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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 storage, via SSH or on the cloud with the same API. No need for your own boilerplate!

    Get started now

  • cloud-ready


    Access image data quickly and in parallel thanks to multiscale OME-Zarr. Easily load data from the CZ cryoET Data Portal!

    Learn more

  • server-less


    No need for a dedicated server or database to access your data, just point copick to your data and go!

    Deploy copick using album

  • cross-platform


    copick works on any platform that supports Python. Compute on Linux, visualize on Windows or Mac!

    Learn about copick and HPC

  • ecosystem


    Using the copick API allows visualizing and curating data in ChimeraX and Napari right away!

    Explore tools

  • open source


    Copick is released under the open source MIT license.

    License

Data

Currently, copick supports the following types of data frequently encountered in cryoET datasets:

  • tomograms
  • feature maps
  • dense segmentations
  • mesh annotations
  • point annotations

Storage backends

Copick should support any storage backend that is supported by fsspec.

The following backends are included in tests and should work out of the box:

  • local filesystem
  • s3
  • smb
  • access via ssh