.gitignore
LICENSE
README.md
buf.gen.yaml
buf.yaml
development.md
package.json
pnpm-lock.yaml
pnpm-workspace.yaml
pom.xml
pyproject.toml
.github/copilot-instructions.md
.github/workflows/buf-ci.yaml
.github/workflows/image-runtime-ci.yaml
.github/workflows/java-ci.yaml
.github/workflows/python-ci.yaml
.github/workflows/tensor-server-ci.yaml
biopb-image-runtime/Dockerfile
biopb-image-runtime/README.md
biopb-image-runtime/docker-compose.yaml
biopb-image-runtime/pyproject.toml
biopb-image-runtime/requirements.txt
biopb-image-runtime/scripts/build.sh
biopb-image-runtime/src/biopb_image_base/__init__.py
biopb-image-runtime/src/biopb_image_base/common.py
biopb-image-runtime/src/biopb_image_base/debug.py
biopb-image-runtime/src/biopb_image_base/dynamics_local.py
biopb-image-runtime/src/biopb_image_base/health.py
biopb-image-runtime/src/biopb_image_base/logging_config.py
biopb-image-runtime/src/biopb_image_base/mock_servicer.py
biopb-image-runtime/src/biopb_image_base/server.py
biopb-image-runtime/src/biopb_image_base/stitch.py
biopb-image-runtime/tests/__init__.py
biopb-image-runtime/tests/cli_test.py
biopb-image-runtime/tests/client.py
biopb-image-runtime/tests/conftest.py
biopb-image-runtime/tests/tensor_cache_test.py
biopb-image-runtime/tests/test_dynamics_local.py
biopb-image-runtime/tests/test_image.png
biopb-image-runtime/tests/test_service.py
biopb-image-runtime/tests/test_stitch.py
biopb-tensor-server/ARCHITECTURE.md
biopb-tensor-server/Dockerfile
biopb-tensor-server/README.md
biopb-tensor-server/containerize.md
biopb-tensor-server/entrypoint.sh
biopb-tensor-server/pyproject.toml
biopb-tensor-server/tsconfig.base.json
biopb-tensor-server/benchmarks/__init__.py
biopb-tensor-server/benchmarks/bench_cachefile.py
biopb-tensor-server/benchmarks/concurrent_read_test.py
biopb-tensor-server/benchmarks/conftest.py
biopb-tensor-server/benchmarks/discovery_scan_test.py
biopb-tensor-server/benchmarks/flight_throughput_test.py
biopb-tensor-server/benchmarks/metadata_db_integration_test.py
biopb-tensor-server/benchmarks/metadata_db_test.py
biopb-tensor-server/benchmarks/profile_steps.py
biopb-tensor-server/benchmarks/scan_syscalls_test.py
biopb-tensor-server/benchmarks/utils.py
biopb-tensor-server/benchmarks/data_sources/idr_embl_recommendations.md
biopb-tensor-server/benchmarks/data_sources/placeholder.json
biopb-tensor-server/benchmarks/data_sources/s3_public.json
biopb-tensor-server/benchmarks/data_sources/synthetic.json
biopb-tensor-server/biopb_tensor_server/__init__.py
biopb-tensor-server/biopb_tensor_server/__main__.py
biopb-tensor-server/biopb_tensor_server/base.py
biopb-tensor-server/biopb_tensor_server/chunk.py
biopb-tensor-server/biopb_tensor_server/cli.py
biopb-tensor-server/biopb_tensor_server/config.py
biopb-tensor-server/biopb_tensor_server/conftest.py
biopb-tensor-server/biopb_tensor_server/discovery.py
biopb-tensor-server/biopb_tensor_server/downsample.py
biopb-tensor-server/biopb_tensor_server/fixtures.py
biopb-tensor-server/biopb_tensor_server/http_server.py
biopb-tensor-server/biopb_tensor_server/logging_config.py
biopb-tensor-server/biopb_tensor_server/metadata_db.py
biopb-tensor-server/biopb_tensor_server/precache.py
biopb-tensor-server/biopb_tensor_server/remote.py
biopb-tensor-server/biopb_tensor_server/renderer.py
biopb-tensor-server/biopb_tensor_server/server.py
biopb-tensor-server/biopb_tensor_server/source_manager.py
biopb-tensor-server/biopb_tensor_server/watcher.py
biopb-tensor-server/biopb_tensor_server/adapters/__init__.py
biopb-tensor-server/biopb_tensor_server/adapters/aicsimageio.py
biopb-tensor-server/biopb_tensor_server/adapters/cached_source.py
biopb-tensor-server/biopb_tensor_server/adapters/dicom.py
biopb-tensor-server/biopb_tensor_server/adapters/hdf5.py
