Fail to extract particles from micrograph after volume alignment

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/”, line 95, in*
  • File “/home/wuhu/cryosparc/cryosparc_worker/cryosparc_compute/jobs/extract/”, 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/”, 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?

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?


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

and the output

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 I believe this is because the builder for the old job is out-of-date relative to changes made in v4.4.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


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

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