├── .gitattributes ├── .github ├── copilot-instructions.md └── workflows │ ├── mcp-ci.yml │ ├── python-pixi.yml │ ├── python.yml │ └── typescript.yml ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── AGENTS.md ├── DEVELOPMENT.md ├── LICENSE.txt ├── README.md ├── docs ├── .gitignore ├── Makefile ├── _static │ ├── favicon.png │ └── logo.png ├── cli.md ├── conf.py ├── development.md ├── faq.md ├── hcs.md ├── index.md ├── installation.md ├── itk.md ├── make.bat ├── mcp.md ├── methods.md ├── python.md ├── quick_start.md ├── requirements.txt ├── rfc4.md └── spec_features.md ├── mcp ├── .gitignore ├── CHANGELOG.md ├── README.md ├── examples │ ├── claude-desktop-config.json │ └── sse-config.json ├── ngff_zarr_mcp │ ├── __about__.py │ ├── __init__.py │ ├── models.py │ ├── server.py │ ├── tools.py │ └── utils.py ├── pixi.lock ├── pyproject.toml ├── test │ └── data │ │ └── input │ │ └── MR-head.nrrd └── tests │ ├── conftest.py │ ├── test_basic.py │ ├── test_convert_to_ome_zarr.py │ └── test_tensorstore_compression.py ├── py ├── .gitignore ├── README.md ├── ngff_zarr │ ├── __about__.py │ ├── __init__.py │ ├── _array_split.py │ ├── _zarr_kwargs.py │ ├── _zarr_open_array.py │ ├── cli.py │ ├── cli_input_to_ngff_image.py │ ├── config.py │ ├── detect_cli_io_backend.py │ ├── from_ngff_zarr.py │ ├── hcs.py │ ├── itk_image_to_ngff_image.py │ ├── memory_usage.py │ ├── methods │ │ ├── __init__.py │ │ ├── _dask_image.py │ │ ├── _itk.py │ │ ├── _itkwasm.py │ │ ├── _metadata.py │ │ └── _support.py │ ├── multiscales.py │ ├── ngff_image.py │ ├── ngff_image_to_itk_image.py │ ├── nibabel_image_to_ngff_image.py │ ├── rfc4.py │ ├── rfc4_validation.py │ ├── rfc9_zip.py │ ├── rich_dask_progress.py │ ├── spec │ │ ├── 0.1 │ │ │ ├── copyright.include │ │ │ └── schemas │ │ │ │ ├── image.schema │ │ │ │ ├── plate.schema │ │ │ │ ├── strict_image.schema │ │ │ │ └── well.schema │ │ ├── 0.2 │ │ │ ├── copyright.include │ │ │ └── schemas │ │ │ │ ├── image.schema │ │ │ │ ├── plate.schema │ │ │ │ └── well.schema │ │ ├── 0.3 │ │ │ ├── copyright.include │ │ │ └── schemas │ │ │ │ ├── image.schema │ │ │ │ ├── jsonld │ │ │ │ ├── context.json │ │ │ │ ├── frame.json │ │ │ │ └── shacl.ttl │ │ │ │ ├── plate.schema │ │ │ │ ├── salad_schema │ │ │ │ └── image.yml │ │ │ │ ├── strict_image.schema │ │ │ │ └── well.schema │ │ ├── 0.4 │ │ │ ├── copyright.include │ │ │ └── schemas │ │ │ │ ├── bf2raw.schema │ │ │ │ ├── image.schema │ │ │ │ ├── label.schema │ │ │ │ ├── ome.schema │ │ │ │ ├── plate.schema │ │ │ │ ├── strict_image.schema │ │ │ │ ├── strict_label.schema │ │ │ │ ├── strict_plate.schema │ │ │ │ ├── strict_well.schema │ │ │ │ └── well.schema │ │ ├── 0.5 │ │ │ ├── copyright.include │ │ │ └── schemas │ │ │ │ ├── _version.schema │ │ │ │ ├── bf2raw.schema │ │ │ │ ├── image.schema │ │ │ │ ├── label.schema │ │ │ │ ├── ome.schema │ │ │ │ ├── ome_zarr.schema │ │ │ │ ├── plate.schema │ │ │ │ ├── strict_image.schema │ │ │ │ ├── strict_label.schema │ │ │ │ ├── strict_plate.schema │ │ │ │ ├── strict_well.schema │ │ │ │ └── well.schema │ │ └── rfc │ │ │ └── 4 │ │ │ └── orientation.schema.json │ ├── task_count.py │ ├── to_multiscales.py │ ├── to_ngff_image.py │ ├── to_ngff_zarr.py │ ├── v04 │ │ ├── __init__.py │ │ └── zarr_metadata.py │ ├── v05 │ │ ├── __init__.py │ │ └── zarr_metadata.py │ ├── validate.py │ └── zarr_metadata.py ├── pixi.lock ├── pyproject.toml └── test │ ├── __init__.py │ ├── _data.py │ ├── conftest.py │ ├── test_cache_behavior.py │ ├── test_cli_input_to_ngff_image.py │ ├── test_convert_ome_zarr_version.py │ ├── test_detect_cli_input_backend.py │ ├── test_dimension_separator.py │ ├── test_direct_compression.py │ ├── test_from_ngff_zarr.py │ ├── test_from_ngff_zarr_tensorstore.py │ ├── test_hcs.py │ ├── test_hcs_cache.py │ ├── test_hcs_ozx.py │ ├── test_hcs_plate_writer.py │ ├── test_hcs_simple.py │ ├── test_hcs_zarr_format.py │ ├── test_index_out_of_range.py │ ├── test_itk_image_to_ngff_image.py │ ├── test_large_serialization.py │ ├── test_memory_usage.py │ ├── test_multiscales_metadata.py │ ├── test_multiscales_type.py │ ├── test_ngff_image_scale_factors.py │ ├── test_ngff_image_to_itk_image.py │ ├── test_ngff_validation.py │ ├── test_nibabel_image_to_ngff_image.py │ ├── test_nibabel_integration.py │ ├── test_omero.py │ ├── test_pyramid_integrity.py │ ├── test_rfc4.py │ ├── test_rfc4_integration.py │ ├── test_rfc4_integration_validation.py │ ├── test_rfc4_validation.py │ ├── test_rfc9_ozx.py │ ├── test_simple_cache.py │ ├── test_task_count.py │ ├── test_to_multiscales.py │ ├── test_to_multiscales_translate.py │ ├── test_to_ngff_zarr_dask_image.py │ ├── test_to_ngff_zarr_itk.py │ ├── test_to_ngff_zarr_itkwasm.py │ ├── test_to_ngff_zarr_kvikio.py │ ├── test_to_ngff_zarr_rfc2_zarr_v3.py │ ├── test_to_ngff_zarr_sharding.py │ ├── test_to_ngff_zarr_tensorstore.py │ ├── test_to_ngff_zarr_v3_compression.py │ ├── test_write_hcs_well_image_edge_cases.py │ └── test_write_store_to_zip.py └── ts ├── .gitignore ├── LICENSE.txt ├── README.md ├── deno.json ├── deno.lock ├── examples ├── ome_zarr_validation.ts └── zarrita_v0.5_example.ts ├── pixi.lock ├── pixi.toml ├── scripts ├── build.ts ├── build_npm.ts └── run_playwright.mjs ├── src ├── browser-mod.ts ├── io │ ├── from_ngff_zarr.ts │ ├── hcs.ts │ ├── itk_image_to_ngff_image.ts │ ├── ngff_image_to_itk_image.ts │ ├── to_multiscales.ts │ ├── to_ngff_image.ts │ └── to_ngff_zarr.ts ├── methods │ └── itkwasm.ts ├── mod.ts ├── schemas │ ├── coordinate_systems.ts │ ├── index.ts │ ├── methods.ts │ ├── multiscales.ts │ ├── ngff_image.ts │ ├── ome_zarr.ts │ ├── rfc4.ts │ ├── units.ts │ └── zarr_metadata.ts ├── types │ ├── array_interface.ts │ ├── hcs.ts │ ├── methods.ts │ ├── multiscales.ts │ ├── ngff_image.ts │ ├── rfc4.ts │ ├── units.ts │ └── zarr_metadata.ts └── utils │ ├── create_queue.ts │ ├── factory.ts │ ├── method_metadata.ts │ └── validation.ts └── test ├── baseline_comparison_test.ts ├── browser-npm ├── .gitignore ├── browser-test.html ├── bundle-test.html ├── direct-test.html ├── index.html ├── ngff-zarr.test.js ├── package-lock.json ├── package.json ├── playwright.config.js └── simple-test.html ├── browser └── server.ts ├── convert_ome_zarr_version_test.ts ├── from_ngff_zarr_test.ts ├── hcs_test.ts ├── itk_data_writing_test.ts ├── itk_image_to_ngff_image_simple_test.ts ├── itk_image_to_ngff_image_test.ts ├── itk_zarr_roundtrip_test.ts ├── ngff_image_to_itk_image_test.ts ├── omero_test.ts ├── rfc4_rfc5_schemas_test.ts ├── schemas └── test_ome_zarr.ts ├── schemas_extended_test.ts ├── schemas_test.ts ├── test_data_layout.ts ├── test_multiscales_metadata_test.ts ├── to_multiscales_itkwasm_test.ts ├── typed_array_support_test.ts ├── types_test.ts ├── utils_test.ts └── verify_against_baseline.ts /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/copilot-instructions.