Beam tilt refinement by image shift groups in cryoSPARC for datasets acquired with the Leginon & Appion suite.
kmeans_groups.py
- reads the input.csv file to group the micrographs based on their image shift groups.
- Usage:
kmeans_groups.py k inputcsv
- outputs numbered
km_groups.csv
,km_centers.csv
, andkm_plot.png
files.
add_class.sh
- adds 3 digit class numbers to the symlinked micrographs.
- Usage:
add_class.sh -d DIRECTORY -i FILE
assign_kmeans_exp_groups_pub.ipynb
- a Jupyter notebook to directly assign the exposure group IDs calculated with
kmeans_group.py
to particles viacryosparc-tools
- requires
km_groups.csv
with micrograph names and exp group assignments
K-means script by Bill Rice
You can find the step by step guide in the repository wiki.