Topaz denoised micrographs not showing in Manual Picker

I can see the topaz denoised micrographs in Inspect Picks, but not in Manual Picker. It just appears as a gray image. I am trouble shooting with a subset of 20 images. The corresponding non-denoised images show up fine in Manual Picker. I know the denoised images are not gray because I visualized them in an Inspect Picks job.

On another instance (both running v2.14.2) using other data I don’t have this problem. What could be causing this?

Hi @Geoffrey,

Could you paste the output of the log for this specific job please?

cryosparcm joblog P1 J721

There could also be an error on the browser side. Could you check if there’s an error in the browser console (right click, ‘inspect element’, ‘console’ tab)?

Thanks,
Suhail

Hey @Geoffrey,

Can you also let us know the characteristics of the image? Resolution? Pixel Size?
Can you also send us the image of the micrograph?
Can you also try this in Exposure Curation with the “Calculate Average Intensity” switch on and off and see if it works?

Grayed out image

[mohammad@uhncryoem ~]$ cryosparcm joblog P1 J721
Traceback (most recent call last):
  File "/home/mohammad/cryosparc2c/cryosparc2_master/deps/anaconda/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/home/mohammad/cryosparc2c/cryosparc2_master/deps/anaconda/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/mohammad/cryosparc2c/cryosparc2_master/cryosparc2_compute/client.py", line 83, in <module>
    print eval("cli."+command)
  File "<string>", line 1, in <module>
  File "/home/mohammad/cryosparc2c/cryosparc2_master/cryosparc2_compute/client.py", line 57, in func
    assert False, res['error']
AssertionError: {u'message': u"OtherError: argument of type 'NoneType' is not iterable", u'code': 500, u'data': None, u'name': u'OtherError'}

Image showing normally

[mohammad@uhncryoem ~]$ cryosparcm joblog P1 J720
Traceback (most recent call last):
  File "/home/mohammad/cryosparc2c/cryosparc2_master/deps/anaconda/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/home/mohammad/cryosparc2c/cryosparc2_master/deps/anaconda/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/mohammad/cryosparc2c/cryosparc2_master/cryosparc2_compute/client.py", line 83, in <module>
    print eval("cli."+command)
  File "<string>", line 1, in <module>
  File "/home/mohammad/cryosparc2c/cryosparc2_master/cryosparc2_compute/client.py", line 57, in func
    assert False, res['error']
AssertionError: {u'message': u"OtherError: argument of type 'NoneType' is not iterable", u'code': 500, u'data': None, u'name': u'OtherError'}

I did some more manual picker jobs and found that I got the grayed out image from normal micrographs (referencing a subset made by Curate Exposures job, J746).

So why don’t we bracket out the denoising micrographs, and first resolve this gray image issue for the normal micrographs.

Here is what I see when I do inspect elements (these are normal, rigid aligned migrographs)

When I do inspect picks with the same inputs (from Curate Exposures, J746) I can see the image fine.

From the import of the original movies:

[CPU: 198.6 MB]    mscope_params/accel_kv :  set([300.0])
[CPU: 198.6 MB]     mscope_params/cs_mm :  set([2.7])
[CPU: 198.6 MB]    mscope_params/total_dose_e_per_A2 :  set([45.599998])
[CPU: 198.6 MB]    mscope_params/exp_group_id :  set([1])
[CPU: 198.6 MB]    mscope_params/phase_plate :  set([0])
[CPU: 198.6 MB]    mscope_params/neg_stain :  set([0])
[CPU: 198.6 MB]      movie_blob/psize_A :  set([1.03])
[CPU: 198.6 MB]        movie_blob/shape :  [  30 4096 4096]

The images failing to display are created by a Full-frame motion correction job. At least that’s the filename that the manual picker and inspect picks have in the Name column

I toggled on “Calculate Average Intensity” in Exposure Curation. I could see the images in this interactive job, as I can when I toggle off “Calculate Average Intensity”. I fed this output into some new jobs to see what happened. I could see the image in inspect particle picks, but not in manual picker. So there doesn’t seem to be a change.

Hi @Geoffrey,

Can you try cloning the original manual picker job that produced the gray images? Then in the interactive screen, toggle on “Override” and move the “Contrast Intensity Override” sliders around. Let us know if the images remain gray after moving the sliders in various ways. Specifically try moving one slider closer to the middle and the other to near its extremum for both sliders.

Regards,
Jay Yoo

Hi @Geoffrey,

This bug has been fixed in the latest version of cryoSPARC v2.15.0. Please update to this version and let us know if this issue persists!