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/.github/copilot-instructions.md -------------------------------------------------------------------------------- /.github/workflows/mcp-ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/.github/workflows/mcp-ci.yml -------------------------------------------------------------------------------- /.github/workflows/python-pixi.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/.github/workflows/python-pixi.yml -------------------------------------------------------------------------------- /.github/workflows/python.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/.github/workflows/python.yml -------------------------------------------------------------------------------- /.github/workflows/typescript.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/.github/workflows/typescript.yml -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /AGENTS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/AGENTS.md -------------------------------------------------------------------------------- /DEVELOPMENT.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/DEVELOPMENT.md -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/README.md -------------------------------------------------------------------------------- /docs/.gitignore: -------------------------------------------------------------------------------- 1 | _build/ 2 | apidocs/ 3 | -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/_static/favicon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/_static/favicon.png -------------------------------------------------------------------------------- /docs/_static/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/_static/logo.png -------------------------------------------------------------------------------- /docs/cli.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/cli.md -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/development.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/development.md -------------------------------------------------------------------------------- /docs/faq.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/faq.md -------------------------------------------------------------------------------- /docs/hcs.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/hcs.md -------------------------------------------------------------------------------- /docs/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/index.md -------------------------------------------------------------------------------- /docs/installation.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/installation.md -------------------------------------------------------------------------------- /docs/itk.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/itk.md -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/mcp.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/mcp.md -------------------------------------------------------------------------------- /docs/methods.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/methods.md -------------------------------------------------------------------------------- /docs/python.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/python.md -------------------------------------------------------------------------------- /docs/quick_start.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/quick_start.md -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/requirements.txt -------------------------------------------------------------------------------- /docs/rfc4.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/rfc4.md -------------------------------------------------------------------------------- /docs/spec_features.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/docs/spec_features.md -------------------------------------------------------------------------------- /mcp/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/mcp/.gitignore -------------------------------------------------------------------------------- /mcp/CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/mcp/CHANGELOG.md -------------------------------------------------------------------------------- /mcp/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/mcp/README.md -------------------------------------------------------------------------------- /mcp/examples/claude-desktop-config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/mcp/examples/claude-desktop-config.json -------------------------------------------------------------------------------- /mcp/examples/sse-config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/mcp/examples/sse-config.json -------------------------------------------------------------------------------- /mcp/ngff_zarr_mcp/__about__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/mcp/ngff_zarr_mcp/__about__.py -------------------------------------------------------------------------------- /mcp/ngff_zarr_mcp/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/mcp/ngff_zarr_mcp/__init__.py -------------------------------------------------------------------------------- /mcp/ngff_zarr_mcp/models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/mcp/ngff_zarr_mcp/models.py -------------------------------------------------------------------------------- /mcp/ngff_zarr_mcp/server.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/mcp/ngff_zarr_mcp/server.py -------------------------------------------------------------------------------- /mcp/ngff_zarr_mcp/tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/mcp/ngff_zarr_mcp/tools.py -------------------------------------------------------------------------------- /mcp/ngff_zarr_mcp/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/mcp/ngff_zarr_mcp/utils.py -------------------------------------------------------------------------------- /mcp/pixi.