.gitignore
LICENSE
MANIFEST.in
NOTICE
README.md
THIRD_PARTY_NOTICES.md
mkdocs.yml
pyproject.toml
.github/workflows/ci.yml
.github/workflows/docs.yml
.github/workflows/release.yml
.github/workflows/validate.yml
_agents/skills/use-omero-zarr-viewer/SKILL.md
_agents/skills/use-omero-zarr-viewer/references/REFERENCE.md
deploy/nl-biomero/docker-compose-windows-dev.yml
deploy/nl-biomero/nginx-location.conf
deploy/omero-deployment-kit/Dockerfile-web.fragment
deploy/omero-deployment-kit/nginx-location.conf.j2
deploy/omero-deployment-kit/web-config.omero.j2
docker/90-biomero-zarr-viewer.omero
docker/91-omero-web-zarr.omero
docker/Dockerfile.biomero
docker/Dockerfile.omeroweb
docker/Dockerfile.standalone
docker/check-http-zarr.py
docker/install-http-zarr.py
docker/nginx-biomero-zarr.conf
docker/nginx-local-proxy.conf
docker/provider-README.md
docker/standalone-constraints.txt
docs/api.md
docs/benchmark-cases-2026-10-17.json
docs/benchmark-loading-2026-10-17.md
docs/benchmark-results-2026-10-17.json
docs/compatibility-spike.md
docs/configuration.md
docs/data-and-registration.md
docs/deployment-nl-biomero.md
docs/deployment-omero-deployment-kit.md
docs/development.md
docs/http-zarr.md
docs/index.md
docs/installation.md
docs/large-volumes.md
docs/movies.md
docs/open-source-provenance.md
docs/publicdata-validation-2026-10-18.md
docs/release-0.8.0.md
docs/release-0.8.1.md
docs/requirements.txt
docs/review-2026-10-18.md
docs/review-loading-2026-10-18.json
docs/review-metadata-2026-10-18.json
docs/viewer-guide.md
docs/viv-wsi-performance-20261021.md
docs/assets/biomero-logo.svg
docs/assets/http-ngff-comparison-20261021.json
docs/assets/neuroglancer-startup-20261021.json
docs/assets/viv-wsi-performance-20261021.json
docs/publicdata-validation/data-validation.json
docs/publicdata-validation/loading-timings.json
docs/publicdata-validation/manifest.json
docs/publicdata-validation/movie-validation.json
frontend/package-lock.json
frontend/package.json
frontend/tsconfig.json
frontend/vite.config.ts
frontend/vite.neuroglancer.config.ts
frontend/neuroglancer/index.html
frontend/neuroglancer/mesh-clipping.ts
frontend/neuroglancer/viewer.css
frontend/neuroglancer/viewer.ts
frontend/scripts/benchmark-projections.mjs
frontend/scripts/clean-output.mjs
frontend/scripts/generate-third-party-notices.mjs
frontend/scripts/smoke-movie.mjs
frontend/scripts/smoke-neuroglancer-sections.mjs
frontend/src/App.integration.test.tsx
frontend/src/App.test.tsx
frontend/src/App.tsx
frontend/src/ApplicationBoundary.tsx
frontend/src/ChannelColorPicker.test.tsx
frontend/src/ChannelColorPicker.tsx
frontend/src/ClippingPlanes.test.tsx
frontend/src/ClippingPlanes.tsx
frontend/src/HelpWindow.test.tsx
frontend/src/HelpWindow.tsx
frontend/src/MetadataWindow.test.tsx
frontend/src/MetadataWindow.tsx
frontend/src/MovieBridge.tsx
frontend/src/MovieControls.test.tsx
frontend/src/MovieControls.tsx
frontend/src/NeuroglancerCanvas.test.tsx
frontend/src/NeuroglancerCanvas.tsx
frontend/src/OverviewGrid.tsx
frontend/src/ScaleBar.tsx
frontend/src/ViewerCanvas.test.tsx
frontend/src/ViewerCanvas.tsx
frontend/src/VivSectionsCanvas.tsx
frontend/src/VolumeCanvas.test.tsx
frontend/src/VolumeCanvas.tsx
frontend/src/VolumeViewControls.test.tsx
frontend/src/VolumeViewControls.tsx
frontend/src/api.test.ts
frontend/src/api.ts
frontend/src/authenticated-store.test.ts
frontend/src/authenticated-store.ts
frontend/src/browser-mesh-store.ts
frontend/src/browser-mesh.test.ts
frontend/src/browser-mesh.ts
frontend/src/calibration.ts
frontend/src/categorical-image-layer.test.ts
frontend/src/categorical-image-layer.ts
