Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W | Z _ __all__ (in module ngff_zarr) __contains__() (ngff_zarr.hcs.LRUCache method) __enter__() (ngff_zarr.hcs.HCSPlateWriter method) __exit__() (ngff_zarr.hcs.HCSPlateWriter method) __getattr__() (ngff_zarr.cli._ReplacingTextIO method) __getitem__() (ngff_zarr.hcs.LRUCache method) __post_init__() (ngff_zarr.v06.zarr_metadata.Metadata method) __setitem__() (ngff_zarr.hcs.LRUCache method) __str__() (ngff_zarr.structural_validation.ValidationError method) _align_chunks() (in module ngff_zarr.methods._support) _apply_blosc_codec_compat() (in module ngff_zarr.from_ngff_zarr) _apply_cli_metadata_overrides() (in module ngff_zarr.cli) _apply_omero_metadata() (in module ngff_zarr.cli) _array_split() (in module ngff_zarr._array_split) _array_write_error() (in module ngff_zarr.to_ngff_zarr) _axis_to_validation_dict() (in module ngff_zarr.structural_validation) _AXIS_TYPE_RANK (in module ngff_zarr.structural_validation) _build_console() (in module ngff_zarr.cli) _build_multiscales_from_pyramid() (in module ngff_zarr.tiff_to_ngff_image) _cache_1d_segments() (in module ngff_zarr.to_multiscales) _cache_2d_strips() (in module ngff_zarr.to_multiscales) _can_use_map_blocks_fast_path() (in module ngff_zarr.methods._support) _channel_dim_last() (in module ngff_zarr.methods._support) _channels_to_hex_colors() (in module ngff_zarr.tiff_to_ngff_image) _compute_channel_statistics() (in module ngff_zarr.compute_omero) _compute_itk_gaussian_kernel_radius() (in module ngff_zarr.methods._itk) _compute_next_scale() (in module ngff_zarr.methods._dask_image) _compute_next_translation() (in module ngff_zarr.methods._dask_image) _compute_plane_regions() (in module ngff_zarr.to_ngff_zarr) _compute_quantiles_approximate() (in module ngff_zarr.compute_omero) _compute_quantiles_dense() (in module ngff_zarr.compute_omero) _compute_sigma() (in module ngff_zarr.methods._support) _compute_write_regions() (in module ngff_zarr.to_ngff_zarr) _configure_sharding() (in module ngff_zarr.to_ngff_zarr) _create_zarr_root() (in module ngff_zarr.to_ngff_zarr) _DASK_USES_GROUP_CREATE (in module ngff_zarr.to_ngff_zarr) _delayed_lif_data() (in module ngff_zarr.lif_to_ngff_image) _DEPRECATED_BLOSC_KEYS (in module ngff_zarr.from_ngff_zarr) _detect_version() (in module ngff_zarr.parse_metadata) _dim_scale_factors() (in module ngff_zarr.methods._support) _downsample_dask_image() (in module ngff_zarr.methods._dask_image) _downsample_itk_bin_shrink() (in module ngff_zarr.methods._itk) _downsample_itk_gaussian() (in module ngff_zarr.methods._itk) _downsample_itkwasm() (in module ngff_zarr.methods._itkwasm) _dtype_to_component_type() (in module ngff_zarr.ngff_image_to_itk_image) _enumerate_fs_files() (in module ngff_zarr.rfc9_zip) _extract_array_from_group() (in module ngff_zarr.to_ngff_image) _extract_method_metadata() (in module ngff_zarr.parse_metadata) _extract_ome_channel_colors() (in module ngff_zarr.tiff_to_ngff_image) _extract_ome_channel_names() (in module ngff_zarr.tiff_to_ngff_image) _extract_ome_pixel_metadata() (in module ngff_zarr.tiff_to_ngff_image) _extract_scale_translation() (in module ngff_zarr.lif_to_ngff_image) _filter_axis_dict() (in module ngff_zarr.v04.zarr_metadata) _find_optimal_chunk_size() (in module ngff_zarr.to_multiscales) _finish() (ngff_zarr.rich_dask_progress.NgffProgressCallback method) _first_scale_vector() (in module ngff_zarr.structural_validation) _from_v04() (ngff_zarr.v05.zarr_metadata.Metadata class method) _from_v05() (ngff_zarr.v04.zarr_metadata.Metadata class method) (ngff_zarr.v06.zarr_metadata.Metadata class method) _from_v06() (ngff_zarr.v05.zarr_metadata.Metadata class method) _from_zarr_attrs() (ngff_zarr.v04.zarr_metadata.Metadata class method) (ngff_zarr.v05.zarr_metadata.Metadata class method) (ngff_zarr.v06.zarr_metadata.Metadata class method) _get_axis_fields() (in module ngff_zarr.v04.zarr_metadata) _get_bioformats2raw_series() (in module ngff_zarr.parse_metadata) _get_block() (in module