Quick Start

Requirements

copick runs on Python 3.9 and above on Linux, MacOS, and Windows.

It requires the following packages:

• fsspec
• pydantic
• numpy
• trimesh
• zarr

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.

pip install "copick[all]"

Note

copick==1.2.0 will fail to install with pip>=25. We recommend using uv pip or pip<=25 when installing copick.

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]