frontend/src/channel-scaling.test.ts
frontend/src/channel-scaling.ts
frontend/src/clipping.ts
frontend/src/http-read-cache.test.ts
frontend/src/http-read-cache.ts
frontend/src/image-cursor.test.ts
frontend/src/image-cursor.ts
frontend/src/instance-color-extension.test.ts
frontend/src/instance-color-extension.ts
frontend/src/label-color.test.ts
frontend/src/label-color.ts
frontend/src/label-inspection.test.ts
frontend/src/label-inspection.ts
frontend/src/label-projection.test.ts
frontend/src/label-projection.ts
frontend/src/main.tsx
frontend/src/mesh-clipping.test.ts
frontend/src/movie-encoder.worker.ts
frontend/src/movie-recipe.test.ts
frontend/src/movie-recipe.ts
frontend/src/movie-renderer.ts
frontend/src/multiplex-views.test.ts
frontend/src/multiplex-views.ts
frontend/src/native-samples.test.ts
frontend/src/native-samples.ts
frontend/src/navigation.test.ts
frontend/src/navigation.ts
frontend/src/neuroglancer-controls.test.ts
frontend/src/neuroglancer-controls.ts
frontend/src/neuroglancer-state.test.ts
frontend/src/neuroglancer-state.ts
frontend/src/ngff-physical-sizes.test.ts
frontend/src/ngff-physical-sizes.ts
frontend/src/orthographic-volume.test.ts
frontend/src/orthographic-volume.ts
frontend/src/physical-scale.ts
frontend/src/physical-tile.ts
frontend/src/plate-default-field.test.ts
frontend/src/plate-geometry.ts
frontend/src/plate.test.ts
frontend/src/preview-client.test.ts
frontend/src/preview-client.ts
frontend/src/preview-resolution.test.ts
frontend/src/preview-resolution.ts
frontend/src/preview-source.test.ts
frontend/src/preview-source.ts
frontend/src/projection-loader.test.ts
frontend/src/projection-loader.ts
frontend/src/pyramid-layers.test.ts
frontend/src/pyramid-layers.ts
frontend/src/read-cache-pixels.test.ts
frontend/src/shared-request.test.ts
frontend/src/shared-request.ts
frontend/src/store-read-gate.test.ts
frontend/src/store-read-gate.ts
frontend/src/styles.css
frontend/src/types.ts
frontend/src/use-image-cursor.ts
frontend/src/viewer-appearance.ts
frontend/src/viewer-context.test.ts
frontend/src/viewer-context.ts
frontend/src/viewer-state.test.ts
frontend/src/viewer-state.ts
frontend/src/virtual-chunk-cache.test.ts
frontend/src/virtual-chunk-cache.ts
frontend/src/vite-env.d.ts
frontend/src/viv-navigation.test.ts
frontend/src/viv-navigation.ts
frontend/src/viv-slices.test.ts
frontend/src/viv-slices.ts
frontend/src/volume-loader.test.ts
frontend/src/volume-loader.ts
frontend/src/volume-memory.test.tsx
frontend/src/volume-memory.tsx
frontend/src/volume-movie.test.ts
frontend/src/volume-movie.ts
frontend/src/volume-utils.test.ts
frontend/src/volume-utils.ts
frontend/src/test/setup.ts
scripts/benchmark_loading.py
scripts/benchmark_neuroglancer.mjs
scripts/build-docker-image.ps1
scripts/build_frontend.py
scripts/manage-docker-plugin.ps1
scripts/smoke-test.ps1
scripts/sync_analysis_skills.py
scripts/verify_wheel.py
src/biomero_zarr_viewer/__init__.py
src/biomero_zarr_viewer/analysis_skill_provider.py
src/biomero_zarr_viewer/apps.py
src/biomero_zarr_viewer/calibration.py
src/biomero_zarr_viewer/errors.py
src/biomero_zarr_viewer/http_source.py
src/biomero_zarr_viewer/http_statistics.py
src/biomero_zarr_viewer/metadata.py
src/biomero_zarr_viewer/metadata_details.py
src/biomero_zarr_viewer/neuroglancer.py
src/biomero_zarr_viewer/neuroglancer_contexts.py
src/biomero_zarr_viewer/physical_pixels.py
src/biomero_zarr_viewer/preview_cache.py
src/biomero_zarr_viewer/resolver.py
src/biomero_zarr_viewer/roi.py
src/biomero_zarr_viewer/settings.py
src/biomero_zarr_viewer/tokens.py
src/biomero_zarr_viewer/urls.py