ngff_zarr.methods._support) _get_lif_image_data_delayed() (in module ngff_zarr.lif_to_ngff_image) _get_store_root_path() (in module ngff_zarr.rfc9_zip) _get_truncate() (in module ngff_zarr.methods._dask_image) _handle_large_array_writing() (in module ngff_zarr.to_ngff_zarr) _image_dims (in module ngff_zarr.methods._itk) (in module ngff_zarr.methods._itkwasm) _is_bioformats2raw() (in module ngff_zarr.parse_metadata) _is_hcs_plate() (in module ngff_zarr.parse_metadata) _is_remote_store() (in module ngff_zarr.from_ngff_zarr) _itk_blur_and_downsample() (in module ngff_zarr.methods._itk) _itkwasm_blur_and_downsample() (in module ngff_zarr.methods._itkwasm) _itkwasm_chunk_bin_shrink() (in module ngff_zarr.methods._itkwasm) _itkwasm_chunk_bin_shrink_nd() (in module ngff_zarr.methods._itkwasm) _large_image_serialization() (in module ngff_zarr.to_multiscales) _lif_reopen_locator() (in module ngff_zarr.lif_to_ngff_image) _LPS_ORIENTATION_PAIRS (in module ngff_zarr.rfc4) _map_lif_dims_to_ngff() (in module ngff_zarr.lif_to_ngff_image) _map_tiff_axes_to_ngff() (in module ngff_zarr.tiff_to_ngff_image) _matches_extension() (in module ngff_zarr.detect_cli_io_backend) _MAX_SPATIAL_DIMENSIONS (in module ngff_zarr.rfc4) _MAX_VECTOR_COMPONENTS (in module ngff_zarr.methods._itkwasm) _METHOD_INFO (in module ngff_zarr.methods._metadata) _MULTISCALE_ENTRY_FIELDS (in module ngff_zarr.v04.zarr_metadata) _multiscales_to_ngff_zarr() (in module ngff_zarr.cli) _next_block_shape() (in module ngff_zarr.methods._support) _next_scale_metadata() (in module ngff_zarr.methods._support) _ngff_image_scale_factors() (in module ngff_zarr.to_multiscales) _ngff_image_to_multiscales() (in module ngff_zarr.cli) _normalize_unit() (in module ngff_zarr.tiff_to_ngff_image) _numcodecs_to_zarr_v3_codec() (in module ngff_zarr.to_ngff_zarr) _numpy_to_zarr_dtype() (in module ngff_zarr.to_ngff_zarr) _ome_color_int_to_hex() (in module ngff_zarr.tiff_to_ngff_image) _OMERO_STATS_LARGE_IMAGE_THRESHOLD (in module ngff_zarr.compute_omero) _OMERO_STATS_MIN_PIXELS (in module ngff_zarr.compute_omero) _order_files_rfc9() (in module ngff_zarr.rfc9_zip) _ORIENTATION_PRESETS (in module ngff_zarr.rfc4) _parse_hcs_path() (in module ngff_zarr.parse_metadata) _parse_omero() (in module ngff_zarr.parse_metadata) _parse_orientation_arg() (in module ngff_zarr.cli) _parse_transforms() (ngff_zarr.v06.zarr_metadata.Metadata class method) _PATH_ACCESS_ERRORS (in module ngff_zarr.tiff_to_ngff_image) _pop_metadata_optionals() (in module ngff_zarr.to_ngff_zarr) _posttask() (ngff_zarr.rich_dask_progress.NgffProgressCallback method) _prep_for_to_zarr() (in module ngff_zarr.to_ngff_zarr) _prepare_metadata() (in module ngff_zarr.to_ngff_zarr) _prepare_next_scale() (in module ngff_zarr.to_ngff_zarr) _prepare_zarr_kwargs() (in module ngff_zarr.to_ngff_zarr) _pretask() (ngff_zarr.rich_dask_progress.NgffProgressCallback method) _read_lif_image_array() (in module ngff_zarr.lif_to_ngff_image) _read_tiff_series() (in module ngff_zarr.tiff_to_ngff_image) _remote_backend_import_error() (in module ngff_zarr.from_ngff_zarr) _remove_none_values() (in module ngff_zarr.to_ngff_zarr) _ReplacingTextIO (class in ngff_zarr.cli) _reshape_for_flattened_channels() (in module ngff_zarr.lif_to_ngff_image) _reshape_tiff_for_channels() (in module ngff_zarr.tiff_to_ngff_image) _sanitize_series_name() (in module ngff_zarr.tiff_to_ngff_image) _select_image_for_omero_stats() (in module ngff_zarr.compute_omero) _series_output_target() (in module ngff_zarr.cli) _SPATIAL_AXIS_NAMES (in module ngff_zarr.structural_validation) _spatial_dims (in module ngff_zarr.methods._support) _SPATIAL_DIMS (in module ngff_zarr.tiff_to_ngff_image) _spatial_dims_last() (in module ngff_zarr.methods._support) _spatial_dims_last_zyx() (in module ngff_zarr.methods._support) _start() (ngff_zarr.rich_dask_progress.NgffProgressCallback method) _start_state() (ngff_zarr.rich_dask_progress.NgffProgressCallback method) _summarize_tiff_error_messages() (in module ngff_zarr.tiff_to_ngff_image) _tiff_open_error() (in module