Index

_

__all__ (in module ngff_zarr) __contains__() (ngff_zarr.hcs.LRUCache method) __enter__() (ngff_zarr.hcs.HCSPlateWriter method) __exit__() (ngff_zarr.hcs.HCSPlateWriter method) __getitem__() (ngff_zarr.hcs.LRUCache method) __setitem__() (ngff_zarr.hcs.LRUCache method) _align_chunks() (in module ngff_zarr.methods._support) _array_split() (in module ngff_zarr._array_split) _channel_dim_last() (in module ngff_zarr.methods._support) _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_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) _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) _extract_method_metadata() (in module ngff_zarr.parse_metadata) _extract_scale_translation() (in module ngff_zarr.lif_to_ngff_image) _finish() (ngff_zarr.rich_dask_progress.NgffProgressCallback method) _from_v04() (ngff_zarr.v05.zarr_metadata.Metadata class method) _from_v05() (ngff_zarr.v04.zarr_metadata.Metadata class method) _from_zarr_attrs() (ngff_zarr.v04.zarr_metadata.Metadata class method) (ngff_zarr.v05.zarr_metadata.Metadata class method) _get_block() (in module ngff_zarr.methods._support) _get_lif_image_data_delayed() (in module ngff_zarr.lif_to_ngff_image) _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)

_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) _large_image_serialization() (in module ngff_zarr.to_multiscales) _map_lif_dims_to_ngff() (in module ngff_zarr.lif_to_ngff_image) _matches_extension() (in module ngff_zarr.detect_cli_io_backend) _MAX_VECTOR_COMPONENTS (in module ngff_zarr.methods._itkwasm) _METHOD_INFO (in module ngff_zarr.methods._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) _numpy_to_zarr_dtype() (in module ngff_zarr.to_ngff_zarr) _parse_omero() (in module ngff_zarr.parse_metadata) _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) _reshape_for_flattened_channels() (in module ngff_zarr.lif_to_ngff_image) _spatial_dims (in module ngff_zarr.methods._support) _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) _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) _update_previous_dim_factors() (in module ngff_zarr.methods._support) _validate_ngff_parameters() (in module ngff_zarr.to_ngff_zarr) _write_array_direct() (in module ngff_zarr.to_ngff_zarr) _write_array_with_tensorstore() (in module ngff_zarr.to_ngff_zarr) _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) AnatomicalOrientation (class in ngff_zarr.rfc4)

AnatomicalOrientationValues (class in ngff_zarr.rfc4) anterior_to_posterior (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) axes (ngff_zarr.v04.zarr_metadata.Metadata attribute) (ngff_zarr.v05.zarr_metadata.Metadata 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)

C

cache_store (ngff_zarr.config.NgffZarrConfig attribute) caudal_to_cranial (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) caudal_to_rostral (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) channels (ngff_zarr.v04.zarr_metadata.Omero attribute) chunks (ngff_zarr.multiscales.Multiscales attribute) clear() (ngff_zarr.hcs.LRUCache method) cli_input_to_ngff_image() (in module ngff_zarr.cli_input_to_ngff_image) 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)

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) coordinateTransformations (ngff_zarr.v04.zarr_metadata.Dataset attribute) (ngff_zarr.v04.zarr_metadata.Metadata attribute) (ngff_zarr.v05.zarr_metadata.Metadata attribute) cranial_to_caudal (ngff_zarr.rfc4.AnatomicalOrientationValues attribute)

D

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) datasets (ngff_zarr.v04.zarr_metadata.Metadata attribute) (ngff_zarr.v05.zarr_metadata.Metadata attribute) decompose_affine_with_shear() (in module ngff_zarr.nibabel_image_to_ngff_image) 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) 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

end (ngff_zarr.v04.zarr_metadata.OmeroWindow attribute) endtime (ngff_zarr.v04.zarr_metadata.PlateAcquisition 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) from_hcs_zarr() (in module ngff_zarr.hcs)

from_ngff_zarr() (in module ngff_zarr.from_ngff_zarr) 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)

G

get() (ngff_zarr.hcs.LRUCache method) 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)

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) images (ngff_zarr.hcs.HCSWell property) (ngff_zarr.multiscales.Multiscales attribute) (ngff_zarr.v04.zarr_metadata.Well attribute) inferior_to_superior (ngff_zarr.rfc4.AnatomicalOrientationValues attribute)

is_dimension_supported() (in module ngff_zarr.v04.zarr_metadata) is_ozx_path() (in module ngff_zarr.rfc9_zip) is_rfc4_enabled() (in module ngff_zarr.rfc4) is_unit_supported() (in module ngff_zarr.v04.zarr_metadata) IS_ZARR_V3_PLUS (in module ngff_zarr.to_ngff_zarr) itk_image_to_ngff_image() (in module ngff_zarr.itk_image_to_ngff_image) itk_lps_to_anatomical_orientation() (in module ngff_zarr.rfc4)

L

label (ngff_zarr.v04.zarr_metadata.OmeroChannel attribute) LATEST (ngff_zarr._supported_versions.NgffVersion attribute) left_to_right (ngff_zarr.rfc4.AnatomicalOrientationValues 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) 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) metadata (ngff_zarr.multiscales.Multiscales attribute) (ngff_zarr.v04.zarr_metadata.Metadata attribute) (ngff_zarr.v05.zarr_metadata.Metadata attribute) method (ngff_zarr.multiscales.Multiscales attribute) (ngff_zarr.v04.zarr_metadata.MethodMetadata attribute) MethodMetadata (class in ngff_zarr.v04.zarr_metadata) Methods (in module 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.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.task_count 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.validate ngff_zarr.zarr_metadata

Multiscales (class in 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_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.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.task_count 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.validate module ngff_zarr.zarr_metadata module NgffImage (class in ngff_zarr.ngff_image) 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

Omero (class in ngff_zarr.v04.zarr_metadata) omero (ngff_zarr.v04.zarr_metadata.Metadata attribute) (ngff_zarr.v05.zarr_metadata.Metadata 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)

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) plantar_to_dorsal (ngff_zarr.rfc4.AnatomicalOrientationValues attribute) Plate (class in ngff_zarr.v04.zarr_metadata)

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) 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) 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) scale (ngff_zarr.ngff_image.NgffImage attribute) (ngff_zarr.v04.zarr_metadata.Scale attribute) scale_factors (ngff_zarr.multiscales.Multiscales 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) SpatialDims (in module ngff_zarr.v04.zarr_metadata) start (ngff_zarr.v04.zarr_metadata.OmeroWindow attribute) starttime (ngff_zarr.v04.zarr_metadata.PlateAcquisition 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) time_units (in module ngff_zarr.v04.zarr_metadata) TimeUnits (in module ngff_zarr.v04.zarr_metadata) 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_version() (ngff_zarr.v04.zarr_metadata.Metadata method) (ngff_zarr.v05.zarr_metadata.Metadata method)

Transform (in module ngff_zarr.v04.zarr_metadata) Translation (class in ngff_zarr.v04.zarr_metadata) translation (ngff_zarr.ngff_image.NgffImage attribute) (ngff_zarr.v04.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)

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) validate() (in module ngff_zarr.validate) validate_color() (ngff_zarr.v04.zarr_metadata.OmeroChannel method)

validate_rfc4_orientation() (in module ngff_zarr.rfc4_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) 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_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_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)