Vesicle Segmentation Pipeline
A Segment Anything–based pipeline for automated vesicle segmentation in cryo-EM micrographs, deployed on our HPC cluster for large data.
Python SAM Cryo-EM HPC
Overview
A wrapper pipeline around Segment Anything (SAM) and vesicle_picker for automated vesicle segmentation in electron micrographs. Designed for batch processing on NEMO (the Crick HPC cluster), submitting SLURM array jobs for parallelisation over large data.
Key Features
- SAM-backed segmentation with user-friendly configuration
- Configurable preprocessing — downsampling, Gaussian, median, or bilateral lowpass filtering before segmentation
- Postprocessing filters to filter out SAM’s dense segmentations and extract only vesicles
- Pydantic config validation that checks all parameters before a job starts, with a standalone
config_checker.pyscript - SLURM array job submission for fully parallel processing across hundreds of MRC files