ngff_zarr.tiff_to_ngff_image) _TiffStructuralErrorHandler (class in ngff_zarr.tiff_to_ngff_image) _to_ngff_zarr_impl() (in module ngff_zarr.to_ngff_zarr) _to_v04() (ngff_zarr.v05.zarr_metadata.Metadata method) _to_v05() (ngff_zarr.v04.zarr_metadata.Metadata method) (ngff_zarr.v06.zarr_metadata.Metadata method) _to_v06() (ngff_zarr.v05.zarr_metadata.Metadata method) _transform_len_mismatch() (in module ngff_zarr.structural_validation) _update_previous_dim_factors() (in module ngff_zarr.methods._support) _validate_color() (in module ngff_zarr.compute_omero) _validate_ngff_parameters() (in module ngff_zarr.to_ngff_zarr) _validate_quantiles() (in module ngff_zarr.compute_omero) _write_array_direct() (in module ngff_zarr.to_ngff_zarr) _write_array_with_tensorstore() (in module ngff_zarr.to_ngff_zarr) _write_rfc9_comment() (in module ngff_zarr.rfc9_zip) _write_with_tensorstore() (in module ngff_zarr.to_ngff_zarr) A acquisition (ngff_zarr.v04.zarr_metadata.WellImage attribute) acquisitions (ngff_zarr.hcs.HCSPlate property) (ngff_zarr.v04.zarr_metadata.Plate attribute) add_anatomical_orientation_to_axis() (in module ngff_zarr.rfc4) add_cache_task() (ngff_zarr.rich_dask_progress.NgffProgress method) add_callback_task() (ngff_zarr.rich_dask_progress.NgffProgressCallback method) add_multiscales_task() (ngff_zarr.rich_dask_progress.NgffProgress method) Affine (class in ngff_zarr.v06.zarr_metadata) affine (ngff_zarr.v06.zarr_metadata.Affine attribute) allow_unknown_fields (ngff_zarr.structural_validation.ValidateOptions attribute) anatomical_orientation_to_itk_direction() (in module ngff_zarr.rfc4) AnatomicalOrientation (class in ngff_zarr.rfc4) AnatomicalOrientationValues (class in ngff_zarr.rfc4) anterior_to_posterior (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) apex_to_base (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) apical_to_basal (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) axes (ngff_zarr.v04.zarr_metadata.Metadata attribute) (ngff_zarr.v05.zarr_metadata.Metadata attribute) (ngff_zarr.v06.zarr_metadata.CoordinateSystem attribute) axes_orientations (ngff_zarr.ngff_image.NgffImage attribute) axes_units (ngff_zarr.ngff_image.NgffImage attribute) AxesType (in module ngff_zarr.v04.zarr_metadata) Axis (class in ngff_zarr.v04.zarr_metadata) AXIS_COUNT (ngff_zarr.structural_validation.SpecRule attribute) AXIS_ORDER (ngff_zarr.structural_validation.SpecRule attribute) AXIS_ORIENTATION_COMPLETENESS (ngff_zarr.structural_validation.SpecRule attribute) AXIS_ORIENTATION_CONSISTENT_TYPE (ngff_zarr.structural_validation.SpecRule attribute) AXIS_TYPE (ngff_zarr.structural_validation.SpecRule attribute) B basal_to_apical (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) base_to_apex (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) BaseTransform (class in ngff_zarr.v06.zarr_metadata) C cache_store (ngff_zarr.config.NgffZarrConfig attribute) caudal_to_cranial (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) caudal_to_rostral (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) channel_colors (ngff_zarr.ngff_image.NgffImage attribute) channel_names (ngff_zarr.ngff_image.NgffImage attribute) channels (ngff_zarr.v04.zarr_metadata.Omero attribute) chunks (ngff_zarr.multiscales.NgffMultiscales attribute) clear() (ngff_zarr.hcs.LRUCache method) cli_input_to_ngff_image() (in module ngff_zarr.cli_input_to_ngff_image) codec_from_name() (in module ngff_zarr.codecs) color (ngff_zarr.v04.zarr_metadata.OmeroChannel attribute) column_index (ngff_zarr.hcs.HCSWell property) columnIndex (ngff_zarr.v04.zarr_metadata.PlateWell attribute) columns (ngff_zarr.hcs.HCSPlate property) (ngff_zarr.v04.zarr_metadata.Plate attribute) compute_omero_from_multiscales() (in module ngff_zarr.compute_omero) compute_omero_from_ngff_image() (in module ngff_zarr.compute_omero) computed_callbacks (ngff_zarr.ngff_image.NgffImage attribute) ComputedCallback (in module ngff_zarr.ngff_image) config (in module ngff_zarr.config) conversion_backends (in module