biopb-tensor-server/biopb_tensor_server/adapters/ndtiff.py
biopb-tensor-server/biopb_tensor_server/adapters/nifti.py
biopb-tensor-server/biopb_tensor_server/adapters/ome_zarr.py
biopb-tensor-server/biopb_tensor_server/adapters/tiff.py
biopb-tensor-server/biopb_tensor_server/adapters/zarr.py
biopb-tensor-server/biopb_tensor_server/cache/__init__.py
biopb-tensor-server/biopb_tensor_server/cache/base.py
biopb-tensor-server/biopb_tensor_server/cache/file_backend.py
biopb-tensor-server/biopb_tensor_server/cache/manager.py
biopb-tensor-server/biopb_tensor_server/cache/memory_backend.py
biopb-tensor-server/biopb_tensor_server/cache/recovery.py
biopb-tensor-server/packages/tensor-flight-client/TODO.md
biopb-tensor-server/packages/tensor-flight-client/package.json
biopb-tensor-server/packages/tensor-flight-client/tsconfig.json
biopb-tensor-server/packages/tensor-flight-client/vitest.config.ts
biopb-tensor-server/packages/tensor-flight-client/coverage/base.css
biopb-tensor-server/packages/tensor-flight-client/coverage/block-navigation.js
biopb-tensor-server/packages/tensor-flight-client/coverage/client.ts.html
biopb-tensor-server/packages/tensor-flight-client/coverage/clover.xml
biopb-tensor-server/packages/tensor-flight-client/coverage/coverage-final.json
biopb-tensor-server/packages/tensor-flight-client/coverage/favicon.png
biopb-tensor-server/packages/tensor-flight-client/coverage/index.html
biopb-tensor-server/packages/tensor-flight-client/coverage/prettify.css
biopb-tensor-server/packages/tensor-flight-client/coverage/prettify.js
biopb-tensor-server/packages/tensor-flight-client/coverage/sort-arrow-sprite.png
biopb-tensor-server/packages/tensor-flight-client/coverage/sorter.js
biopb-tensor-server/packages/tensor-flight-client/coverage/tensor-array.ts.html
biopb-tensor-server/packages/tensor-flight-client/src/client.test.ts
biopb-tensor-server/packages/tensor-flight-client/src/client.ts
biopb-tensor-server/packages/tensor-flight-client/src/index.ts
biopb-tensor-server/packages/tensor-flight-client/src/tensor-array.test.ts
biopb-tensor-server/packages/tensor-flight-client/src/tensor-array.ts
biopb-tensor-server/packages/tensor-flight-client/src/tensor-flight-client.ts
biopb-tensor-server/packages/tensor-flight-client/src/types.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/image/bindata_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/image/detection_request_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/image/detection_response_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/image/detection_settings_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/image/image_data_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/image/op_schema_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/image/roi_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/image/rpc_object_detection_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/image/rpc_process_image_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/annotation_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/bindata_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/dataset_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/detector_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/detector_setting_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/experiment_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/experimenter_group_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/experimenter_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/filter_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/filter_set_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/folder_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/image_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/