Lodstone

Lodstone is a renderer-neutral engine for view-dependent streaming of multiscale chunked arrays. Given a pyramid, camera, and renderer target, it selects visible levels and chunks, prioritizes them by visual value, and delivers updates without blocking the viewer.

Lodstone is an alpha. The core supports Python 3.11–3.14 and only requires NumPy. Viewer integrations currently use development branches while their streaming APIs stabilize.

Install

pip install lodstone==0.1.0a1
pip install "lodstone[ome-zarr]==0.1.0a1"  # remote OME-Zarr sources

For the runnable viewer demos below, clone Lodstone so the example scripts are available:

git clone --depth 1 https://github.com/kephale/lodstone.git
cd lodstone

All commands use the public ZSNS001 Zebrahub light-sheet dataset at timepoint 400. Clone the viewer repositories next to lodstone, giving this layout:

work/
├── lodstone/
├── napari/
├── ndv/
└── chimerax-ome-zarr/

Run with napari

The napari integration uses a single multiscale layer, bounded resident intervals, partial texture uploads, and a shared Lodstone runtime.

cd ..
git clone --depth 1 --single-branch --branch lodstone-integration \
  https://github.com/kephale/napari.git
cd napari
python3 -m venv .venv
.venv/bin/python -m pip install -e ".[pyqt6,progressive]"
.venv/bin/python -m pip install -e "../lodstone[ome-zarr]"

cd ../lodstone
../napari/.venv/bin/python examples/napari_zebrahub.py \
  --time 400 --ndisplay 3

Add --trace-chunks to log plans, cache hits, source reads, and evictions, or --diagnostic-levels to color pixels by the pyramid level that supplied them.

Run with ndv

Both ndv backends use the same source, planner, runtime, and dense clipmap target. Only the canvas renderer changes.

cd ..
git clone --depth 1 --single-branch --branch lodstone-integration \
  https://github.com/kephale/ndv.git
cd ndv
python3 -m venv .venv
.venv/bin/python -m pip install -e ".[pyqt,vispy,pygfx]"
.venv/bin/python -m pip install -e "../lodstone[ome-zarr]"

cd ../lodstone
../ndv/.venv/bin/python examples/ndv_dense.py \
  --backend vispy --time 400

Close the VisPy window, then run the identical data path with PyGFX:

../ndv/.venv/bin/python examples/ndv_dense.py \
  --backend pygfx --time 400

VisPy	PyGFX

Run with ChimeraX

The ChimeraX integration is provided by the OME-Zarr bundle's streaming branch. The commands below use ChimeraX Daily on macOS; adjust CHIMERAX_PYTHON and CHIMERAX for another installation.

cd ..
git clone --depth 1 --single-branch --branch codex/lodstone-streaming \
  https://github.com/kephale/chimerax-ome-zarr.git
cd chimerax-ome-zarr

export CHIMERAX=/Applications/ChimeraX_Daily.app/Contents/bin/ChimeraX
export CHIMERAX_PYTHON=/Applications/ChimeraX_Daily.app/Contents/bin/python3.14

"$CHIMERAX_PYTHON" -m pip install --no-deps --force-reinstall ../lodstone
PYTHONPATH="$PWD" "$CHIMERAX_PYTHON" -m chimerax.core --nogui --exit \
  --cmd "devel build ."
"$CHIMERAX_PYTHON" -m chimerax.core --nogui --exit --cmd \
  "toolshed install $PWD/dist/chimerax_ome_zarr-1.0.0a1-py3-none-any.whl noDeps true reinstall true"

"$CHIMERAX" --cmd \
  "open ngff:https://public.czbiohub.org/royerlab/zebrahub/imaging/single-objective/ZSNS001.ome.zarr streaming true"

Restart ChimeraX after replacing Lodstone or reinstalling the bundle.

How it fits

Source + View + Target
          │
        Planner
          │
        Stream

• Source exposes pyramid metadata and asynchronous regional reads.
• View captures displayed axes, selections, viewport, and camera matrix.
• Target describes renderer residency and applies completed updates.
• Planner selects visible levels and chunks within the target budget.
• Stream owns scheduling, cancellation, caching, batching, and stale-work rejection.

Storage chunks and display tiles are independent. A renderer may request small bricks while a remote Zarr source stores larger chunks; Lodstone coalesces and caches the native reads needed to assemble those updates. Multiple layers can share one Runtime while retaining independent stream state.

See Camera-aware multiscale rendering for the planner math and the roadmap for metadata culling, sharding, and virtual texture residency.

Viewer status

Integrations should pin an exact Lodstone prerelease. Compatibility is claimed only for combinations covered by native tests and visual smoke tests.

Develop

uv run --extra test pytest
uv run --group dev ruff check .
uv run --group dev pyright src

The test suite is network-independent. See CHANGELOG.md, RELEASING.md, and the renderer architecture for deeper reference material.