Cryosparc-tools query

Scripting
1

Hi,

I’m trying to get my head around cryosparc-tools. A simple use case might be to take a particle set (e.g. from a refinement job) and edit one parameter (e.g. Cs or amplitude contrast for example) and output a modified particle set. How would I go about doing that?

Cheers
Oli

2

Hi @olibclarke, you can use a combination of CryoSPARC.find_job, Job.load_output, CryoSPARC.save_external_result and dataset operations to achieve this. Here’s some partial code:

from cryosparc.tools import CryoSPARC

cs = CryoSPARC(...)  # fill in credentials and instance info here
puid = "PX"  # substitute with project UID
wuid = "WY"  # substitute with workspace UID
juid = "JZ"  # substitute with job UID
output = "particles"  # substitute with job output name

job = cs.find_job(puid, juid)
particles = job.load_output(output, slots=["ctf"])

# == Modify output dataset here ==
particles["ctf/cs_mm"] = ...
particles["ctf/amp_contrast"] = ...

cs.save_external_result(puid, wuid, "particle", particles, 
    name=output 
    slots=["ctf"],
    passthrough=(juid, output),
    title="Modified particles",
    desc="set cs to ... and amplitude contrast to ...",
)

This creates a new External job in the target workspace with a modified particles.ctf output group that inherits other output groups from the given refinement job.

I used the Re-center Particles example as a template for this code, I recommend reading that and the other examples to learn more about cryosparc-tools’s capabilities.

Hope that helps!

3 Likes
3

That is exceptionally helpful, thanks @nfrasser!

1 Like