Open-source tools for collaborative cryoET annotation and analysis
copick is an open-source ecosystem for collaborative cryogenic Electron Tomography (cryoET) annotation and analysis.
We provide a cross-platform, storage-agnostic, and server-less dataset API that enables researchers to access and manage tomography data seamlessly—regardless of where it's stored.
| Package | PyPI | Zenodo | Description | Install |
|---|---|---|---|---|
| copick |  |
 |
Core data model and API for cryoET datasets | pip install "copick[all]" |
| copick-utils |  |
 |
CLI utilities for data processing and conversion | pip install copick-utils |
| Package | PyPI | Zenodo | Description | Install |
|---|---|---|---|---|
| copick-torch |  |
 |
PyTorch dataset classes and augmentations | pip install copick-torch |
| Package | PyPI | Zenodo | Description | Install |
|---|---|---|---|---|
| napari-copick |  |
 |
Napari plugin for interactive annotation | pip install napari-copick |
| chimerax-copick |  |
UCSF ChimeraX plugin for 3D visualization | ChimeraX Toolshed | |
| copick-shared-ui |  |
 |
Shared Qt UI components for plugins | pip install copick-shared-ui |
| Package | PyPI | Zenodo | Description | Install |
|---|---|---|---|---|
| copick-mcp |  |
 |
MCP server for Claude AI integration | pip install copick-mcp |
| octopi |  |
 |
Deep learning framework for cryoET 3D particle picking | pip install octopi |
| saber |  |
Autonomous segmentation of organelles from cryoET | pip install saber-em |
|
| py2rely | Sub-tomogram averaging workflows for SLURM-based HPC | see repo | ||
| topcup |  |
Winning models for CZII cryoET ML Challenge | pip install topcup |
|
| slabpick | Particle picking from 2D projections of tomography data | see repo |
# Install core package with all storage backends
pip install "copick[all]"# Access data from the CZ cryoET Data Portal
from copick.impl.cryoet_data_portal import CopickRootCDP
# Open a dataset from the portal
root = CopickRootCDP.from_dataset_id(10301)
# List runs (tomograms)
for run in root.runs:
print(run.name)- Documentation — Full documentation and tutorials
- Quickstart Guide — Get started in minutes
- Data Model — Understand the copick data structure
- CLI Reference — Command-line tools
- CZ cryoET Data Portal — Public repository of cryoET datasets
- Example Dataset — Sample copick project on Zenodo
| GitHub | Packages | |
|---|---|---|
 |
@uermel | copick, copick-utils, napari-copick, chimerax-copick, copick-torch, copick-mcp |
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@kephale | copick, copick-utils, napari-copick, copick-torch, copick-mcp |
 |
@jtschwar | copick, copick-utils, copick-torch |
 |
@zhuowenzhao | copick, copick-utils |
 |
@daniel-ji | copick |
 |
@andy-sweet | copick |
We welcome contributions! See our Contributing Guide for development setup and guidelines.
All projects follow the Contributor Covenant Code of Conduct.
If you use copick in your research, please cite:
@article{harrington2024open,
title={Open-source Tools for CryoET Particle Picking Machine Learning Competitions},
author={Harrington, Kyle I. and Zhao, Zhuowen and Schwartz, Jonathan and Kandel, Saugat and Ermel, Utz and Paraan, Mohammadreza and Potter, Clinton and Carragher, Bridget},
journal={NeurIPS 2024 Workshop on Machine Learning in Structural Biology},
year={2024},
doi={10.1101/2024.11.04.621608}
}All copick packages are released under the MIT License.
