slabpick 1.0.2

Tools for particle picking from 2d projections.

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

Slabpick with CryoSPARC

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.

Slabpick with RELION

Refer to the Documentation for details