Picking jobs error

Troubleshooting
1

Hi,

I am having a problem running manual picking job in cryosparc v2.13.2 version. Here is the error message that it reported:

[CPU: 563.9 MB] Traceback (most recent call last):
File “cryosparc2_master/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main
File “cryosparc2_compute/jobs/manual_picker/run.py”, line 739, in run_manual_picker
arr_tile = arr_bin[tile_start_y[y]:tile_end_y[y], tile_start_x[x]:tile_end_x[x]]
IndexError: index 8 is out of bounds for axis 0 with size 8

So I tried blob picking instead. Blob picking was somehow working but it showed a blank region on the top of the image and didn’t pick anything in that region. The contrast of the other region is also weird that I couldn’t see any particles that should be there.

image
image720×720 70.8 KB

2

Hi @Chen,

What camera were these images captured with?
Did you import the raw movies and use patch motion correction to create micrographs? Or did you import the micrographs directly?

3

Hi @stephan,

Thank you for your swift response. We used Gatan K3 camera to collect these images and we directly imported the motion corrected micrographs.

Thanks,
Chen

4

Hi @Chen

Thats great, take a look at this post. I believe other users are reporting similar issues. There are a few workarounds for now until we deploy the next release:

5

Hey @Chen,

This issue has been fixed and released in cryoSPARC v2.14.0, out now. Can you update and see if it solves your issue?

6

Sorry for the late reply. Yes, it is fine in the latest version.