/kmeans-beamtilt

Primary LanguageJupyter Notebook

kmeans-beamtilt

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, and km_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 via cryosparc-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.