Copick Server

A server for copick projects.

Installation

pip install .

Usage

Launch a server

Using a config file

python -m copick_server.server serve --config path/to/copick_config.json --cors "*" --port 8000

Using dataset IDs from CZ cryoET Data Portal

python -m copick_server.server serve --dataset-ids 10440 --cors "*" --port 8017

You can use multiple dataset IDs by repeating the option:

python -m copick_server.server serve --dataset-ids 10440 --dataset-ids 10441 --cors "*" --port 8017

Using uv run

With config file:

uv run copick_server/server.py serve --config ~/Data/copick/full_ml_challenge_czcdp.json --cors "*" --port 8017

With dataset IDs:

uv run copick_server/server.py serve --dataset-ids 10440 --cors "*" --port 8017

Launch a client

uv run copick_server/client.py

Running Tests

pip install ".[test]"
pytest

For coverage report:

pytest --cov=copick_server

CLI Options

python -m copick_server.server serve --help

Option	Description	Default
-c, --config	Path to the configuration file	None
-ds, --dataset-ids	Dataset IDs to include in the project	None
--overlay-root	Root URL for the overlay storage	/tmp/overlay_root
--cors	Origin to allow CORS. Use wildcard '*' to allow all	None
--host	Bind socket to this host	127.0.0.1
--port	Bind socket to this port	8000
--reload	Enable auto-reload	False

Use in other projects

CryoLens extends copick-server to support generative models of cryo-ET particles.

References

The idea is influenced by https://github.com/manzt/simple-zarr-server, but aimed at supporting https://github.com/copick/copick.

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.