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?
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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.
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