrection/refmotion.py”, line
1289, in
cryosparc_master.cryosparc_compute.jobs.motioncorrection.refmotion.mainfn_reconstruct
AssertionError

2

I suppose the other fix would be to manually input the hyperparameters.

As an update the hyperparameters ended up being similar:

Unbinned Hyperparameters:
Spatial prior strength: 5.4929e-03
Spatial correlation distance: 500
Acceleration prior strength: 5.4929e-03

Bin2 Hyperparameters:
Spatial prior strength: 5.4788e-03
Spatial correlation distance: 500
Acceleration prior strength: 1.4751e-02

3

Hi @JamesLeCornu,

The error you experienced is because the box sizes were different between the two runs, meaning the dose weights (not the motion model hyperparameters) weren’t transferable between the two datasets. In and of itself, that is expected behaviour. But, the AssertionError doesn’t give any indication of the cause, so I’ve made a note to add a better error message for future versions of CryoSPARC.

Thanks for bringing this to our attention!

– Harris

4

Just to confirm, the box sizes were different (608 then binned to 304 and 448 unbinned).