Overview
Setup
copick projects can be distributed across multiple storage backends. The following short tutorials outline the most common setups, and provide template configuration files for each case.
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Local Project
All data is accessible on the local filesystem.
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cryoET Data Portal Project
Static data is accessed via the CZ cryoET Data Portal.
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Shared Project
Some or all data is stored on a shared filesystem.
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S3 Project
Some or all data is stored on AWS or local S3.
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SSH Project
Some or all data is stored on a filesystem accessible via SSH.
Tutorials
The following tutorials provide step-by-step instructions for using copick to perform specific curation or analysis tasks.
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Quickstart
Install copick and set up a simple project.
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Data Portal
Accessing data from the CZ cryoET Data Portal and creating new annotations for data portal tomograms.
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ChimeraX-copick
Using the ChimeraX-copick interface to visualize data from a copick project.
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Album
Creating album-based solutions to process copick data.
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Sample Boundaries
An end-to-end tutorial on how to train a neural network to predict sample boundaries.
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membrain-seg
Running the Membrain-seg segmentation pipeline on a copick project.