opusTomo

Cryo-ET data processing pipeline using WARP, AreTomo2, PyTOM, and OPUS-ET. Use this skill whenever the user is processing cryo-electron tomography (cryo-ET) data, including: importing frame series or tilt series from MDOC files, CTF estimation, AreTomo2 alignment, template matching with PyTOM, exporting subtomograms, or training OPUS-ET heterogeneity models. Also use when the user mentions tomostar files, WarpTools commands, tilt stacks (.st, .rawtlt), defocus handedness, ts_export_particles, or SLURM job submission for GPU tomography processing.

Cryo-ET data processing and analysis workflows using opus-et training results. Handles PCA/kmeans clustering, volume generation from latent codes, pose parsing, and star file manipulation. Use when processing training results from a specific epoch, generating volumes for cluster centers or principal components, parsing poses, or combining star files from cryo-ET reconstructions.