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 | |
| @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{ermel2026copick,
title={copick: An open dataset interface and toolkit for collaborative annotation and analysis of cryo-electron tomography data},
author={Ermel, Utz Heinrich and Schwartz, Jonathan and Zhao, Zhuowen and Ji, Daniel and Peck, Ariana and Yu, Yue and Paraan, Mohammadreza and Carragher, Bridget and Frangakis, Achilleas S. and Harrington, Kyle I. S.},
journal={Protein Science},
volume={35},
number={5},
pages={e70578},
year={2026},
doi={10.1002/pro.70578}
}📄 https://doi.org/10.1002/pro.70578
All copick packages are released under the MIT License.