ngff_zarr.detect_cli_io_backend) conversion_backends_values (in module ngff_zarr.detect_cli_io_backend) ConversionBackend (in module ngff_zarr.detect_cli_io_backend) CoordinateSystem (class in ngff_zarr.v06.zarr_metadata) CoordinateSystemIdentifier (class in ngff_zarr.v06.zarr_metadata) coordinateSystems (ngff_zarr.v06.zarr_metadata.Metadata attribute) coordinateTransformations (ngff_zarr.v04.zarr_metadata.Dataset attribute) (ngff_zarr.v04.zarr_metadata.Metadata attribute) (ngff_zarr.v05.zarr_metadata.Metadata attribute) (ngff_zarr.v06.zarr_metadata.Dataset attribute) (ngff_zarr.v06.zarr_metadata.Metadata attribute) cranial_to_caudal (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) D DASK_IMAGE_GAUSSIAN (ngff_zarr.methods.Methods attribute) DASK_IMAGE_MODE (ngff_zarr.methods.Methods attribute) DASK_IMAGE_NEAREST (ngff_zarr.methods.Methods attribute) DASK_SUPPORTS_SHARDING (in module ngff_zarr.to_ngff_zarr) data (ngff_zarr.ngff_image.NgffImage attribute) Dataset (class in ngff_zarr.v04.zarr_metadata) (class in ngff_zarr.v06.zarr_metadata) DATASET_ORDER_HIGHEST_TO_LOWEST (ngff_zarr.structural_validation.SpecRule attribute) datasets (ngff_zarr.v04.zarr_metadata.Metadata attribute) (ngff_zarr.v05.zarr_metadata.Metadata attribute) (ngff_zarr.v06.zarr_metadata.Metadata attribute) decompose_affine_with_shear() (in module ngff_zarr.nibabel_image_to_ngff_image) deep_to_superficial (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) default_store_factory() (in module ngff_zarr.config) description (ngff_zarr.v04.zarr_metadata.MethodMetadata attribute) (ngff_zarr.v04.zarr_metadata.PlateAcquisition attribute) detect_cli_io_backend() (in module ngff_zarr.detect_cli_io_backend) dimension_names (ngff_zarr.v04.zarr_metadata.Metadata property) (ngff_zarr.v05.zarr_metadata.Metadata property) (ngff_zarr.v06.zarr_metadata.Metadata property) dims (ngff_zarr.ngff_image.NgffImage attribute) distal_to_proximal (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) dorsal_to_palmar (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) dorsal_to_plantar (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) dorsal_to_ventral (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) E emit() (ngff_zarr.tiff_to_ngff_image._TiffStructuralErrorHandler method) end (ngff_zarr.v04.zarr_metadata.OmeroWindow attribute) endtime (ngff_zarr.v04.zarr_metadata.PlateAcquisition attribute) extra (ngff_zarr.v04.zarr_metadata.Metadata attribute) (ngff_zarr.v05.zarr_metadata.Metadata attribute) (ngff_zarr.v06.zarr_metadata.Metadata attribute) extract_omero_metadata_from_nibabel() (in module ngff_zarr.nibabel_image_to_ngff_image) extract_spatial_metadata() (in module ngff_zarr.nibabel_image_to_ngff_image) F field_count (ngff_zarr.hcs.HCSPlate property) (ngff_zarr.v04.zarr_metadata.Plate attribute) flush() (ngff_zarr.cli._ReplacingTextIO method) from_dict() (ngff_zarr.v06.zarr_metadata.BaseTransform class method) from_hcs_zarr() (in module ngff_zarr.hcs) from_ngff_zarr (in module ngff_zarr.from_ngff_zarr) from_ome_zarr() (in module ngff_zarr.from_ngff_zarr) (ngff_zarr.multiscales.NgffMultiscales class method) from_store() (ngff_zarr.hcs.HCSWell class method) from_version() (ngff_zarr.v04.zarr_metadata.Metadata class method) (ngff_zarr.v05.zarr_metadata.Metadata class method) (ngff_zarr.v06.zarr_metadata.Metadata class method) G get() (ngff_zarr.hcs.LRUCache method) get_available_codecs() (in module ngff_zarr.codecs) get_default_colors() (in module ngff_zarr.compute_omero) get_image() (ngff_zarr.hcs.HCSWell method) get_image_by_acquisition() (ngff_zarr.hcs.HCSWell method) get_method_metadata() (in module ngff_zarr.methods._metadata) get_well() (ngff_zarr.hcs.HCSPlate method) get_well_by_indices() (ngff_zarr.hcs.HCSPlate method) GLASBEY_COLORS (in module ngff_zarr.compute_omero) GLOBAL_COORD_TRANSFORM_AFTER_PER_LEVEL (ngff_zarr.structural_validation.SpecRule attribute) H has_mosaic_dimension() (in module ngff_zarr.lif_to_ngff_image) has_rfc4_orientation_metadata() (in module ngff_zarr.rfc4_validation) hcs_image_cache_size (ngff_zarr.config.NgffZarrConfig attribute) hcs_well_cache_size (ngff_zarr.config.NgffZarrConfig attribute) HCSPlate (class in ngff_zarr.hcs) HCSPlateWriter (class in ngff_zarr.hcs) HCSWell (class in ngff_zarr.hcs) I id (ngff_zarr.v04.zarr_metadata.PlateAcquisition attribute) Identity (class in ngff_zarr.v04.zarr_metadata) (class in ngff_zarr.v06.zarr_metadata) images (ngff_zarr.hcs.HCSWell property) (ngff_zarr.multiscales.NgffMultiscales attribute) (ngff_zarr.v04.zarr_metadata.Well attribute) inferior_to_superior (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) input (ngff_zarr.v06.zarr_metadata.BaseTransform attribute) intrinsic_coordinate_system (ngff_zarr.v06.zarr_metadata.Metadata property) is_dimension_supported() (in module ngff_zarr.v04.zarr_metadata) is_ozx_path() (in module ngff_zarr.rfc9_zip) is_unit_supported() (in module ngff_zarr.v04.zarr_metadata) IS_ZARR_V3_PLUS (in module ngff_zarr.to_ngff_zarr) ITK_BIN_SHRINK (ngff_zarr.methods.Methods attribute) itk_direction_to_anatomical_orientation() (in module ngff_zarr.rfc4) ITK_GAUSSIAN (ngff_zarr.methods.Methods attribute) itk_image_to_ngff_image() (in module ngff_zarr.itk_image_to_ngff_image) itk_lps_to_anatomical_orientation() (in module ngff_zarr.rfc4) ITKWASM_BIN_SHRINK (ngff_zarr.methods.Methods attribute) ITKWASM_GAUSSIAN (ngff_zarr.methods.Methods attribute) ITKWASM_LABEL_IMAGE (ngff_zarr.methods.Methods attribute) L label (ngff_zarr.v04.zarr_metadata.OmeroChannel attribute) LATEST (ngff_zarr._supported_versions.NgffVersion attribute) left_to_right (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) level (ngff_zarr.structural_validation.ValidateOptions attribute) LIF_DIM_TO_NGFF (in module ngff_zarr.lif_to_ngff_image) lif_file_to_ngff_images() (in module ngff_zarr.lif_to_ngff_image) lif_to_hcs_plate() (in module ngff_zarr.lif_to_ngff_image) lif_to_ngff_image() (in module ngff_zarr.lif_to_ngff_image) load_rfc4_orientation_schema() (in module ngff_zarr.rfc4_validation) load_schema() (in module ngff_zarr.validate) logger (in module ngff_zarr.v04.zarr_metadata) LPS (in module ngff_zarr.rfc4) LRUCache (class in ngff_zarr.hcs) M main() (in module ngff_zarr.cli) max (ngff_zarr.v04.zarr_metadata.OmeroWindow attribute) maximumfieldcount (ngff_zarr.v04.zarr_metadata.PlateAcquisition attribute) memory_target (ngff_zarr.config.NgffZarrConfig attribute) memory_usage() (in module ngff_zarr.memory_usage) Metadata (class in ngff_zarr.v04.zarr_metadata) (class in ngff_zarr.v05.zarr_metadata) (class in ngff_zarr.v06.zarr_metadata) metadata (ngff_zarr.multiscales.NgffMultiscales attribute) (ngff_zarr.v04.zarr_metadata.Metadata attribute) (ngff_zarr.v05.zarr_metadata.Metadata attribute) (ngff_zarr.v06.zarr_metadata.Metadata attribute) method (ngff_zarr.multiscales.NgffMultiscales attribute) (ngff_zarr.v04.zarr_metadata.MethodMetadata attribute) MethodMetadata (class in ngff_zarr.v04.zarr_metadata) Methods (class in ngff_zarr.methods) methods (in module ngff_zarr.methods) methods_values (in module ngff_zarr.methods) min (ngff_zarr.v04.zarr_metadata.OmeroWindow attribute) module ngff_zarr ngff_zarr._array_split ngff_zarr._supported_versions ngff_zarr._zarr_kwargs ngff_zarr._zarr_open_array ngff_zarr._zarr_types ngff_zarr.cli ngff_zarr.cli_input_to_ngff_image ngff_zarr.codecs ngff_zarr.compute_omero ngff_zarr.config ngff_zarr.detect_cli_io_backend ngff_zarr.from_ngff_zarr ngff_zarr.hcs ngff_zarr.itk_image_to_ngff_image ngff_zarr.lif_to_ngff_image ngff_zarr.memory_usage ngff_zarr.methods ngff_zarr.methods._dask_image ngff_zarr.methods._itk ngff_zarr.methods._itkwasm ngff_zarr.methods._metadata ngff_zarr.methods._support ngff_zarr.multiscales ngff_zarr.ngff_image ngff_zarr.ngff_image_to_itk_image ngff_zarr.nibabel_image_to_ngff_image ngff_zarr.parse_metadata ngff_zarr.rfc4 ngff_zarr.rfc4_validation ngff_zarr.rfc9_zip ngff_zarr.rich_dask_progress ngff_zarr.structural_validation ngff_zarr.task_count ngff_zarr.tiff_to_ngff_image ngff_zarr.to_multiscales ngff_zarr.to_ngff_image ngff_zarr.to_ngff_zarr