Index

_

__enter__() (Omero.Omero method) (OmeroLabelReader.OmeroLabelReader method) __exit__() (Omero.Omero method) (OmeroLabelReader.OmeroLabelReader method) __getitem__() (XmlDict.XmlDict method) (XmlDict.XmlList method) __iter__() (XmlDict.XmlList method) __next__() (XmlDict.XmlList method) _asarray_level() (BioSource.BioSource method) (GeneratorSource.GeneratorSource method) (OmeroSource.OmeroSource method) (OmeSource.OmeSource method) (OmeZarrSource.OmeZarrSource method) (PlainImageSource.PlainImageSource method) (TiffSource.TiffSource method) _connect() (Omero.Omero method) _decode() (TiffSource.TiffSource method) _decompress() (TiffSource.TiffSource method)

_disconnect() (Omero.Omero method) _find_metadata() (BioSource.BioSource method) (GeneratorSource.GeneratorSource method) (OmeroSource.OmeroSource method) (OmeSource.OmeSource method) (OmeZarrSource.OmeZarrSource method) (PlainImageSource.PlainImageSource method) (TiffSource.TiffSource method) _get_dataset() (Omero.Omero method) _get_dataset_images() (Omero.Omero method) _get_image_annotations() (Omero.Omero method) _get_ome_metadata() (OmeSource.OmeSource method) _get_project() (Omero.Omero method) _init_metadata() (OmeSource.OmeSource method) _init_sizes() (OmeSource.OmeSource method) _load_as_dask() (TiffSource.TiffSource method) _load_as_zarr() (TiffSource.TiffSource method) _segments() (TiffSource.TiffSource method) _switch_user_group() (Omero.Omero method)

A

arrays (PlainImageSource.PlainImageSource attribute) (TiffSource.TiffSource attribute)

asarray() (OmeSource.OmeSource method) asarray_um() (OmeSource.OmeSource method) asdask() (OmeSource.OmeSource method)

B

bio_ome_metadata (BioSource.BioSource attribute) BioSource module

BioSource (class in BioSource) blur_image() (in module image_util) blur_image_single() (in module image_util)

C

calc_color() (GeneratorSource.GeneratorSource method) calc_fraction_used() (in module image_util) calc_pyramid() (in module image_util) calc_tiles_median() (in module image_util) calc_tiles_quantiles() (in module image_util) ChannelOperation (class in parameters) channels (OmeSource.OmeSource attribute) check_image() (in module conversion) check_round_significants() (in module util) check_versions() (in module image_util) chunk_shapes (OmeZarrSource.OmeZarrSource attribute) clear_arrays() (TiffSource.TiffSource method) clone_empty() (OmeSource.OmeSource method) close() (BioSource.BioSource method) (Omero.Omero method) (OmeroSource.OmeroSource method) (OmeSource.OmeSource method) (TiffSource.TiffSource method) close_javabridge() (in module BioSource) color_conversion module color_value_table (GeneratorSource.GeneratorSource attribute) COMBINE (parameters.ChannelOperation attribute) combine_images() (in module conversion) compare_image() (in module image_util)

compare_image_dist() (in module image_util) compare_image_dist_simple() (in module image_util) compressed (TiffSource.TiffSource attribute) connected (Omero.Omero attribute) conversion module convert_image() (in module conversion) convert_image_sign_type() (in module image_util) convert_rational_value() (in module util) copy() (XmlDict.XmlDict method) create() (Zarr.Zarr method) create_axes_metadata() (in module ome_zarr_util) create_channel_metadata() (in module ome_zarr_util) create_compression_codecs() (in module image_util) create_compression_filter() (in module image_util) create_credentials_file() (in module omero_credentials) create_label_csv() (OmeroLabelReader.OmeroLabelReader method) create_ome_metadata() (in module ome_metadata) create_ome_metadata_from_omero() (in module omero_metadata) create_pixels_store() (Omero.Omero method) create_source() (in module conversion) create_transformation_metadata() (in module ome_zarr_util) create_xml_metadata() (OmeroSource.OmeroSource method) (OmeSource.OmeSource method) credentials_filename (Omero.Omero attribute)

D

data (TiffSource.TiffSource attribute) (Zarr.Zarr attribute) dct (in module XmlDict) decompress() (TiffSource.TiffSource method) decompressed (TiffSource.TiffSource attribute) decrypt_credentials() (in module omero_credentials) default_physical_unit (OmeSource.OmeSource attribute) default_properties_order (OmeSource.OmeSource attribute)

desc_to_dict() (in module util) dict2xml() (in module XmlDict) dimension_order (BioSource.BioSource attribute) (OmeroSource.OmeroSource attribute) (OmeSource.OmeSource attribute) (PlainImageSource.PlainImageSource attribute) (TiffSource.TiffSource attribute) dtype (GeneratorSource.GeneratorSource attribute)

