| Name | copick JSON |
| Version |
1.11.0
JSON |
| download |
| home_page | None |
| Summary | Definitions for a collaborative cryoET annotation tool. |
| upload_time | 2025-07-22 21:05:26 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.9 |
| 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
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE. |
| keywords |
annotation
collaborative
copick
cryo-et
cryoet
segmentation
tomography
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# copick
<div align="center">
[](https://opensource.org/licenses/MIT)
[](https://badge.fury.io/py/copick)
[](https://pypi.org/project/copick/)
[](https://github.com/copick/copick/actions/workflows/test.yml)
[](https://codecov.io/gh/copick/copick)
[](https://copick.github.io/copick/)
</div>
**copick** is a cross-platform, storage-agnostic and server-less dataset API for cryoET datasets. Access to the data is
provided through an object-oriented API that abstracts away the underlying storage using the
[fsspec](https://filesystem-spec.readthedocs.io/en/latest/)-family of libraries.
## Why copick?
- **storage-agnostic**: Access data on local or shared filesystems, via SSH or on the cloud with the same API. No
need for your own boilerplate!
- **cloud-ready**: Access image data quickly and in parallel thanks to multiscale OME-Zarr!
- **server-less**: No need for a dedicated server or database to access your data, just point **copick** to your data
and go!
- **cross-platform**: **copick** works on any platform that supports Python. Compute on Linux, visualize on Windows or
Mac, all with the same dataset API!
- **ecosystem**: Using the **copick** API allows visualizing and curating data in ChimeraX and Napari right away!
## Documentation
For more information, see the [documentation](https://copick.github.io/copick/).
## Installation
copick can be installed using pip. Using the `all` extra installs necessary requirements for all tested filesystem
implementations from the fsspec family (`local`, `s3fs`, `smb`, `sshfs`). A separate `smb` extra is available.
```shell
pip install "copick[all]"
```
> [!NOTE]
> `copick==1.2.0` will fail to install with `pip>=25`. We recommend using [`uv pip`](https://docs.astral.sh/uv/pip/) or `pip<=25` when installing copick.
## Example dataset
An example dataset can be obtained from [Zenodo](https://doi.org/10.5281/zenodo.11238625).
To test with the example dataset:
1. Download and unpack the example dataset
2. Add the location of the `sample_project`-directory in the unpacked dataset to `filesystem_overlay_only.json`
```json
{
"name": "test",
"description": "A test project.",
"version": "1.0.0",
"pickable_objects": [
{
"name": "proteasome",
"is_particle": true,
"pdb_id": "3J9I",
"label": 1,
"color": [255, 0, 0, 255],
"radius": 60,
"map_threshold": 0.0418
},
{
"name": "ribosome",
"is_particle": true,
"pdb_id": "7P6Z",
"label": 2,
"color": [0, 255, 0, 255],
"radius": 150,
"map_threshold": 0.037
},
{
"name": "membrane",
"is_particle": false,
"label": 3,
"color": [0, 0, 0, 255]
}
],
// Change this path to the location of sample_project
"overlay_root": "local:///PATH/TO/EXTRACTED/PROJECT/",
"overlay_fs_args": {
"auto_mkdir": true
}
}
```
3. Start copick with the configuration file
```python
from copick.impl.filesystem import CopickRootFSSpec
root = CopickRootFSSpec.from_file('path/to/filesystem_overlay_only.json')
```
4. Access the data using the copick API
```python
import zarr
from copick.impl.filesystem import CopickRootFSSpec
root = CopickRootFSSpec.from_file('path/to/filesystem_overlay_only.json')
# Get a run by name
run = root.get_run("TS_001")
# Get a tomogram by name
tomogram = run.get_voxel_spacing(10).get_tomogram("wbp")
# Access the data
group = zarr.open(tomogram.zarr())
arrays = list(group.arrays())
_, array = arrays[0]
```
## Contributing
We welcome contributions to copick! Here's how to get started:
### Development Setup
1. Clone the repository and install with development dependencies:
```bash
git clone https://github.com/copick/copick.git
cd copick
pip install -e ".[dev,test]"
```
2. Install pre-commit hooks:
```bash
pre-commit install
```
3. Run tests to ensure everything is working:
```bash
pytest
```
### Code Quality
We use several tools to maintain code quality:
- **Black** for code formatting
- **Ruff** for linting and import sorting
- **Pre-commit hooks** to enforce standards
Before submitting a PR, ensure your code passes all checks:
```bash
black src/ tests/
ruff check --fix src/ tests/
pytest
```
### Conventional Commits
All pull requests must use [Conventional Commits](https://www.conventionalcommits.org/) for commit messages. This helps us automatically generate changelogs and determine version bumps.
Examples:
- `feat: add support for new tomogram format`
- `fix: resolve memory leak in zarr loading`
- `docs: update installation instructions`
- `test: add unit tests for mesh operations`
### Plugin System
Copick supports a plugin system that allows external Python packages to register CLI commands. Commands can be added to the main CLI or organized into groups like `inference`, `training`, `evaluation`, `process`, and `convert`.
See the [CLI documentation](https://copick.github.io/copick/cli/#plugin-system) for detailed plugin development instructions and the [copick-plugin-demo](https://github.com/copick/copick-plugin-demo) repository for a complete example.
## Code of Conduct
This project adheres to the Contributor Covenant [code of conduct](https://github.com/chanzuckerberg/.github/blob/main/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to [opensource@chanzuckerberg.com](mailto: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](mailto:security@chanzuckerberg.com).