ngff_zarr.v04 ngff_zarr.v04.zarr_metadata ngff_zarr.v05 ngff_zarr.v05.zarr_metadata ngff_zarr.v06 ngff_zarr.v06.zarr_metadata ngff_zarr.validate ngff_zarr.zarr_metadata Multiscales (in module ngff_zarr.multiscales) N name (ngff_zarr.hcs.HCSPlate property) (ngff_zarr.ngff_image.NgffImage attribute) (ngff_zarr.v04.zarr_metadata.Axis attribute) (ngff_zarr.v04.zarr_metadata.Metadata attribute) (ngff_zarr.v04.zarr_metadata.Plate attribute) (ngff_zarr.v04.zarr_metadata.PlateAcquisition attribute) (ngff_zarr.v04.zarr_metadata.PlateColumn attribute) (ngff_zarr.v04.zarr_metadata.PlateRow attribute) (ngff_zarr.v05.zarr_metadata.Metadata attribute) (ngff_zarr.v06.zarr_metadata.BaseTransform attribute) (ngff_zarr.v06.zarr_metadata.CoordinateSystem attribute) (ngff_zarr.v06.zarr_metadata.CoordinateSystemIdentifier attribute) (ngff_zarr.v06.zarr_metadata.Metadata attribute) (ngff_zarr.v06.zarr_metadata.TransformSequence attribute) ngff_image_to_itk_image() (in module ngff_zarr.ngff_image_to_itk_image) NGFF_URI (in module ngff_zarr.validate) ngff_zarr module ngff_zarr._array_split module ngff_zarr._supported_versions module ngff_zarr._zarr_kwargs module ngff_zarr._zarr_open_array module ngff_zarr._zarr_types module ngff_zarr.cli module ngff_zarr.cli_input_to_ngff_image module ngff_zarr.codecs module ngff_zarr.compute_omero module ngff_zarr.config module ngff_zarr.detect_cli_io_backend module ngff_zarr.from_ngff_zarr module ngff_zarr.hcs module ngff_zarr.itk_image_to_ngff_image module ngff_zarr.lif_to_ngff_image module ngff_zarr.memory_usage module ngff_zarr.methods module ngff_zarr.methods._dask_image module ngff_zarr.methods._itk module ngff_zarr.methods._itkwasm module ngff_zarr.methods._metadata module ngff_zarr.methods._support module ngff_zarr.multiscales module ngff_zarr.ngff_image module ngff_zarr.ngff_image_to_itk_image module ngff_zarr.nibabel_image_to_ngff_image module ngff_zarr.parse_metadata module ngff_zarr.rfc4 module ngff_zarr.rfc4_validation module ngff_zarr.rfc9_zip module ngff_zarr.rich_dask_progress module ngff_zarr.structural_validation module ngff_zarr.task_count module ngff_zarr.tiff_to_ngff_image module ngff_zarr.to_multiscales module ngff_zarr.to_ngff_image module ngff_zarr.to_ngff_zarr module ngff_zarr.v04 module ngff_zarr.v04.zarr_metadata module ngff_zarr.v05 module ngff_zarr.v05.zarr_metadata module ngff_zarr.v06 module ngff_zarr.v06.zarr_metadata module ngff_zarr.validate module ngff_zarr.zarr_metadata module NgffImage (class in ngff_zarr.ngff_image) NgffMultiscales (class in ngff_zarr.multiscales) NgffProgress (class in ngff_zarr.rich_dask_progress) NgffProgressCallback (class in ngff_zarr.rich_dask_progress) NgffVersion (class in ngff_zarr._supported_versions) NgffZarrConfig (class in ngff_zarr.config) nibabel_image_to_ngff_image() (in module ngff_zarr.nibabel_image_to_ngff_image) O OME_NAMESPACE (ngff_zarr.structural_validation.SpecRule attribute) OME_UNIT_TO_NGFF (in module ngff_zarr.tiff_to_ngff_image) Omero (class in ngff_zarr.v04.zarr_metadata) omero (ngff_zarr.v04.zarr_metadata.Metadata attribute) (ngff_zarr.v05.zarr_metadata.Metadata attribute) (ngff_zarr.v06.zarr_metadata.Metadata attribute) OMERO_CHANNEL_COLOR_FORMAT (ngff_zarr.structural_validation.SpecRule attribute) OmeroChannel (class in ngff_zarr.v04.zarr_metadata) OmeroWindow (class in ngff_zarr.v04.zarr_metadata) open_array (in module ngff_zarr._zarr_open_array) orientation (ngff_zarr.v04.zarr_metadata.Axis attribute) orientation_from_name() (in module ngff_zarr.rfc4) output (ngff_zarr.v06.zarr_metadata.BaseTransform attribute) P palmar_to_dorsal (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) path (ngff_zarr.v04.zarr_metadata.Dataset attribute) (ngff_zarr.v04.zarr_metadata.PlateWell attribute) (ngff_zarr.v04.zarr_metadata.WellImage attribute) (ngff_zarr.v06.zarr_metadata.Affine attribute) (ngff_zarr.v06.zarr_metadata.CoordinateSystemIdentifier attribute) (ngff_zarr.v06.zarr_metadata.Dataset attribute) (ngff_zarr.v06.zarr_metadata.Rotation attribute) plantar_to_dorsal (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) Plate (class in ngff_zarr.v04.zarr_metadata) PLATE_ROW_INDEX_CONSISTENCY (ngff_zarr.structural_validation.SpecRule attribute) PlateAcquisition (class in ngff_zarr.v04.zarr_metadata) PlateColumn (class in ngff_zarr.v04.zarr_metadata) PlateRow (class in ngff_zarr.v04.zarr_metadata) PlateWell (class in ngff_zarr.v04.zarr_metadata) posterior_to_anterior (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) proximal_to_distal (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) R RAS (in module ngff_zarr.rfc4) read_ozx_json_first() (in module ngff_zarr.rfc9_zip) read_ozx_version() (in module ngff_zarr.rfc9_zip) REMOTE_FS_PROTOCOLS (in module ngff_zarr.from_ngff_zarr) REMOTE_URL_SCHEMES (in module ngff_zarr.from_ngff_zarr) remove_anatomical_orientation_from_axis() (in module ngff_zarr.rfc4) right_to_left (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) rostral_to_caudal (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) Rotation (class in ngff_zarr.v06.zarr_metadata) rotation (ngff_zarr.v06.zarr_metadata.Rotation attribute) row_index (ngff_zarr.hcs.HCSWell property) rowIndex (ngff_zarr.v04.zarr_metadata.PlateWell attribute) rows (ngff_zarr.hcs.HCSPlate property) (ngff_zarr.v04.zarr_metadata.Plate attribute) S Scale (class in ngff_zarr.v04.zarr_metadata) (class in ngff_zarr.v06.zarr_metadata) scale (ngff_zarr.ngff_image.NgffImage attribute) (ngff_zarr.v04.zarr_metadata.Scale attribute) (ngff_zarr.v06.zarr_metadata.Scale attribute) scale_factors (ngff_zarr.multiscales.NgffMultiscales attribute) SCALE_LENGTH_MISMATCH (ngff_zarr.structural_validation.SpecRule attribute) ScaleStrategy (in module ngff_zarr.to_ngff_zarr) SCHEMA_ONLY (ngff_zarr.structural_validation.ValidationLevel attribute) set() (ngff_zarr.hcs.LRUCache method) space_units (in module ngff_zarr.v04.zarr_metadata) SpaceUnits (in module ngff_zarr.v04.zarr_metadata) SPATIAL_DIMS (in module ngff_zarr.lif_to_ngff_image) (in module ngff_zarr.tiff_to_ngff_image) SpatialDims (in module ngff_zarr.v04.zarr_metadata) SpecRule (class in ngff_zarr.structural_validation) start (ngff_zarr.v04.zarr_metadata.OmeroWindow attribute) starttime (ngff_zarr.v04.zarr_metadata.PlateAcquisition attribute) STRICT (ngff_zarr.structural_validation.ValidationLevel attribute) superficial_to_deep (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) superior_to_inferior (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) supported_dims (in module ngff_zarr.v04.zarr_metadata) SUPPORTED_VERSIONS (in module ngff_zarr._supported_versions) SupportedDims (in module ngff_zarr.v04.zarr_metadata) T task_count() (in module ngff_zarr.task_count) task_target (ngff_zarr.config.NgffZarrConfig attribute) TIFF_AXIS_TO_NGFF (in module ngff_zarr.tiff_to_ngff_image) TIFF_CHANNEL_AXES (in module ngff_zarr.tiff_to_ngff_image) tiff_file_to_ngff_images() (in module ngff_zarr.tiff_to_ngff_image) time_units (in module ngff_zarr.v04.zarr_metadata) TimeUnits (in module ngff_zarr.v04.zarr_metadata) to_dict() (ngff_zarr.v06.zarr_metadata.BaseTransform method) to_hcs_zarr() (in module ngff_zarr.hcs) to_multiscales() (in module ngff_zarr.to_multiscales) to_ngff_image() (in module ngff_zarr.to_ngff_image) to_ngff_zarr (in module ngff_zarr.to_ngff_zarr) to_ome_zarr() (in module ngff_zarr.to_ngff_zarr) (ngff_zarr.multiscales.NgffMultiscales method) to_version() (ngff_zarr.v04.zarr_metadata.Metadata method) (ngff_zarr.v05.zarr_metadata.Metadata method) (ngff_zarr.v06.zarr_metadata.Metadata method) Transform (in module ngff_zarr.v04.zarr_metadata) (in module ngff_zarr.v06.zarr_metadata) transformations (ngff_zarr.v06.zarr_metadata.TransformSequence attribute) TransformSequence (class in ngff_zarr.v06.zarr_metadata) Translation (class in ngff_zarr.v04.zarr_metadata) (class in ngff_zarr.v06.zarr_metadata) translation (ngff_zarr.ngff_image.NgffImage attribute) (ngff_zarr.v04.zarr_metadata.Translation attribute) (ngff_zarr.v06.zarr_metadata.Translation attribute) type (ngff_zarr.rfc4.AnatomicalOrientation