I tried to make a list of all the parameters which can be used for exposure curation. I’ve used ChatGPT to sort it according to importance and what it means. It looks reasonable to me, but I thought I would value input on where it needs improving on. Some of the parameters will only be available if a junk detector or particles have been picked before. Bonus question: I am using cryoSparc 4.7.0 (am not in control of updating), and the junk detector fails if I don’t pick particles. This seems to be a bug. Is that fixed in later versions?
Hi,
I’m a huge fan of making things like this to understand parameters and their importance! I haven’t had time to fully look at each chart item and I’m sure people who have been around for longer than I am will have good things to weigh in on, but here are some thoughts from a quick glance to get a discussion going:
(1) The average defocus reported is estimated, not set by the microscope (the microscope of course sets a value, but the one reported in cryosparc is not that set value but rather what cryosparc estimates from the micrograph)
(2) The defocus range can also be affected by the tilt angle (pretty sure on this one but haven’t looked into it consistently)
(3) I would be somewhat careful about using the picked particles to curate exposures if you don’t visually inspect the particle picks. Of course this can be useful, but if the particle pickers aren’t picking well, or are picking junk and not your particles, or you are trying to pick certain views, you can’t know this only from the numerical data. Perhaps this is obvious, but I find lots of newer cryo-EM people don’t actually look at their micrographs at all or how the picking has gone in favor of trying to do everything on numbers alone.
(4) Simliar with the ice thickness. Thin but not empty is ideal, but sometimes particles need thicker ice than “thinnest without breaking” for some reason (orientation, particle partitioning into ice, etc)
Bonus – we’re on 4.7.1 and I just ran a junk detector with no particles attached and it worked fine. So seems to be fixed, maybe you can push for the update 
1 Like
@ehmerb If an upgrade to v4.7.1 is not possible or if the junk detector continues to fail after the updated, please can you post your “Bonus question” as a new topic and include there additional information:
- the error message
- a screenshot of the expanded Inputs (with Show slots checked)
- the job type(s) for the job(s) that provided the inputs
It seems to work now, I think somebody upgraded it. Thank you.
1 Like