Inspect picks in 2.15.0

Troubleshooting
1

It seems like the inspect picks job has a few issues in 2.15:

  • A lot of micrographs are shown (more than 10)
  • low-pass slider starts at 5 (the fixed increments are great, but the old default of 20 was more appropriate)
  • Contrast adjustment seems off
2

Hi @DanielAsarnow,

Do you mean the Number of mics. to plot parameter is not working properly?
low-pass slider starts at 5 (the fixed increments are great, but the old default of 20 was more appropriate)

In v2.15.0, a bug in the Inspect Picks job was fixed where the cutoff value was incorrectly calculated from the original micrograph shape and being applied to the 1024x1024 mic. You correct, the slider’s max value decreased from 200Å to 60Å, and the default value is 5Å instead of 20Å. However, there is a small bug- when you first load the Interactive tab, the lowpass value that is applied to the micrograph is 20Å, even though the slider is set to 5Å. If you click the slider and re-apply a lowpass value of 5, you’ll notice the micrograph changes- is it possible if you can let me know if after trying this, what you think the best default value for this slider is?

Is is possible if you can send a screenshot of your job?

3

If I leave the number of mics to plot as the default of 10, but set the pick frequency to 300 (there are > 3,000 micrographs), then ~100 are displayed.

image
image854Ă—156 5.83 KB

image
image486Ă—943 46.5 KB

As to the low pass and contrast, when I open the job I see the image at “20A” even though the slider is at 5A, like you mentioned. To my eye this is more than 20A, or something is up with the contrast adjustment.

image
image704Ă—501 104 KB

When I reset it to 5A, I find it looks much closer to my expectation:

image
image691Ă—494 176 KB

Here’s the 5A one again with some high NCC and power particles circled, for aid of comparison.

image
image695Ă—492 229 KB

4

Hey @DanielAsarnow,

Thanks for the detailed response! We’ll fix these bugs asap.

5

I just wanted to bump this and ask if it would be fixed in the next release.

After I click the low-pass slider to reset the filter to “5Å”, I see something like this for most micrographs:
image

The same image in Curate Exposures:
image

The slight intensity gradient in the image is much more apparent in Inspect Picks, and gets in the way of choosing the right parameters. Personally, I would recommend a simple fixed 500 Ă… high-pass filter as the only form of local contrast adjustment.

1 Like