Connecting CS Live micrographs and external particle coordinates

How do I connect external particle coordinates with CTF estimated micrographs from CS Live?

There is no ‘job’ for the CTF estimation when you run this in CS live and the ‘Export Exposure from CS Live’ does not contain the CTF estimation.


Hi,@jarmko. I think we are talking the same topic and you may refer to dicussions in #To extract particles using coordinates from relion in cryosparc for more details.

Hi @Verdandy,

The post is similar, but not the same. In CS, you have the CTF output available, but in CS live there is no CTF output for connecting external particles, only exposure without the CTF information.

I can always re-run CTF estimation after connecting the exposures, but that would be redundant and inefficient.


Hi Matt,

Interesting. Please can you expand the CryoSPARC Live Exposure Export job and share a screenshot of the Outputs tab’s accepted_exposures section (see example below) with us?

Hi @wtempel ,

My Live Exposure Export job does have all these outputs. I am assuming the CTF information is there.

Here is my problem, I’ve used external particles coordinates in star format to extract from the CS live exposures (ignoring the raw data), but after extraction the 2D classes like fuzzy:
Do you know how to resolve this?

Thank you,

Am I correctly assuming that these these thumbnails are from a 2D classification job?
Please can you post a screenshot of the continuous workflow (with visible job types), including but not limited to

  1. the job where the *.star file was input
  2. the job that output exposures used in particle extraction
  3. the 2d classification job

as well as
Inputs screenshots of 1. and 3., Outputs screenshot for 2.

Here is the continuous workflow:

Input screenshot of 1:

Everything else is default

Outputs of 2:

Inputs of 3: