Particle extraction error

Troubleshooting
1

Hi,

I am trying out manual picker to pick particles to train deep picker. I picked ~1500 particles and tried to extract them. I am getting the following error:

[CPU: 772.2 MB]  Traceback (most recent call last):
  File "cryosparc_master/cryosparc_compute/run.py", line 84, in cryosparc_compute.run.main
  File "/media/raid/cryosparc/cryosparc_master/cryosparc_compute/jobs/manual_picker/run.py", line 643, in run_manual_picker
    do_extract_particles_from_micrographs(state['box_size_pix'], state['bin_size_pix'])
  File "/media/raid/cryosparc/cryosparc_master/cryosparc_compute/jobs/manual_picker/run.py", line 492, in do_extract_particles_from_micrographs
    scale_const, overall_normalizer, bg_fwhm_A = 200, has_ctf=state['has_ctf'])
  File "/media/raid/cryosparc/cryosparc_master/cryosparc_compute/jobs/extract/extraction.py", line 90, in do_extract_particles_single_mic
    mic -= bg_full # bg subtracted
ValueError: operands could not be broadcast together with shapes (4092,5760) (5760,4092) (4092,5760)

Could you help me fix this?

Thanks

Abhilash.

2

Hi @Abhilash, what job/program did you use for motion correction? If you didn’t use the Patch Motion job, can you try that?

3

Hi,
I used Motioncorr 2 for this particular set. I can try using Patch Motion.

Thanks

Abhilash.

4

Okay, there is a bug in cryoSPARC’s Motioncor2 implementation that causes this issue. It will be fixed in the next release. I would recommend Patch Motion until then. Sorry about that!

5

Patch v3.2.0+210601 released yesterday resolves this issue: Patch 210601 is available for cryoSPARC v3.2.0