Interactive Vitessce visualizations for Harpy workflows

Documentation · Quick Start · Tutorials

Harpy-Vitessce

harpy-vitessce helps you turn Harpy outputs into shareable, interactive Vitessce configurations.

For more information on Harpy, see the Harpy documentation.

Why Use Harpy-Vitessce?

• Build Vitessce configs directly from SpatialData or from seperate files on disk.
• Get ready-to-share, interactive visualizations for transcriptomics and proteomics
• Use sensible defaults while keeping control over layout and rendering options

Installation (uv)

Install the current main branch:

uv venv .venv_harpy_vitessce_zarr2 --python=3.12
source .venv_harpy_vitessce_zarr2/bin/activate
uv pip install "harpy-vitessce[vitessce] @ git+https://github.com/vibspatial/harpy_vitessce.git@main"

Add it as a project dependency managed by uv:

uv add "harpy-vitessce[vitessce] @ git+https://github.com/vibspatial/harpy_vitessce.git@main"

Quick Start

The full quick-start guide lives in docs/quickstart.md.

Tutorials

• Visium HD (bins): docs/tutorials/visium_hd/visium_hd_bins_from_spatialdata.ipynb
• Visium HD (spots): docs/tutorials/visium_hd/visium_hd_spots.ipynb
• Proteomics SpatialData blobs: docs/tutorials/proteomics/spatialdata_blobs.ipynb

Live Examples

Example Visium HD visualization: Open in Vitessce

Example proteomics (CODEX) visualization: Open in Vitessce

Example proteomics visualization (dummy dataset): Open in Vitessce

Disclaimer

This is an independent, third-party integration project and is not affiliated with, endorsed by, or sponsored by the Vitessce maintainers. Vitessce and related names may be trademarks of their respective owners.