Metadata-Version: 2.4
Name: slabpick
Version: 1.0.2
Summary: Tools for particle picking from 2d projections.
Project-URL: Repository, https://github.com/slabpick/slabpick.git
Project-URL: Issues, https://github.com/slabpick/slabpick/issues
Author-email: Ariana Peck <ariana.peck@czii.org>
License: MIT License
        
        Copyright (c) 2024 Utz Ermel
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
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        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
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        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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License-File: LICENSE
Keywords: cryo-et,cryoet,tomography
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Requires-Python: >=3.9
Requires-Dist: copick
Requires-Dist: matplotlib
Requires-Dist: mrcfile
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: pydantic
Requires-Dist: pytest
Requires-Dist: scipy
Requires-Dist: starfile
Requires-Dist: typing
Requires-Dist: zarr
Provides-Extra: dev
Requires-Dist: black; extra == 'dev'
Requires-Dist: ipython; extra == 'dev'
Requires-Dist: notebook; extra == 'dev'
Requires-Dist: pre-commit; extra == 'dev'
Requires-Dist: ruff; extra == 'dev'
Provides-Extra: test
Requires-Dist: pytest; extra == 'test'
Description-Content-Type: text/markdown

# 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](https://chanzuckerberg.github.io/py2rely/user-guide/2d-slab-classification/) for details