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/mcp/pixi.lock -------------------------------------------------------------------------------- /mcp/pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/mcp/pyproject.toml -------------------------------------------------------------------------------- /mcp/test/data/input/MR-head.nrrd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/mcp/test/data/input/MR-head.nrrd -------------------------------------------------------------------------------- /mcp/tests/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/mcp/tests/conftest.py -------------------------------------------------------------------------------- /mcp/tests/test_basic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/mcp/tests/test_basic.py -------------------------------------------------------------------------------- /mcp/tests/test_convert_to_ome_zarr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/mcp/tests/test_convert_to_ome_zarr.py -------------------------------------------------------------------------------- /mcp/tests/test_tensorstore_compression.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/mcp/tests/test_tensorstore_compression.py -------------------------------------------------------------------------------- /py/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/.gitignore -------------------------------------------------------------------------------- /py/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/README.md -------------------------------------------------------------------------------- /py/ngff_zarr/__about__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/__about__.py -------------------------------------------------------------------------------- /py/ngff_zarr/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/__init__.py -------------------------------------------------------------------------------- /py/ngff_zarr/_array_split.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/_array_split.py -------------------------------------------------------------------------------- /py/ngff_zarr/_zarr_kwargs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/_zarr_kwargs.py -------------------------------------------------------------------------------- /py/ngff_zarr/_zarr_open_array.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/_zarr_open_array.py -------------------------------------------------------------------------------- /py/ngff_zarr/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/cli.py -------------------------------------------------------------------------------- /py/ngff_zarr/cli_input_to_ngff_image.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/cli_input_to_ngff_image.py -------------------------------------------------------------------------------- /py/ngff_zarr/config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/config.py -------------------------------------------------------------------------------- /py/ngff_zarr/detect_cli_io_backend.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/detect_cli_io_backend.py -------------------------------------------------------------------------------- /py/ngff_zarr/from_ngff_zarr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/from_ngff_zarr.py -------------------------------------------------------------------------------- /py/ngff_zarr/hcs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/hcs.py -------------------------------------------------------------------------------- /py/ngff_zarr/itk_image_to_ngff_image.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/itk_image_to_ngff_image.py -------------------------------------------------------------------------------- /py/ngff_zarr/memory_usage.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/memory_usage.py -------------------------------------------------------------------------------- /py/ngff_zarr/methods/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/methods/__init__.py -------------------------------------------------------------------------------- /py/ngff_zarr/methods/_dask_image.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/methods/_dask_image.py -------------------------------------------------------------------------------- /py/ngff_zarr/methods/_itk.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/methods/_itk.py -------------------------------------------------------------------------------- /py/ngff_zarr/methods/_itkwasm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/methods/_itkwasm.py -------------------------------------------------------------------------------- /py/ngff_zarr/methods/_metadata.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/methods/_metadata.py -------------------------------------------------------------------------------- /py/ngff_zarr/methods/_support.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/methods/_support.py -------------------------------------------------------------------------------- /py/ngff_zarr/multiscales.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/multiscales.py -------------------------------------------------------------------------------- /py/ngff_zarr/ngff_image.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/ngff_image.py -------------------------------------------------------------------------------- /py/ngff_zarr/ngff_image_to_itk_image.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/ngff_image_to_itk_image.py -------------------------------------------------------------------------------- /py/ngff_zarr/nibabel_image_to_ngff_image.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/nibabel_image_to_ngff_image.py -------------------------------------------------------------------------------- /py/ngff_zarr/rfc4.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/rfc4.py -------------------------------------------------------------------------------- /py/ngff_zarr/rfc4_validation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/rfc4_validation.py -------------------------------------------------------------------------------- /py/ngff_zarr/rfc9_zip.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/rfc9_zip.py -------------------------------------------------------------------------------- /py/ngff_zarr/rich_dask_progress.