Hi everyone
Does anyone know how I can view the parameters I had picked for selecting micrographs in manual curation? For example, my cutoff from Ctf Resolution and range of defocus values etc.
Thank you
Prash
Doesn’t exist right now - I requested some time ago (Exposure Curation: Suggestions and Feature Requests) so hopefully will be included in the forthcoming overhaul of exposure and pick curation
Bummer. I really wanted to show in my paper how it helped me achieve high resolution structure, specially with the ice thickness selection.
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Hi @prash,
It is technically possible to obtain this information retroactively, although a bit cumbersome and requires working with the cs files directly. For more information on how to programmatically interact with cs files, see Tutorial: Manipulating .cs files created by cryoSPARC.
To obtain the path to the cs file you need to open, navigate to the Outputs tab of the Curate Exposures job, and click the copy icon next to the CTF result field (or whichever field’s attributes you’re interested in) on the exposures accepted output. This should copy the path of the cs file that contains the dataset fields of the accepted exposures to your clipboard.
From there, you can load the file into a python environment. The easiest way is to use the provided interactive python shell by running cryosparcm icli. Then you can run the commands below, for example:
import numpy as np
from cryosparc_compute import dataset
exp_dataset = dataset.Dataset().from_file('<cs file path here>')
exp_dataset #prints out list of available fields
print('Min val:', np.amin(exp_dataset.data['<field of interest here>']))
print('Max val:', np.amax(exp_dataset.data['<field of interest here>']))
This will print the min and max of your dataset field of interest, which should indicate the threshold values you used. You can see the fields available in the dataset just by entering exp_dataset into the shell, which should print a list of them.
E.g. if you wanted the CTF fit resolution, you can set the field to 'ctf/ctf_fit_to_A'; if you wanted ice thickness, you could look at 'ctf_stats/ice_thickness_rel', etc.
You could go a step further and repeat this for the parent job’s exposure output (probably from a CTF estimation job) and print the original ranges of the dataset, which would show you the original ranges of any field. In a future update, we hope to make this information much more easily available through the UI!
Best,
Michael
3 Likes
for detailed instructions. It worked like a charm.