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Tools

There is a growing list of tools that support the copick dataset API, some of them are listed below:

Visualization

ChimeraX-copick

chimerax-copick interface
ChimeraX-copick interface with dataset 10301, Run 14069

A UCSF ChimeraX plugin for visualizing copick datasets and particle curation. The plugin is available in the ChimeraX Toolshed and can be installed from within ChimeraX.

CellCanvas

A Napari plugin for interactive segmentation and visualization of 3D images, supporting the copick dataset API.

napari-copick

A Napari plugin for visualizing copick datasets and particle curation.

copick-live

CopickLive is a Dash Plotly web server for tracking progress of collaborative particle picking and curation projects using copick.

Analysis

deepfinder

A deep learning-based tool for particle picking in cryo-EM data. It uses a U-Net architecture to detect particles in tomograms. Images can be loaded from the copick dataset API, and results can be saved back to the copick project.

copick-catalog

An album-catalog for manipulating copick data entities. Includes solutions to fit planes to points, manipulate meshes and more.

cellcanvas-catalog

An album-catalog for CellCanvas, including solutions creating and manipulating copick data.