Index

_

__init__() (aicsimageio.aics_image.AICSImage method) (aicsimageio.readers.ome_tiff_reader.OmeTiffReader method) (aicsimageio.readers.reader.Reader method) (aicsimageio.readers.tiff_reader.TiffReader method) (aicsimageio.writers.ome_tiff_writer.OmeTiffWriter method)

A

AICSImage (class in aicsimageio.aics_image), [1] aicsimageio module aicsimageio.aics_image module aicsimageio.constants module aicsimageio.dimensions module aicsimageio.exceptions module aicsimageio.formats module aicsimageio.image_container module aicsimageio.metadata module aicsimageio.metadata.utils module aicsimageio.readers module aicsimageio.readers.array_like_reader module aicsimageio.readers.bfio_reader module aicsimageio.readers.bioformats_reader module aicsimageio.readers.czi_reader module aicsimageio.readers.default_reader module aicsimageio.readers.dv_reader module aicsimageio.readers.lif_reader module aicsimageio.readers.nd2_reader module

aicsimageio.readers.ome_tiff_reader module aicsimageio.readers.ome_zarr_reader module aicsimageio.readers.reader module aicsimageio.readers.sldy_reader module aicsimageio.readers.sldy_reader.sldy_image module aicsimageio.readers.tiff_glob_reader module aicsimageio.readers.tiff_reader module aicsimageio.transforms module aicsimageio.types module aicsimageio.utils module aicsimageio.utils.io_utils module aicsimageio.writers module aicsimageio.writers.ome_tiff_writer module aicsimageio.writers.ome_zarr_writer module aicsimageio.writers.timeseries_writer module aicsimageio.writers.two_d_writer module aicsimageio.writers.writer module ArrayLikeReader (class in aicsimageio.readers.array_like_reader)

B

backend (aicsimageio.readers.bfio_reader.BfioReader attribute) (aicsimageio.readers.bfio_reader.OmeTiledTiffReader attribute) BfioReader (class in aicsimageio.readers.bfio_reader) BioFile (class in aicsimageio.readers.bioformats_reader)

bioformats_ome() (in module aicsimageio.metadata.utils) bioformats_version() (aicsimageio.readers.bioformats_reader.BioformatsReader static method) BioformatsReader (class in aicsimageio.readers.bioformats_reader) build_ome() (aicsimageio.writers.ome_tiff_writer.OmeTiffWriter static method) (aicsimageio.writers.ome_zarr_writer.OmeZarrWriter static method)

C

Channel (aicsimageio.dimensions.DimensionNames attribute) channel_names (aicsimageio.aics_image.AICSImage property) (aicsimageio.image_container.ImageContainer property) (aicsimageio.readers.bfio_reader.BfioReader property) (aicsimageio.readers.ome_zarr_reader.OmeZarrReader property) (aicsimageio.readers.reader.Reader property) clean_ome_xml_for_known_issues() (in module aicsimageio.metadata.utils) close() (aicsimageio.readers.bioformats_reader.BioFile method) closed (aicsimageio.readers.bioformats_reader.BioFile property) ConflictingArgumentsError

core_meta (aicsimageio.readers.bioformats_reader.BioFile property) CoreMeta (class in aicsimageio.readers.bioformats_reader) current_scene (aicsimageio.aics_image.AICSImage property) (aicsimageio.image_container.ImageContainer property) (aicsimageio.readers.bfio_reader.BfioReader property) (aicsimageio.readers.reader.Reader property) current_scene_index (aicsimageio.aics_image.AICSImage property) (aicsimageio.image_container.ImageContainer property) (aicsimageio.readers.bfio_reader.BfioReader property) (aicsimageio.readers.reader.Reader property) CziReader (class in aicsimageio.readers.czi_reader)

D

dask_data (aicsimageio.aics_image.AICSImage property) (aicsimageio.image_container.ImageContainer property) (aicsimageio.readers.reader.Reader property) data (aicsimageio.aics_image.AICSImage property) (aicsimageio.image_container.ImageContainer property) (aicsimageio.readers.reader.Reader property) DefaultReader (class in aicsimageio.readers.default_reader) determine_reader() (aicsimageio.aics_image.AICSImage static method) DIM_ORDERS (aicsimageio.writers.timeseries_writer.TimeseriesWriter attribute) (aicsimageio.writers.two_d_writer.TwoDWriter attribute) dimension_order (aicsimageio.readers.bioformats_reader.CoreMeta attribute)

DimensionNames (class in aicsimageio.dimensions) Dimensions (class in aicsimageio.dimensions) dims (aicsimageio.aics_image.AICSImage property) (aicsimageio.image_container.ImageContainer property) (aicsimageio.readers.reader.Reader property) dtype (aicsimageio.aics_image.AICSImage property) (aicsimageio.image_container.ImageContainer property) (aicsimageio.readers.bioformats_reader.CoreMeta attribute) (aicsimageio.readers.reader.Reader property) dtype_to_ome_type() (in module aicsimageio.metadata.utils) DVReader (class in aicsimageio.readers.dv_reader)

F

FFMPEG_FORMATS (aicsimageio.readers.default_reader.DefaultReader attribute)

filename (aicsimageio.readers.bioformats_reader.BioFile property)