Raw data
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"description": "# copick\n\n<div align=\"center\">\n\n[](https://opensource.org/licenses/MIT)\n[](https://badge.fury.io/py/copick)\n[](https://pypi.org/project/copick/)\n[](https://github.com/copick/copick/actions/workflows/test.yml)\n[](https://codecov.io/gh/copick/copick)\n[](https://copick.github.io/copick/)\n\n</div>\n\n**copick** is a cross-platform, storage-agnostic and server-less dataset API for cryoET datasets. Access to the data is\nprovided through an object-oriented API that abstracts away the underlying storage using the\n[fsspec](https://filesystem-spec.readthedocs.io/en/latest/)-family of libraries.\n\n## Why copick?\n\n- **storage-agnostic**: Access data on local or shared filesystems, via SSH or on the cloud with the same API. No\n need for your own boilerplate!\n- **cloud-ready**: Access image data quickly and in parallel thanks to multiscale OME-Zarr!\n- **server-less**: No need for a dedicated server or database to access your data, just point **copick** to your data\n and go!\n- **cross-platform**: **copick** works on any platform that supports Python. Compute on Linux, visualize on Windows or\n Mac, all with the same dataset API!\n- **ecosystem**: Using the **copick** API allows visualizing and curating data in ChimeraX and Napari right away!\n\n## Documentation\n\nFor more information, see the [documentation](https://copick.github.io/copick/).\n\n## Installation\n\ncopick can be installed using pip. Using the `all` extra installs necessary requirements for all tested filesystem\nimplementations from the fsspec family (`local`, `s3fs`, `smb`, `sshfs`). A separate `smb` extra is available.\n\n```shell\npip install \"copick[all]\"\n```\n\n> [!NOTE]\n> `copick==1.2.0` will fail to install with `pip>=25`. We recommend using [`uv pip`](https://docs.astral.sh/uv/pip/) or `pip<=25` when installing copick.\n\n\n## Example dataset\n\nAn example dataset can be obtained from [Zenodo](https://doi.org/10.5281/zenodo.11238625).\n\nTo test with the example dataset:\n\n1. Download and unpack the example dataset\n2. Add the location of the `sample_project`-directory in the unpacked dataset to `filesystem_overlay_only.json`\n ```json\n {\n \"name\": \"test\",\n \"description\": \"A test project.\",\n \"version\": \"1.0.0\",\n\n \"pickable_objects\": [\n {\n \"name\": \"proteasome\",\n \"is_particle\": true,\n \"pdb_id\": \"3J9I\",\n \"label\": 1,\n \"color\": [255, 0, 0, 255],\n \"radius\": 60,\n \"map_threshold\": 0.0418\n },\n {\n \"name\": \"ribosome\",\n \"is_particle\": true,\n \"pdb_id\": \"7P6Z\",\n \"label\": 2,\n \"color\": [0, 255, 0, 255],\n \"radius\": 150,\n \"map_threshold\": 0.037\n\n },\n {\n \"name\": \"membrane\",\n \"is_particle\": false,\n \"label\": 3,\n \"color\": [0, 0, 0, 255]\n }\n ],\n\n // Change this path to the location of sample_project\n \"overlay_root\": \"local:///PATH/TO/EXTRACTED/PROJECT/\",\n\n \"overlay_fs_args\": {\n \"auto_mkdir\": true\n }\n }\n ```\n\n3. Start copick with the configuration file\n\n ```python\n from copick.impl.filesystem import CopickRootFSSpec\n root = CopickRootFSSpec.from_file('path/to/filesystem_overlay_only.json')\n ```\n\n4. Access the data using the copick API\n\n ```python\n import zarr\n\n from copick.impl.filesystem import CopickRootFSSpec\n root = CopickRootFSSpec.from_file('path/to/filesystem_overlay_only.json')\n\n # Get a run by name\n run = root.get_run(\"TS_001\")\n\n # Get a tomogram by name\n tomogram = run.get_voxel_spacing(10).get_tomogram(\"wbp\")\n\n # Access the data\n group = zarr.open(tomogram.zarr())\n arrays = list(group.arrays())\n _, array = arrays[0]\n ```\n\n## Contributing\n\nWe welcome contributions to copick! Here's how to get started:\n\n### Development Setup\n\n1. Clone the repository and install with development dependencies:\n ```bash\n git clone https://github.com/copick/copick.git\n cd copick\n pip install -e \".[dev,test]\"\n ```\n\n2. Install pre-commit hooks:\n ```bash\n pre-commit install\n ```\n\n3. Run tests to ensure everything is working:\n ```bash\n pytest\n ```\n\n### Code Quality\n\nWe use several tools to maintain code quality:\n\n- **Black** for code formatting\n- **Ruff** for linting and import sorting\n- **Pre-commit hooks** to enforce standards\n\nBefore submitting a PR, ensure your code passes all checks:\n```bash\nblack src/ tests/\nruff check --fix src/ tests/\npytest\n```\n\n### Conventional Commits\n\nAll pull requests must use [Conventional Commits](https://www.conventionalcommits.org/) for commit messages. This helps us automatically generate changelogs and determine version bumps.\n\nExamples:\n- `feat: add support for new tomogram format`\n- `fix: resolve memory leak in zarr loading`\n- `docs: update installation instructions`\n- `test: add unit tests for mesh operations`\n\n### Plugin System\n\nCopick supports a plugin system that allows external Python packages to register CLI commands. 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