E

ensure_list() (in module util) ensure_unsigned_image() (in module image_util)

ensure_unsigned_type() (in module image_util) executor (TiffSource.TiffSource attribute) extract_thumbnail() (in module conversion)

F

fh (TiffSource.TiffSource attribute) file_to_dict() (in module util) filename (BioSource.BioSource attribute) (OmeZarr.OmeZarr attribute) (OmeZarrSource.OmeZarrSource attribute) (PlainImageSource.PlainImageSource attribute) (TiffSource.TiffSource attribute) (Zarr.Zarr attribute)

filter_dict() (in module util) first_page (TiffSource.TiffSource attribute) float2int_image() (in module image_util)

G

generate_asymmetric_keys() (in module omero_credentials) GeneratorSource module GeneratorSource (class in GeneratorSource) get() (XmlDict.XmlDict method) (Zarr.Zarr method) get_annotation_image_ids() (Omero.Omero method) get_best_level_factor() (in module OmeSource) get_best_size() (in module OmeSource) get_channel_window() (OmeSource.OmeSource method) get_channels() (OmeSource.OmeSource method) get_default() (in module util) get_dimension_order() (OmeSource.OmeSource method) get_filetitle() (in module util) get_image_annotation() (Omero.Omero method) get_image_info() (in module conversion) get_image_object() (Omero.Omero method) get_image_quantile() (in module image_util) get_image_size_info() (in module image_util) get_mag() (OmeSource.OmeSource method) get_metadata() (OmeSource.OmeSource method) get_nchannels() (OmeSource.OmeSource method) get_numpy_slicing() (in module image_util)

get_physical_size() (OmeSource.OmeSource method) get_pil_metadata() (in module image_util) get_pixel_nbytes() (OmeSource.OmeSource method) get_pixel_size() (OmeSource.OmeSource method) get_pixel_size_micrometer() (OmeSource.OmeSource method) get_pixel_type() (OmeSource.OmeSource method) get_position() (OmeSource.OmeSource method) get_position_micrometer() (OmeSource.OmeSource method) get_resolution_from_pixel_size() (in module OmeSource) get_rotation() (OmeSource.OmeSource method) get_shape() (OmeSource.OmeSource method) get_size() (OmeSource.OmeSource method) get_size_xyzct() (OmeSource.OmeSource method) get_source_dask() (OmeSource.OmeSource method) (OmeZarrSource.OmeZarrSource method) (TiffSource.TiffSource method) get_source_image() (in module conversion) get_source_image_chunked() (in module conversion) get_source_image_dask() (in module conversion) get_thumbnail() (OmeroSource.OmeroSource method) (OmeSource.OmeSource method) get_tiff_pages() (in module image_util) get_tile() (GeneratorSource.GeneratorSource method) get_value_units_micrometer() (in module util)

H

has_ome_metadata (OmeSource.OmeSource attribute)

hexrgb_to_rgba() (in module color_conversion)

I

image (PlainImageSource.PlainImageSource attribute) IMAGE_DIR (in module parameters) image_id (OmeroSource.OmeroSource attribute) image_object (OmeroSource.OmeroSource attribute) image_reshape() (in module image_util) image_resize() (in module image_util) image_util module indexes (BioSource.BioSource attribute)

init() (Omero.Omero method) int2float_image() (in module image_util) int_to_rgba() (in module color_conversion) is_rgb (BioSource.BioSource attribute) (GeneratorSource.GeneratorSource attribute) (OmeroSource.OmeroSource attribute) (OmeZarrSource.OmeZarrSource attribute) (PlainImageSource.PlainImageSource attribute) (TiffSource.TiffSource attribute)

J

javabridge_open (in module BioSource)

L

level_scales (OmeZarrSource.OmeZarrSource attribute) levels (OmeZarrSource.OmeZarrSource attribute)

load() (PlainImageSource.PlainImageSource method) (TiffSource.TiffSource method) loaded (PlainImageSource.PlainImageSource attribute)