instrument_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/light_source_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/light_source_setting_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/lightpath_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/manufacturer_spec_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/metadata_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/metadata_ref_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/microbeam_manipulation_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/microscope_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/objective_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/objective_setting_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/ome_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/pixel_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/plate_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/project_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/reagent_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/rights_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/roi_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/ome/screen_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/tensor/descriptor_pb.ts
biopb-tensor-server/packages/tensor-flight-client/src/gen/biopb/tensor/ticket_pb.ts
biopb-tensor-server/packages/web/index.html
biopb-tensor-server/packages/web/next.config.mjs
biopb-tensor-server/packages/web/package.json
biopb-tensor-server/packages/web/tsconfig.json
biopb-tensor-server/packages/web/vite.config.ts
biopb-tensor-server/packages/web/app/ClientBootstrap.tsx
biopb-tensor-server/packages/web/app/store.ts
biopb-tensor-server/packages/web/app/unlock/page.tsx
biopb-tensor-server/packages/web/src/ClientBootstrap.tsx
biopb-tensor-server/packages/web/src/index.css
biopb-tensor-server/packages/web/src/main.tsx
biopb-tensor-server/packages/web/src/store.ts
biopb-tensor-server/packages/web/src/components/ImageViewer.tsx
biopb-tensor-server/packages/web/src/components/MetaPanel.tsx
biopb-tensor-server/packages/web/src/components/SliceControls.tsx
biopb-tensor-server/packages/web/src/components/SourceTree.tsx
biopb-tensor-server/packages/web/src/hooks/useRenderWebSocket.ts
biopb-tensor-server/packages/web/src/pages/HomePage.tsx
biopb-tensor-server/packages/web/src/pages/UnlockPage.tsx
biopb-tensor-server/packages/web/src/utils/colorUtils.ts
biopb-tensor-server/packages/web/src/utils/regionUtils.ts
biopb-tensor-server/scripts/sync-version.js
biopb-tensor-server/tests/__init__.py
biopb-tensor-server/tests/adapter_integration_test.py
biopb-tensor-server/tests/adapter_unit_test.py
biopb-tensor-server/tests/cache_test.py
biopb-tensor-server/tests/cachefile_test.py
biopb-tensor-server/tests/cli_resolve_sources_test.py
biopb-tensor-server/tests/cli_test.py
biopb-tensor-server/tests/config_discovery_test.py
biopb-tensor-server/tests/conftest.py
biopb-tensor-server/tests/dicom_test.py
biopb-tensor-server/tests/discovery_claim_descent_test.py
biopb-tensor-server/tests/discovery_from_entries_test.py
biopb-tensor-server/tests/discovery_skip_test.py
biopb-tensor-server/tests/do_action_test.py
biopb-tensor-server/tests/health_status_test.py
biopb-tensor-server/tests/http_server_test.py
biopb-tensor-server/tests/list_flights_test.py
biopb-tensor-server/tests/multifield_test.py
biopb-tensor-server/tests/ndtiff_test.py
biopb-tensor-server/tests/nifti_test.py
biopb-tensor-server/tests/ome_metadata_cache_test.py
biopb-tensor-server/tests/precache_test.py
biopb-tensor-server/tests/register_source_test.py
biopb-tensor-server/tests/remote_test.py
biopb-tensor-server/tests/source_manager_test.py
biopb-tensor-server/tests/tensor_extended_test.py
biopb-tensor-server/tests/test_metadata_db.py