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/rich_dask_progress.py -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.1/copyright.include: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.1/copyright.include -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.1/schemas/image.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.1/schemas/image.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.1/schemas/plate.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.1/schemas/plate.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.1/schemas/strict_image.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.1/schemas/strict_image.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.1/schemas/well.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.1/schemas/well.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.2/copyright.include: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.2/copyright.include -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.2/schemas/image.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.2/schemas/image.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.2/schemas/plate.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.2/schemas/plate.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.2/schemas/well.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.2/schemas/well.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.3/copyright.include: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.3/copyright.include -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.3/schemas/image.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.3/schemas/image.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.3/schemas/jsonld/context.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.3/schemas/jsonld/context.json -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.3/schemas/jsonld/frame.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.3/schemas/jsonld/frame.json -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.3/schemas/jsonld/shacl.ttl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.3/schemas/jsonld/shacl.ttl -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.3/schemas/plate.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.3/schemas/plate.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.3/schemas/salad_schema/image.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.3/schemas/salad_schema/image.yml -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.3/schemas/strict_image.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.3/schemas/strict_image.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.3/schemas/well.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.3/schemas/well.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.4/copyright.include: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.4/copyright.include -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.4/schemas/bf2raw.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.4/schemas/bf2raw.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.4/schemas/image.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.4/schemas/image.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.4/schemas/label.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.4/schemas/label.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.4/schemas/ome.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.4/schemas/ome.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.4/schemas/plate.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.4/schemas/plate.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.4/schemas/strict_image.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.4/schemas/strict_image.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.4/schemas/strict_label.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.4/schemas/strict_label.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.4/schemas/strict_plate.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.4/schemas/strict_plate.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.4/schemas/strict_well.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.4/schemas/strict_well.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.4/schemas/well.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.4/schemas/well.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.5/copyright.include: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.5/copyright.include -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.5/schemas/_version.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.5/schemas/_version.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.5/schemas/bf2raw.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.5/schemas/bf2raw.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.5/schemas/image.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.5/schemas/image.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.5/schemas/label.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.5/schemas/label.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.5/schemas/ome.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.5/schemas/ome.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.5/schemas/ome_zarr.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.5/schemas/ome_zarr.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.5/schemas/plate.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.5/schemas/plate.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.5/schemas/strict_image.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.5/schemas/strict_image.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.5/schemas/strict_label.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.5/schemas/strict_label.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.5/schemas/strict_plate.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.5/schemas/strict_plate.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.5/schemas/strict_well.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.5/schemas/strict_well.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/0.5/schemas/well.schema: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/0.5/schemas/well.schema -------------------------------------------------------------------------------- /py/ngff_zarr/spec/rfc/4/orientation.schema.