attribute) (ngff_zarr.v04.zarr_metadata.Axis attribute) (ngff_zarr.v04.zarr_metadata.Identity attribute) (ngff_zarr.v04.zarr_metadata.Metadata attribute) (ngff_zarr.v04.zarr_metadata.Scale attribute) (ngff_zarr.v04.zarr_metadata.Translation attribute) (ngff_zarr.v05.zarr_metadata.Metadata attribute) (ngff_zarr.v06.zarr_metadata.Affine attribute) (ngff_zarr.v06.zarr_metadata.BaseTransform attribute) (ngff_zarr.v06.zarr_metadata.Identity attribute) (ngff_zarr.v06.zarr_metadata.Metadata attribute) (ngff_zarr.v06.zarr_metadata.Rotation attribute) (ngff_zarr.v06.zarr_metadata.Scale attribute) (ngff_zarr.v06.zarr_metadata.TransformSequence attribute) (ngff_zarr.v06.zarr_metadata.Translation attribute) U unit (ngff_zarr.v04.zarr_metadata.Axis attribute) Units (in module ngff_zarr.v04.zarr_metadata) update_cache_task_completed() (ngff_zarr.rich_dask_progress.NgffProgress method) update_multiscales_task_completed() (ngff_zarr.rich_dask_progress.NgffProgress method) V V01 (ngff_zarr._supported_versions.NgffVersion attribute) V02 (ngff_zarr._supported_versions.NgffVersion attribute) V03 (ngff_zarr._supported_versions.NgffVersion attribute) V04 (ngff_zarr._supported_versions.NgffVersion attribute) V05 (ngff_zarr._supported_versions.NgffVersion attribute) V06 (ngff_zarr._supported_versions.NgffVersion attribute) V06dev4 (ngff_zarr._supported_versions.NgffVersion attribute) validate() (in module ngff_zarr.validate) validate_axis_count() (in module ngff_zarr.structural_validation) validate_axis_order() (in module ngff_zarr.structural_validation) validate_axis_orientation() (in module ngff_zarr.structural_validation) validate_axis_type() (in module ngff_zarr.structural_validation) validate_color() (ngff_zarr.v04.zarr_metadata.OmeroChannel method) validate_dataset_order() (in module ngff_zarr.structural_validation) validate_ome_namespace() (in module ngff_zarr.structural_validation) validate_omero_color_hex() (in module ngff_zarr.structural_validation) validate_per_dataset_scale_count() (in module ngff_zarr.structural_validation) validate_plate() (in module ngff_zarr.structural_validation) validate_plate_well_index_consistency() (in module ngff_zarr.structural_validation) validate_rfc4_orientation() (in module ngff_zarr.rfc4_validation) validate_scale_length() (in module ngff_zarr.structural_validation) validate_spatial_axis_order() (in module ngff_zarr.structural_validation) validate_structural() (in module ngff_zarr.structural_validation) validate_transform_order() (in module ngff_zarr.structural_validation) validate_well() (in module ngff_zarr.structural_validation) validate_well_acquisition() (in module ngff_zarr.structural_validation) validate_zarr_format_for_version() (in module ngff_zarr.structural_validation) ValidateOptions (class in ngff_zarr.structural_validation) ValidationError ValidationLevel (class in ngff_zarr.structural_validation) value (ngff_zarr.rfc4.AnatomicalOrientation attribute) ventral_to_dorsal (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) version (ngff_zarr.v04.zarr_metadata.Metadata attribute) (ngff_zarr.v04.zarr_metadata.MethodMetadata attribute) (ngff_zarr.v04.zarr_metadata.Plate attribute) (ngff_zarr.v04.zarr_metadata.Well attribute) W Well (class in ngff_zarr.v04.zarr_metadata) WELL_ACQUISITION_MISSING (ngff_zarr.structural_validation.SpecRule attribute) WellImage (class in ngff_zarr.v04.zarr_metadata) wells (ngff_zarr.hcs.HCSPlate property) (ngff_zarr.v04.zarr_metadata.Plate attribute) window (ngff_zarr.v04.zarr_metadata.OmeroChannel attribute) write() (ngff_zarr.cli._ReplacingTextIO method) write_hcs_well_image() (in module ngff_zarr.hcs) write_store_to_zip() (in module ngff_zarr.rfc9_zip) write_well_image() (ngff_zarr.hcs.HCSPlateWriter method) Z ZARR_FORMAT (ngff_zarr.structural_validation.SpecRule attribute) zarr_version (in module ngff_zarr._zarr_kwargs) (in module ngff_zarr._zarr_open_array) (in module ngff_zarr.from_ngff_zarr) (in module ngff_zarr.to_ngff_zarr) zarr_version_major (in module ngff_zarr.from_ngff_zarr)