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). 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]