napari-copick

A plugin for collaborative annotation in cryoET using copick

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Installation

You can install napari-copick via pip:

pip install napari-copick

Copick 2 / OME-Zarr 0.5 prereleases use the alpha channel:

pip install --pre napari-copick

To install latest development version:

pip install git+https://github.com/copick/napari-copick.git@v2.0

Usage

Using a copick config file

napari-copick run --config path/to/copick_config.json

Using dataset IDs from CZ cryoET Data Portal

napari-copick run --dataset-ids 10440 10441 --overlay-root /path/to/overlay_root

You can specify multiple dataset IDs separated by spaces.

GUI Usage

The plugin provides an intuitive interface with two loading options:

1. Load Config File: Opens a file dialog to select a copick configuration JSON file
2. Load from Dataset IDs: Opens a dialog to enter CZ cryoET Data Portal dataset IDs and overlay root path

After loading, you'll see a hierarchical tree of the project structure that you can navigate to access tomograms, segmentations, and picks.

Tomogram Handling

napari-copick handles multiscale OME-Zarr arrays directly:

• Selects resolution levels from OME multiscale metadata, including non-numeric dataset paths
• Reads both legacy OME-Zarr 0.4 / Zarr v2 and OME-Zarr 0.5 / Zarr v3 stores
• Loads the selected resolution level into memory before adding it to napari
• Applies the selected dataset's OME coordinate transformation as the layer scale

This direct zarr handling provides better performance and more flexibility compared to relying on external plugins.

Volume reads use the Zarr store supplied by copick and require OME multiscales metadata. Stores written by copick 1.x (OME-Zarr 0.4 / Zarr v2) and copick 2.x (OME-Zarr 0.5 / Zarr v3) are supported. Third-party stores that expose only a root data array without OME multiscales metadata are intentionally unsupported; napari-copick does not infer a dataset path from array names or root-key order. Storage backend access and retry behavior remain owned by copick.

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the MIT license, "napari-copick" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.

Code of Conduct

This project adheres to the Contributor Covenant code of conduct. By participating, you are expected to uphold this code. Please report unacceptable behavior to opensource@chanzuckerberg.com.

Reporting Security Issues

If you believe you have found a security issue, please responsibly disclose by contacting us at security@chanzuckerberg.com.