copick 0.6.0

Definitions for a collaborative cryoET annotation tool.

copick

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-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.

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). Separate s3, smb, and ssh extras are available.

pip install "copick[all]"

Example dataset

An example dataset can be obtained from Zenodo.

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

   {
       "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

   from copick.impl.filesystem import CopickRootFSSpec
   root = CopickRootFSSpec.from_file('path/to/filesystem_overlay_only.json')
   

4. Access the data using the copick API

   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]
   

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 [e-mail].

Reporting Security Issues

If you believe you have found a security issue, please responsibly disclose by contacting us at [e-mail].