slabpick

Tools to facilitate particle picking and curation from 2D projections of tomography data from either slabs (projected slices through the full tomogram) or minislabs (projections of per-particle subvolumes). Minslabs can be formatted as a particle stack for cryoDRGN and Relion compatibility or a gallery of tiled particle projections for use in CryoSPARC. Functions to generate Relion-4 starfiles or copick-formatted annotations from particles curated in CryoSPARC or by Relion's 2D class averaging routine are also included.

Instructions for use

The make_minislabs command will generate either galleries (per-particle projections tiled into mock micrographs) for use in CryoSPARC or particle stacks for use in Relion.

For use in CryoSPARC, an example workflow would be:

1. Import the galleries as micrographs with the "Output Constant CTF" option turned on.
2. Perform a round of blob picking, with the settings set to ensure that each gallery has more picks than the number of tiles per gallery.
3. Run cs_center_picks to center the mock picks from blob-picking in each tile and remove excess picks, e.g.

cs_center_picks —cs_file /path/to/picked_particles.cs —map_file path/to/gallery/particle_map.csv

4. After 2D classification, particles can be mapped back to a copick project or a Relion-4 starfile using the cs_map_particles command.

Details for use in Relion to follow.