Fail to extract particles from micrograph after volume alignment

Particle Picking
1

In V4.4.0, after a volume alignment tools job, I found that the passthrough_particles.cs file was missing, then I try to re-extract particles from micrograph, it show me that
Traceback (most recent call last):

  • File “cryosparc_master/cryosparc_compute/run.py”, line 95, in cryosparc_master.cryosparc_compute.run.main*
  • File “/home/wuhu/cryosparc/cryosparc_worker/cryosparc_compute/jobs/extract/run.py”, line 350, in run_extract_micrographs_multi*
  • particles_dset = rc.load_input_group(input_group_name=‘particles’)*
  • File “/home/wuhu/cryosparc/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 675, in load_input_group*
  • assert is_connected, “Slot %s.%s must be connected!” % (input_group_name, slot[‘name’])*
    AssertionError: Slot particles.location must be connected!

but it works in V4.2.0, I don’t know if there are any bugs?

2

Hi @wuhucryoem,

Could you show a screenshot of the fully-expanded inputs and outputs tabs in the Volume Alignment Tools job (in v4.4.0), so we can see where location may have been lost?

Michael

3

of course, I’m glad to show you thr screenshot.For the sake of confidentiality, I mosaiced the volume part of pictures.

IMG_20231116_003204
IMG_20231116_0032041906×1240 183 KB

4

and the output

IMG_20231116_003444
IMG_20231116_0034442222×1239 171 KB

5

Hi @Wuhucryoem

Thank you very much. I believe this is because the builder for the old job is out-of-date relative to changes made in v4.4.

To fix this, could you try building a new Volume Alignment Tools job from the builder (i.e. fresh from the job builder, without cloning the old one)? Then, could you connect the same volume/mask/particle inputs to this job and use the same parameters as before, and re-run the job? Then, I believe downstream particles should have location as well as all other slots retained.

Michael

6

Yeah, that building a new Volume Alignment Tools job from the builder is worked.Thank you.
best wishes.

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