src/biomero_zarr_viewer/vector_overlays.py
src/biomero_zarr_viewer/views.py
src/biomero_zarr_viewer/volume_cache.py
src/biomero_zarr_viewer.egg-info/PKG-INFO
src/biomero_zarr_viewer.egg-info/SOURCES.txt
src/biomero_zarr_viewer.egg-info/dependency_links.txt
src/biomero_zarr_viewer.egg-info/requires.txt
src/biomero_zarr_viewer.egg-info/scm_file_list.json
src/biomero_zarr_viewer.egg-info/scm_version.json
src/biomero_zarr_viewer.egg-info/top_level.txt
src/biomero_zarr_viewer/analysis_skills/use-omero-zarr-viewer/SKILL.md
src/biomero_zarr_viewer/analysis_skills/use-omero-zarr-viewer/references/REFERENCE.md
src/biomero_zarr_viewer/static/biomero_zarr_viewer/app.css
src/biomero_zarr_viewer/static/biomero_zarr_viewer/app.js
src/biomero_zarr_viewer/static/biomero_zarr_viewer/blosc-D1xNXZJs.js
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src/biomero_zarr_viewer/static/biomero_zarr_viewer/index-BnNK-MDH.js
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src/biomero_zarr_viewer/static/biomero_zarr_viewer/jpeg-NQwUIPY4.js
src/biomero_zarr_viewer/static/biomero_zarr_viewer/lerc-B2Wf11nu.js
src/biomero_zarr_viewer/static/biomero_zarr_viewer/lz4-1Ws5oVWR.js
src/biomero_zarr_viewer/static/biomero_zarr_viewer/lzw-D7iK439X.js
src/biomero_zarr_viewer/static/biomero_zarr_viewer/main-Bulu4T8V.js
src/biomero_zarr_viewer/static/biomero_zarr_viewer/openwith-v2.js
src/biomero_zarr_viewer/static/biomero_zarr_viewer/packbits-BN2Noezu.js
src/biomero_zarr_viewer/static/biomero_zarr_viewer/pako.esm-DLNJzcmj.js
src/biomero_zarr_viewer/static/biomero_zarr_viewer/raw-DNBozhfO.js
src/biomero_zarr_viewer/static/biomero_zarr_viewer/webimage-CKZXMzdz.js
src/biomero_zarr_viewer/static/biomero_zarr_viewer/zstd-C4EcZnjq.js
src/biomero_zarr_viewer/static/biomero_zarr_viewer/assets/movie-encoder.worker-CdGROEWz.js
src/biomero_zarr_viewer/static/biomero_zarr_viewer/neuroglancer/index.html
src/biomero_zarr_viewer/static/biomero_zarr_viewer/neuroglancer/assets/async_computation.bundle-zNIszY_L.js
src/biomero_zarr_viewer/static/biomero_zarr_viewer/neuroglancer/assets/blosc-CrUiACa7.js
src/biomero_zarr_viewer/static/biomero_zarr_viewer/neuroglancer/assets/chunk-INHXZS53-D3tQiqtZ.js
src/biomero_zarr_viewer/static/biomero_zarr_viewer/neuroglancer/assets/chunk_worker.bundle-BaiGaFj1.js
src/biomero_zarr_viewer/static/biomero_zarr_viewer/neuroglancer/assets/compresso-B_JvYEj-.wasm
src/biomero_zarr_viewer/static/biomero_zarr_viewer/neuroglancer/assets/index-BZCepui2.css
src/biomero_zarr_viewer/static/biomero_zarr_viewer/neuroglancer/assets/index-BoQ-OPiJ.js
src/biomero_zarr_viewer/static/biomero_zarr_viewer/neuroglancer/assets/jxl_decoder-4GmTkijA.wasm
src/biomero_zarr_viewer/static/biomero_zarr_viewer/neuroglancer/assets/libpng-KHGPusr3.wasm
src/biomero_zarr_viewer/static/biomero_zarr_viewer/neuroglancer/assets/neuroglancer_draco-DghDCUD5.wasm
src/biomero_zarr_viewer/static/biomero_zarr_viewer/neuroglancer/assets/zstd-u5eweWyS.js
src/biomero_zarr_viewer/templates/biomero_zarr_viewer/viewer.html
tests/__init__.py
tests/conftest.py
tests/fakes.py
tests/test_bundled_frontend.py
tests/test_external_info.py
tests/test_http_source.py
tests/test_http_statistics.py
tests/test_metadata.py
tests/test_metadata_details.py
tests/test_neuroglancer.py
tests/test_neuroglancer_contexts.py
tests/test_physical_tiles.py
tests/test_preview_cache.py
tests/test_resolver.py
tests/test_roi.py
tests/test_shallow_identity.py
tests/test_streaming.py
tests/test_tokens.py
tests/test_vector_overlays.py
tests/test_views.py
tests/test_volume_cache.py
tests/test_volume_selection.py
tests/zarr_helpers.py