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/spec/rfc/4/orientation.schema.json -------------------------------------------------------------------------------- /py/ngff_zarr/task_count.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/task_count.py -------------------------------------------------------------------------------- /py/ngff_zarr/to_multiscales.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/to_multiscales.py -------------------------------------------------------------------------------- /py/ngff_zarr/to_ngff_image.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/to_ngff_image.py -------------------------------------------------------------------------------- /py/ngff_zarr/to_ngff_zarr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/to_ngff_zarr.py -------------------------------------------------------------------------------- /py/ngff_zarr/v04/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/v04/__init__.py -------------------------------------------------------------------------------- /py/ngff_zarr/v04/zarr_metadata.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/v04/zarr_metadata.py -------------------------------------------------------------------------------- /py/ngff_zarr/v05/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/v05/__init__.py -------------------------------------------------------------------------------- /py/ngff_zarr/v05/zarr_metadata.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/v05/zarr_metadata.py -------------------------------------------------------------------------------- /py/ngff_zarr/validate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/validate.py -------------------------------------------------------------------------------- /py/ngff_zarr/zarr_metadata.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/ngff_zarr/zarr_metadata.py -------------------------------------------------------------------------------- /py/pixi.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/pixi.lock -------------------------------------------------------------------------------- /py/pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/pyproject.toml -------------------------------------------------------------------------------- /py/test/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/__init__.py -------------------------------------------------------------------------------- /py/test/_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/_data.py -------------------------------------------------------------------------------- /py/test/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/conftest.py -------------------------------------------------------------------------------- /py/test/test_cache_behavior.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_cache_behavior.py -------------------------------------------------------------------------------- /py/test/test_cli_input_to_ngff_image.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_cli_input_to_ngff_image.py -------------------------------------------------------------------------------- /py/test/test_convert_ome_zarr_version.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_convert_ome_zarr_version.py -------------------------------------------------------------------------------- /py/test/test_detect_cli_input_backend.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_detect_cli_input_backend.py -------------------------------------------------------------------------------- /py/test/test_dimension_separator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_dimension_separator.py -------------------------------------------------------------------------------- /py/test/test_direct_compression.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_direct_compression.py -------------------------------------------------------------------------------- /py/test/test_from_ngff_zarr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_from_ngff_zarr.py -------------------------------------------------------------------------------- /py/test/test_from_ngff_zarr_tensorstore.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_from_ngff_zarr_tensorstore.py -------------------------------------------------------------------------------- /py/test/test_hcs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_hcs.py -------------------------------------------------------------------------------- /py/test/test_hcs_cache.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_hcs_cache.py -------------------------------------------------------------------------------- /py/test/test_hcs_ozx.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_hcs_ozx.py -------------------------------------------------------------------------------- /py/test/test_hcs_plate_writer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_hcs_plate_writer.py -------------------------------------------------------------------------------- /py/test/test_hcs_simple.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_hcs_simple.py -------------------------------------------------------------------------------- /py/test/test_hcs_zarr_format.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_hcs_zarr_format.py -------------------------------------------------------------------------------- /py/test/test_index_out_of_range.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_index_out_of_range.py -------------------------------------------------------------------------------- /py/test/test_itk_image_to_ngff_image.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_itk_image_to_ngff_image.py -------------------------------------------------------------------------------- /py/test/test_large_serialization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_large_serialization.py -------------------------------------------------------------------------------- /py/test/test_memory_usage.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_memory_usage.py -------------------------------------------------------------------------------- /py/test/test_multiscales_metadata.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_multiscales_metadata.py -------------------------------------------------------------------------------- /py/test/test_multiscales_type.