copick: An open dataset interface and toolkit for collaborative annotation and analysis of cryo-electron tomography...

Area of Science:

• Structural Biology
• Cell Biology
• Biophysics

Background:

• Cryo-electron tomography (cryoET) is crucial for visualizing cellular structures at high resolution.
• Increasingly large and complex cryoET datasets pose challenges for manual analysis and collaboration.

Purpose of the Study:

• To develop an open-source tool suite, copick, for scalable and collaborative cryo-electron tomography analysis.
• To standardize data access and facilitate human-in-the-loop workflows for annotation and machine learning integration.

Main Methods:

• Developed copick, an open-source API and tool suite for cryoET data.
• Integrated plugins for napari and ChimeraX for interactive analysis.
• Implemented a multi-resolution OME-Zarr architecture for efficient data handling.
• Introduced a Model Context Protocol for automated pipeline generation.

Main Results:

• Copick provides standardized access to diverse cryoET data types across various storage platforms.
• Plugins enable collaborative particle picking, segmentation, and machine learning output inspection.
• The OME-Zarr architecture ensures responsive visualization and cross-platform compatibility.
• Automated pipeline generation streamlines annotation and curation processes.

Conclusions:

• Copick enhances the scalability, reproducibility, and collaborative nature of cryoET data analysis.
• The tool suite addresses the growing complexity of cryoET datasets, supporting advanced structural biology research.
• Copick facilitates efficient integration of manual and automated analysis methods in cryoET workflows.