copick
A storage-agnostic, server-less dataset API for cryo-electron tomography. Access tomograms, segmentations, meshes, and point annotations through one object-oriented Python API — backed by fsspec and multiscale OME-Zarr, from a laptop to the cloud.
Visualization & curation
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Visualize and curate copick datasets in UCSF ChimeraX.
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Browse and curate copick datasets in napari.
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View copick datasets in the browser — tomograms, picks, and segmentations.
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Interactive 3D segmentation in napari, backed by copick.
Processing & conversion
Workflows & tutorials
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Visualize and curate a copick project in ChimeraX.
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Filtering by Sample Boundaries
Filter particle picks by their position relative to the sample boundaries.
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Work with copick projects described by an ML Commons Croissant manifest.
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Drive copick from an MCP-enabled assistant.
Supported data types
copick represents the data types frequently encountered in cryoET datasets through a single object-oriented API.
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Tomograms
Multiscale 3D reconstructions stored as OME-Zarr.
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Feature maps
Derived voxel-wise feature volumes computed from tomograms.
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Segmentations
Dense, multiscale volumetric labels.
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Meshes
Surface annotations stored as GLB.
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Picks
Point annotations with per-particle position and orientation.
Why copick?
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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!
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cloud-ready
Access image data quickly and in parallel thanks to multiscale OME-Zarr. Easily load data from the CZ cryoET Data Portal!
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server-less
No need for a dedicated server or database to access your data, just point copick to your data and go!
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cross-platform
copick works on any platform that supports Python. Compute on Linux, visualize on Windows or Mac!
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ecosystem
Using the copick API allows visualizing and curating data in ChimeraX and Napari right away!
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open source
Copick is released under the open source MIT license.