Random numbers being added in Import Micrographs Job

Import and Export
1

Hi!

I noticed since updating cryoSPARC random numbers are being added to the Micrograph name in Import Micrograph job.

Original name: 04_00003_UnderDefocus1_0um_frameImage.mrc

cryoSPARC output: 018167810604403721854_04_00003_UnderDefocus1_0um_frameImage.mrc

I cloned an Import job from before the update and it also added these numbers.

Thanks!
Arnold

1 Like
2

Hi @am2837,

In some cases, movies are imported from different base directories but have the same filename (as a result of some image capture software). In order to account for all scenarios, a unique identifier is prepended to micrograph and particle .mrc files created by cryoSPARC for internal bookkeeping and in general to maintain uniqueness.

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3

hi!

I guess my problem is when I try to import a particle stack it cant link the particles to the micrographs. I get this error:

[CPU: 779.6 MB] Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 85, in cryosparc_compute.run.main
File “/mnt/int6_3/working3/cryosparc2/cryosparc2_master/cryosparc_compute/jobs/imports/run.py”, line 223, in run_import_particles
assert qname in inv_index_source, “Could not find match for %s” % qname
AssertionError: Could not find match for 04_00003_UnderDefocus1_0um_frameImage.mrc

These are motion corrected micrographs from RELION and the particles are from relion as well.

1 Like
4

There is an option for stripping the UUID from input micrographs, for this reason:

image
image1576×638 120 KB

3 Likes
6

So is there any way to remove the numbers in the star file? I imported the particles from relion, and after 2D/3D refinement, I hope to import them back to relion, but I found after transfer cs file to star file, all the names of mrcs files have extra number before them.

7

Yes, you can do this using sed or vi

8

Hi All, I turned on this option “Remove leading UID in input micrograph path” using v3.3.1, but still got UID when importing a Relion particle star file. Why is this option not working? Any suggestions? Thanks!

9

@stephan How can I do “Import Particle Stack” without leading UID added? I need to import a particle stack again without leading UID added for my previous 3DVA jobs (whose imported particle stacks did not add leading UID). Thank you!