M

manage_omero (OmeroLabelReader.OmeroLabelReader attribute) metadata (BioSource.BioSource attribute) (OmeSource.OmeSource attribute) (PlainImageSource.PlainImageSource attribute) module BioSource color_conversion conversion GeneratorSource image_util ome_metadata ome_zarr_util Omero omero_credentials omero_metadata OmeroLabelReader OmeroSource OmeSource OmeZarr OmeZarrSource parameters PlainImageSource TiffSource util XmlDict Zarr

N

NONE (parameters.ChannelOperation attribute)

normalise_values() (in module image_util)

O

ome_metadata module OME_SCHEMA_LOC (in module ome_metadata) (in module omero_metadata) OME_URI (in module ome_metadata) (in module omero_metadata) OME_XSI (in module ome_metadata) (in module omero_metadata) ome_zarr_util module Omero module Omero (class in Omero) omero (OmeroLabelReader.OmeroLabelReader attribute) (OmeroSource.OmeroSource attribute) omero_credentials module omero_metadata module

OmeroLabelReader module OmeroLabelReader (class in OmeroLabelReader) OmeroSource module OmeroSource (class in OmeroSource) OmeSource module OmeSource (class in OmeSource) OmeZarr module OmeZarr (class in OmeZarr) OmeZarrSource module OmeZarrSource (class in OmeZarrSource) open_javabridge() (in module BioSource) output_dimension_order (OmeSource.OmeSource attribute)

P

pages (TiffSource.TiffSource attribute) PARAMETER_FILE (in module parameters) parameters module params (Omero.Omero attribute) (OmeroLabelReader.OmeroLabelReader attribute) pilmode_to_pixelinfo() (in module image_util) pixel_nbits (OmeSource.OmeSource attribute) (PlainImageSource.PlainImageSource attribute) pixel_types (GeneratorSource.GeneratorSource attribute) (OmeSource.OmeSource attribute) (PlainImageSource.PlainImageSource attribute)

pixels_store (OmeroSource.OmeroSource attribute) pixels_store_pyramid_order (OmeroSource.OmeroSource attribute) PlainImageSource module PlainImageSource (class in PlainImageSource) position (OmeSource.OmeSource attribute) precise_resize() (in module image_util) print_dict() (in module util) print_hbytes() (in module util) print_omero_object() (in module Omero) print_projects() (Omero.Omero method) private_key_filename (Omero.Omero attribute) produce_chunks() (OmeSource.OmeSource method)

R

reader (BioSource.BioSource attribute) redimension_data() (in module image_util) render() (OmeSource.OmeSource method) reorder() (in module util)

RESOURCE_DIR (in module parameters) rgba_to_hexrgb() (in module color_conversion) rgba_to_int() (in module color_conversion) rotation (OmeSource.OmeSource attribute) round_significants() (in module util)

S

save_image() (in module image_util) save_image_as_ome_zarr() (in module conversion) save_image_as_tiff() (in module conversion) save_image_as_zarr() (in module conversion) save_tiff() (in module conversion) scale_dimensions_dict() (in module ome_zarr_util) scale_dimensions_xy() (in module ome_zarr_util) set() (Zarr.Zarr method) set_level() (Zarr.Zarr method) shapes (OmeZarrSource.OmeZarrSource attribute) show_image() (in module image_util) show_image_gray() (in module image_util)

size (GeneratorSource.GeneratorSource attribute) (in module GeneratorSource) sizes (GeneratorSource.GeneratorSource attribute) (OmeSource.OmeSource attribute) (PlainImageSource.PlainImageSource attribute) sizes_xyzct (GeneratorSource.GeneratorSource attribute) (OmeSource.OmeSource attribute) (PlainImageSource.PlainImageSource attribute) source_pixel_size (OmeSource.OmeSource attribute) SPLIT (parameters.ChannelOperation attribute) split_num_text() (in module util) split_value_unit_list() (in module util) store_tiles() (in module conversion)

T

tags (TiffSource.TiffSource attribute) tags_to_dict() (in module image_util) target_pixel_size (OmeSource.OmeSource attribute) tiff (TiffSource.TiffSource attribute) tiff_info() (in module image_util)

tiff_info_short() (in module image_util) TiffSource module TiffSource (class in TiffSource) tile_shape (GeneratorSource.GeneratorSource attribute)

U

unload() (PlainImageSource.PlainImageSource method) (TiffSource.TiffSource method)

util module

V

v3 (Zarr.Zarr attribute)

W

write() (OmeZarr.OmeZarr method)

write_dataset() (OmeZarr.OmeZarr method)

X

xml2dict() (in module XmlDict) XmlDict module

XmlDict (class in XmlDict) XmlList (class in XmlDict)

Z

Zarr module

Zarr (class in Zarr)