2D classification error invalid entry in index array



The particles (inverted and normalized) are picked in Warp are imported in cryosparc and feeded into 2D class with the following error.

I was running a 2D class in cryosparc with the following error output:

[CPU: 2.85 GB]   Traceback (most recent call last):
  File "cryosparc2_compute/jobs/runcommon.py", line 1547, in run_with_except_hook
    run_old(*args, **kw)
  File "cryosparc2_worker/cryosparc2_compute/engine/cuda_core.py", line 110, in cryosparc2_compute.engine.cuda_core.GPUThread.run
  File "cryosparc2_worker/cryosparc2_compute/engine/cuda_core.py", line 111, in cryosparc2_compute.engine.cuda_core.GPUThread.run
  File "cryosparc2_worker/cryosparc2_compute/engine/engine.py", line 1072, in cryosparc2_compute.engine.engine.process.work
  File "cryosparc2_worker/cryosparc2_compute/engine/engine.py", line 392, in cryosparc2_compute.engine.engine.EngineThread.find_and_set_best_pose_shift
ValueError: invalid entry in index array

What I found suspicious that the particles did not look inverted (they look dark-on-white) while I defined them as light-on-dark (according to Warp). In the import I defined Amplitude Contrast (fraction) as the absolute dose (e.g. 43.57) but I am not sure if this was correct. Its rougly 360000 particles and I wanted a rough first classification with 100 classes, defined a mask of 320 A with an expected particle of 250 A, else I used the standard parameters.

Does anyone have an advice? Maybe I defined something wrongly?

Thanks a lot!


Hi @mica84,

One thing that stands out here is that the Amplitude Contrast (fraction) should be a number between 0 and 1, it is the component of amplitude contrast vs phase contrast in the images. It generally should not be changed (0.07 or 0.1 for cryo-EM data, 0.3 for negative stain).

The 43.57 number you have is the total electron dose, but that is only used for dose-weighting, which cannot be done on particle stacks - we need the movies to be imported into cryoSPARC for motion correction to apply dose-weighting. You would provide the 43.57 number at the time of importing movies rather than particles.