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_multiscales_type.py -------------------------------------------------------------------------------- /py/test/test_ngff_image_scale_factors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_ngff_image_scale_factors.py -------------------------------------------------------------------------------- /py/test/test_ngff_image_to_itk_image.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_ngff_image_to_itk_image.py -------------------------------------------------------------------------------- /py/test/test_ngff_validation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_ngff_validation.py -------------------------------------------------------------------------------- /py/test/test_nibabel_image_to_ngff_image.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_nibabel_image_to_ngff_image.py -------------------------------------------------------------------------------- /py/test/test_nibabel_integration.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_nibabel_integration.py -------------------------------------------------------------------------------- /py/test/test_omero.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_omero.py -------------------------------------------------------------------------------- /py/test/test_pyramid_integrity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_pyramid_integrity.py -------------------------------------------------------------------------------- /py/test/test_rfc4.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_rfc4.py -------------------------------------------------------------------------------- /py/test/test_rfc4_integration.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_rfc4_integration.py -------------------------------------------------------------------------------- /py/test/test_rfc4_integration_validation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_rfc4_integration_validation.py -------------------------------------------------------------------------------- /py/test/test_rfc4_validation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_rfc4_validation.py -------------------------------------------------------------------------------- /py/test/test_rfc9_ozx.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_rfc9_ozx.py -------------------------------------------------------------------------------- /py/test/test_simple_cache.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_simple_cache.py -------------------------------------------------------------------------------- /py/test/test_task_count.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_task_count.py -------------------------------------------------------------------------------- /py/test/test_to_multiscales.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_to_multiscales.py -------------------------------------------------------------------------------- /py/test/test_to_multiscales_translate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_to_multiscales_translate.py -------------------------------------------------------------------------------- /py/test/test_to_ngff_zarr_dask_image.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_to_ngff_zarr_dask_image.py -------------------------------------------------------------------------------- /py/test/test_to_ngff_zarr_itk.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_to_ngff_zarr_itk.py -------------------------------------------------------------------------------- /py/test/test_to_ngff_zarr_itkwasm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_to_ngff_zarr_itkwasm.py -------------------------------------------------------------------------------- /py/test/test_to_ngff_zarr_kvikio.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_to_ngff_zarr_kvikio.py -------------------------------------------------------------------------------- /py/test/test_to_ngff_zarr_rfc2_zarr_v3.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_to_ngff_zarr_rfc2_zarr_v3.py -------------------------------------------------------------------------------- /py/test/test_to_ngff_zarr_sharding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_to_ngff_zarr_sharding.py -------------------------------------------------------------------------------- /py/test/test_to_ngff_zarr_tensorstore.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_to_ngff_zarr_tensorstore.py -------------------------------------------------------------------------------- /py/test/test_to_ngff_zarr_v3_compression.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_to_ngff_zarr_v3_compression.py -------------------------------------------------------------------------------- /py/test/test_write_hcs_well_image_edge_cases.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_write_hcs_well_image_edge_cases.py -------------------------------------------------------------------------------- /py/test/test_write_store_to_zip.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/py/test/test_write_store_to_zip.py -------------------------------------------------------------------------------- /ts/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/.gitignore -------------------------------------------------------------------------------- /ts/LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/LICENSE.txt -------------------------------------------------------------------------------- /ts/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/README.md -------------------------------------------------------------------------------- /ts/deno.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/deno.json -------------------------------------------------------------------------------- /ts/deno.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/deno.lock -------------------------------------------------------------------------------- /ts/examples/ome_zarr_validation.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/examples/ome_zarr_validation.ts -------------------------------------------------------------------------------- /ts/examples/zarrita_v0.5_example.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/examples/zarrita_v0.5_example.ts -------------------------------------------------------------------------------- /ts/pixi.