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Software compatible with the copick API

A growing ecosystem of applications is compatible with copick dataset API — desktop and web viewers, interactive segmentation and picking tools, and AI integrations. Scroll the highlights below, or jump to a category.

  • ChimeraX-copick

    ChimeraX-copick

    Visualize and curate copick datasets in UCSF ChimeraX.

  • napari-copick

    napari-copick

    Browse and curate copick datasets in napari.

  • copick-web

    copick-web

    View copick datasets in the browser — tomograms, picks, and segmentations.

  • CellCanvas

    CellCanvas

    Interactive 3D segmentation in napari, backed by copick.

  • copick-live

    copick-live

    Track collaborative picking and curation in a web dashboard.

Explore the copick ecosystem

AI Integration

copick-mcp

copick-mcp workflow
An AI agent translating a natural-language request into copick CLI commands via copick-mcp.

A Model Context Protocol server that enables Claude AI (Claude Desktop and Claude Code) to explore copick projects and discover CLI commands for building processing pipelines.

Analysis / ML

octopi

octopi

A deep-learning toolkit for training and running particle-picking models on cryoET tomograms, reading and writing annotations through the copick dataset API.

TopCUP

TopCUP (Top CryoET U-Net Picker) is a 3D U-Net ensemble model for particle picking in cryoET volumes using a segmentation-heatmap approach. It won first place in the CryoET Object Identification Kaggle competition and is distributed through CZI Virtual Cell Models.

membrain-seg

membrain-seg input and output membrain-seg input and output
membrain-seg turns a raw tomogram (left) into a membrane segmentation (right).

A pretrained 3D U-Net for segmenting membranes in cryoET tomograms. Via the copick-torch plugin it runs directly on a copick project as copick inference membrain-seg, reading tomograms and writing membrane segmentations back through the copick dataset API.

copick-easymode

easymode input and output easymode input and output
easymode turns a raw tomogram (left) into dense per-feature segmentations (right).

A collection of pretrained, general-purpose 3D U-Nets for segmenting common eukaryotic features in cryoET — membranes, ribosomes, microtubules and more. The copick-easymode plugin runs them directly on a copick project as copick inference easymode, reading tomograms and writing one segmentation per feature back through the copick dataset API.

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.

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.

napari-copick

napari-copick interface
Browsing and curating a copick project in napari-copick.

A Napari plugin for visualizing copick datasets and particle curation.

copick-web

copick-web interface
Browsing tomograms, picks, and segmentations in the copick-web viewer.

copick-web is the official browser-based viewer for copick datasets, built directly on the copick data model. Browse runs, voxel spacings, and tomograms; view tomogram slices with channel controls and a scale bar; and overlay particle picks and multilabel segmentations.

CellCanvas

CellCanvas interface
Interactive 3D segmentation in CellCanvas.

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

copick-live

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