Tutorials

Step-by-step guides for common copick curation and analysis tasks. Looking for installation and project setup instead? Head to Get Started.

Access data from the CZ cryoET Data Portal and create new annotations for portal tomograms.

Visualize and curate data from a copick project in UCSF ChimeraX.

An end-to-end tutorial on training a neural network to predict sample boundaries.

Filter particle picks by their position relative to the detected sample boundaries.

Run the membrain-seg segmentation pipeline on a copick project.

Run easymode's pretrained segmentation networks on a copick project.

Synchronize the CZII Kaggle challenge dataset into a copick project.

Drive copick from an MCP-enabled assistant.

Work with copick projects described by an ML Commons Croissant manifest.

Run copick workflows at scale on HPC clusters.

Create album-based solutions to process copick data.

Snippets

Short, copy-pasteable Python examples for common copick API operations — reading runs, objects, tomograms, picks, segmentations, and meshes.