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/pixi.lock -------------------------------------------------------------------------------- /ts/pixi.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/pixi.toml -------------------------------------------------------------------------------- /ts/scripts/build.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/scripts/build.ts -------------------------------------------------------------------------------- /ts/scripts/build_npm.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/scripts/build_npm.ts -------------------------------------------------------------------------------- /ts/scripts/run_playwright.mjs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/scripts/run_playwright.mjs -------------------------------------------------------------------------------- /ts/src/browser-mod.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/browser-mod.ts -------------------------------------------------------------------------------- /ts/src/io/from_ngff_zarr.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/io/from_ngff_zarr.ts -------------------------------------------------------------------------------- /ts/src/io/hcs.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/io/hcs.ts -------------------------------------------------------------------------------- /ts/src/io/itk_image_to_ngff_image.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/io/itk_image_to_ngff_image.ts -------------------------------------------------------------------------------- /ts/src/io/ngff_image_to_itk_image.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/io/ngff_image_to_itk_image.ts -------------------------------------------------------------------------------- /ts/src/io/to_multiscales.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/io/to_multiscales.ts -------------------------------------------------------------------------------- /ts/src/io/to_ngff_image.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/io/to_ngff_image.ts -------------------------------------------------------------------------------- /ts/src/io/to_ngff_zarr.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/io/to_ngff_zarr.ts -------------------------------------------------------------------------------- /ts/src/methods/itkwasm.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/methods/itkwasm.ts -------------------------------------------------------------------------------- /ts/src/mod.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/mod.ts -------------------------------------------------------------------------------- /ts/src/schemas/coordinate_systems.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/schemas/coordinate_systems.ts -------------------------------------------------------------------------------- /ts/src/schemas/index.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/schemas/index.ts -------------------------------------------------------------------------------- /ts/src/schemas/methods.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/schemas/methods.ts -------------------------------------------------------------------------------- /ts/src/schemas/multiscales.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/schemas/multiscales.ts -------------------------------------------------------------------------------- /ts/src/schemas/ngff_image.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/schemas/ngff_image.ts -------------------------------------------------------------------------------- /ts/src/schemas/ome_zarr.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/schemas/ome_zarr.ts -------------------------------------------------------------------------------- /ts/src/schemas/rfc4.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/schemas/rfc4.ts -------------------------------------------------------------------------------- /ts/src/schemas/units.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/schemas/units.ts -------------------------------------------------------------------------------- /ts/src/schemas/zarr_metadata.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/schemas/zarr_metadata.ts -------------------------------------------------------------------------------- /ts/src/types/array_interface.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/types/array_interface.ts -------------------------------------------------------------------------------- /ts/src/types/hcs.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/types/hcs.ts -------------------------------------------------------------------------------- /ts/src/types/methods.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/types/methods.ts -------------------------------------------------------------------------------- /ts/src/types/multiscales.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/types/multiscales.ts -------------------------------------------------------------------------------- /ts/src/types/ngff_image.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/types/ngff_image.ts -------------------------------------------------------------------------------- /ts/src/types/rfc4.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/types/rfc4.ts -------------------------------------------------------------------------------- /ts/src/types/units.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/types/units.ts -------------------------------------------------------------------------------- /ts/src/types/zarr_metadata.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/types/zarr_metadata.ts -------------------------------------------------------------------------------- /ts/src/utils/create_queue.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/utils/create_queue.ts -------------------------------------------------------------------------------- /ts/src/utils/factory.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/utils/factory.ts -------------------------------------------------------------------------------- /ts/src/utils/method_metadata.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/utils/method_metadata.ts -------------------------------------------------------------------------------- /ts/src/utils/validation.