biopb-tensor-server/tests/tiff_sequence_test.py
biopb-tensor-server/tests/upload_test.py
biopb-tensor-server/tests/watcher_test.py
install/README.md
install/install.ps1
install/install.sh
install/test/Dockerfile.bioformats
install/test/Dockerfile.clean
install/test/Dockerfile.old-python
install/test/Dockerfile.rerun
install/test/Dockerfile.uv-preinstalled
install/test/run.sh
proto/biopb/image/bindata.proto
proto/biopb/image/detection_request.proto
proto/biopb/image/detection_response.proto
proto/biopb/image/detection_settings.proto
proto/biopb/image/image_data.proto
proto/biopb/image/op_schema.proto
proto/biopb/image/roi.proto
proto/biopb/image/rpc_object_detection.proto
proto/biopb/image/rpc_process_image.proto
proto/biopb/ome/annotation.proto
proto/biopb/ome/bindata.proto
proto/biopb/ome/dataset.proto
proto/biopb/ome/detector.proto
proto/biopb/ome/detector_setting.proto
proto/biopb/ome/experiment.proto
proto/biopb/ome/experimenter.proto
proto/biopb/ome/experimenter_group.proto
proto/biopb/ome/filter.proto
proto/biopb/ome/filter_set.proto
proto/biopb/ome/folder.proto
proto/biopb/ome/image.proto
proto/biopb/ome/instrument.proto
proto/biopb/ome/light_source.proto
proto/biopb/ome/light_source_setting.proto
proto/biopb/ome/lightpath.proto
proto/biopb/ome/manufacturer_spec.proto
proto/biopb/ome/metadata.proto
proto/biopb/ome/metadata_ref.proto
proto/biopb/ome/microbeam_manipulation.proto
proto/biopb/ome/microscope.proto
proto/biopb/ome/objective.proto
proto/biopb/ome/objective_setting.proto
proto/biopb/ome/ome.proto
proto/biopb/ome/pixel.proto
proto/biopb/ome/plate.proto
proto/biopb/ome/project.proto
proto/biopb/ome/reagent.proto
proto/biopb/ome/rights.proto
proto/biopb/ome/roi.proto
proto/biopb/ome/screen.proto
proto/biopb/tensor/descriptor.proto
proto/biopb/tensor/serialized.proto
proto/biopb/tensor/ticket.proto
src/VERSIONING.md
src/examples/README.md
src/examples/java/example-client/README.md
src/examples/java/example-client/pom.xml
src/examples/java/example-client/src/main/java/org/biopb/image/example/Client.java
src/examples/python/biopb-image-client/README.md
src/examples/python/biopb-image-client/biopb_image_client.py
src/examples/python/biopb-image-runtime/README.md
src/examples/python/biopb-image-runtime/minimal_cellpose_server.py
src/main/java/README.md
src/main/java/biopb/image/Utils.java
src/main/java/biopb/tensor/SerializableTensorImg.java
src/main/java/biopb/tensor/TensorConnectionPool.java
src/main/java/biopb/tensor/TensorFlightClient.java
src/main/python/build_proto.py
src/main/python/biopb/__init__.py
src/main/python/biopb/_version.py
src/main/python/biopb/cli.py
src/main/python/biopb.egg-info/PKG-INFO
src/main/python/biopb.egg-info/SOURCES.txt
src/main/python/biopb.egg-info/dependency_links.txt
src/main/python/biopb.egg-info/entry_points.txt
src/main/python/biopb.egg-info/requires.txt
src/main/python/biopb.egg-info/top_level.txt
src/main/python/biopb/image/__init__.py
src/main/python/biopb/image/cli.py
src/main/python/biopb/image/utils.py
src/main/python/biopb/tensor/__init__.py
src/main/python/biopb/tensor/cli.py
src/main/python/biopb/tensor/client.py
src/test/java/biopb/image/Imglib2OrderTest.java
src/test/java/biopb/image/UtilsTest.java
src/test/java/biopb/tensor/SerializableTensorImgTest.java
src/test/java/biopb/tensor/TensorConnectionPoolTest.java
src/test/java/biopb/tensor/TensorFlightClientTest.java
src/test/java/biopb/tensor/TensorFlightClientUtilTest.java
src/test/python/README.md
src/test/python/cli_test.py
src/test/python/client_util_test.py
src/test/python/connection_pool_test.py
src/test/python/grpc_services_test.py
src/test/python/image_test.py
src/test/python/roi_test.py
src/test/python/server_cli_test.py
src/test/python/tensor_test.py