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/src/utils/validation.ts -------------------------------------------------------------------------------- /ts/test/baseline_comparison_test.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/baseline_comparison_test.ts -------------------------------------------------------------------------------- /ts/test/browser-npm/.gitignore: -------------------------------------------------------------------------------- 1 | test-results/ 2 | ngff-zarr.bundle.js 3 | -------------------------------------------------------------------------------- /ts/test/browser-npm/browser-test.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/browser-npm/browser-test.html -------------------------------------------------------------------------------- /ts/test/browser-npm/bundle-test.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/browser-npm/bundle-test.html -------------------------------------------------------------------------------- /ts/test/browser-npm/direct-test.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/browser-npm/direct-test.html -------------------------------------------------------------------------------- /ts/test/browser-npm/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/browser-npm/index.html -------------------------------------------------------------------------------- /ts/test/browser-npm/ngff-zarr.test.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/browser-npm/ngff-zarr.test.js -------------------------------------------------------------------------------- /ts/test/browser-npm/package-lock.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/browser-npm/package-lock.json -------------------------------------------------------------------------------- /ts/test/browser-npm/package.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/browser-npm/package.json -------------------------------------------------------------------------------- /ts/test/browser-npm/playwright.config.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/browser-npm/playwright.config.js -------------------------------------------------------------------------------- /ts/test/browser-npm/simple-test.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/browser-npm/simple-test.html -------------------------------------------------------------------------------- /ts/test/browser/server.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/browser/server.ts -------------------------------------------------------------------------------- /ts/test/convert_ome_zarr_version_test.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/convert_ome_zarr_version_test.ts -------------------------------------------------------------------------------- /ts/test/from_ngff_zarr_test.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/from_ngff_zarr_test.ts -------------------------------------------------------------------------------- /ts/test/hcs_test.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/hcs_test.ts -------------------------------------------------------------------------------- /ts/test/itk_data_writing_test.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/itk_data_writing_test.ts -------------------------------------------------------------------------------- /ts/test/itk_image_to_ngff_image_simple_test.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/itk_image_to_ngff_image_simple_test.ts -------------------------------------------------------------------------------- /ts/test/itk_image_to_ngff_image_test.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/itk_image_to_ngff_image_test.ts -------------------------------------------------------------------------------- /ts/test/itk_zarr_roundtrip_test.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/itk_zarr_roundtrip_test.ts -------------------------------------------------------------------------------- /ts/test/ngff_image_to_itk_image_test.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/ngff_image_to_itk_image_test.ts -------------------------------------------------------------------------------- /ts/test/omero_test.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/omero_test.ts -------------------------------------------------------------------------------- /ts/test/rfc4_rfc5_schemas_test.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/rfc4_rfc5_schemas_test.ts -------------------------------------------------------------------------------- /ts/test/schemas/test_ome_zarr.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/schemas/test_ome_zarr.ts -------------------------------------------------------------------------------- /ts/test/schemas_extended_test.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/schemas_extended_test.ts -------------------------------------------------------------------------------- /ts/test/schemas_test.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/schemas_test.ts -------------------------------------------------------------------------------- /ts/test/test_data_layout.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/test_data_layout.ts -------------------------------------------------------------------------------- /ts/test/test_multiscales_metadata_test.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/test_multiscales_metadata_test.ts -------------------------------------------------------------------------------- /ts/test/to_multiscales_itkwasm_test.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/to_multiscales_itkwasm_test.ts -------------------------------------------------------------------------------- /ts/test/typed_array_support_test.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/typed_array_support_test.ts -------------------------------------------------------------------------------- /ts/test/types_test.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/types_test.ts -------------------------------------------------------------------------------- /ts/test/utils_test.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/utils_test.ts -------------------------------------------------------------------------------- /ts/test/verify_against_baseline.ts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fideus-labs/ngff-zarr/HEAD/ts/test/verify_against_baseline.ts --------------------------------------------------------------------------------