G

generate_ome_channel_id() (in module aicsimageio.metadata.utils) generate_ome_detector_id() (in module aicsimageio.metadata.utils) generate_ome_image_id() (in module aicsimageio.metadata.utils) generate_ome_instrument_id() (in module aicsimageio.metadata.utils) generate_stack() (in module aicsimageio.transforms) get_coords_from_ome() (in module aicsimageio.metadata.utils) get_dask_stack() (aicsimageio.aics_image.AICSImage method) (aicsimageio.readers.reader.Reader method) get_data() (aicsimageio.readers.sldy_reader.sldy_image.SldyImage method) get_dims_from_ome() (in module aicsimageio.metadata.utils) get_image_dask_data() (aicsimageio.aics_image.AICSImage method) (aicsimageio.image_container.ImageContainer method) (aicsimageio.readers.reader.Reader method) get_image_data() (aicsimageio.aics_image.AICSImage method) (aicsimageio.image_container.ImageContainer method) (aicsimageio.readers.reader.Reader method)

get_module_version() (in module aicsimageio) get_mosaic_tile_position() (aicsimageio.aics_image.AICSImage method) (aicsimageio.readers.czi_reader.CziReader method) (aicsimageio.readers.lif_reader.LifReader method) (aicsimageio.readers.reader.Reader method) get_mosaic_tile_positions() (aicsimageio.aics_image.AICSImage method) (aicsimageio.readers.czi_reader.CziReader method) (aicsimageio.readers.lif_reader.LifReader method) (aicsimageio.readers.reader.Reader method) get_stack() (aicsimageio.aics_image.AICSImage method) (aicsimageio.readers.reader.Reader method) get_xarray_dask_stack() (aicsimageio.aics_image.AICSImage method) (aicsimageio.readers.reader.Reader method) get_xarray_stack() (aicsimageio.aics_image.AICSImage method) (aicsimageio.readers.reader.Reader method)

I

ImageContainer (class in aicsimageio.image_container) imread() (in module aicsimageio.aics_image) imread_dask() (in module aicsimageio.aics_image) imread_xarray() (in module aicsimageio.aics_image) imread_xarray_dask() (in module aicsimageio.aics_image)

InvalidDimensionOrderingError is_interleaved (aicsimageio.readers.bioformats_reader.CoreMeta attribute) is_rgb (aicsimageio.readers.bioformats_reader.CoreMeta attribute) is_supported_image() (aicsimageio.readers.reader.Reader class method) items() (aicsimageio.dimensions.Dimensions method)

L

LifReader (class in aicsimageio.readers.lif_reader)

M

mapped_dims (aicsimageio.readers.czi_reader.CziReader property) metadata (aicsimageio.aics_image.AICSImage property) (aicsimageio.image_container.ImageContainer property) (aicsimageio.readers.reader.Reader property) (aicsimageio.readers.sldy_reader.sldy_image.SldyImage property) MicroManagerIndexer() (aicsimageio.readers.tiff_glob_reader.TiffGlobReader static method) module aicsimageio aicsimageio.aics_image aicsimageio.constants aicsimageio.dimensions aicsimageio.exceptions aicsimageio.formats aicsimageio.image_container aicsimageio.metadata aicsimageio.metadata.utils aicsimageio.readers aicsimageio.readers.array_like_reader aicsimageio.readers.bfio_reader aicsimageio.readers.bioformats_reader aicsimageio.readers.czi_reader aicsimageio.readers.default_reader aicsimageio.readers.dv_reader aicsimageio.readers.lif_reader aicsimageio.readers.nd2_reader aicsimageio.readers.ome_tiff_reader aicsimageio.readers.ome_zarr_reader aicsimageio.readers.reader aicsimageio.readers.sldy_reader aicsimageio.readers.sldy_reader.sldy_image aicsimageio.readers.tiff_glob_reader aicsimageio.readers.tiff_reader aicsimageio.transforms aicsimageio.types aicsimageio.utils aicsimageio.utils.io_utils aicsimageio.writers aicsimageio.writers.ome_tiff_writer aicsimageio.writers.ome_zarr_writer aicsimageio.writers.timeseries_writer aicsimageio.writers.two_d_writer aicsimageio.writers.writer

mosaic_dask_data (aicsimageio.readers.reader.Reader property) mosaic_data (aicsimageio.readers.reader.Reader property) mosaic_tile_dims (aicsimageio.aics_image.AICSImage property) (aicsimageio.readers.reader.Reader property) mosaic_xarray_dask_data (aicsimageio.readers.reader.Reader property) mosaic_xarray_data (aicsimageio.readers.reader.Reader property) MosaicTile (aicsimageio.dimensions.DimensionNames attribute)

N

ND2Reader (class in aicsimageio.readers.nd2_reader)

O

ome_metadata (aicsimageio.aics_image.AICSImage property) (aicsimageio.readers.bfio_reader.BfioReader property) (aicsimageio.readers.bioformats_reader.BioFile property) (aicsimageio.readers.bioformats_reader.BioformatsReader property) (aicsimageio.readers.czi_reader.CziReader property) (aicsimageio.readers.nd2_reader.ND2Reader property) (aicsimageio.readers.ome_tiff_reader.OmeTiffReader property) (aicsimageio.readers.reader.Reader property)

ome_to_numpy_dtype() (in module aicsimageio.metadata.utils) ome_xml (aicsimageio.readers.bioformats_reader.BioFile property) OmeTiffReader (class in aicsimageio.readers.ome_tiff_reader), [1] OmeTiffWriter (class in aicsimageio.writers.ome_tiff_writer), [1] OmeTiledTiffReader (class in aicsimageio.readers.bfio_reader) OmeZarrReader (class in aicsimageio.readers.ome_zarr_reader) OmeZarrWriter (class in aicsimageio.writers.ome_zarr_writer) open() (aicsimageio.readers.bioformats_reader.BioFile method) order (aicsimageio.dimensions.Dimensions property)

P

pathlike_to_fs() (in module aicsimageio.utils.io_utils) physical_pixel_sizes (aicsimageio.aics_image.AICSImage property) (aicsimageio.image_container.ImageContainer property) (aicsimageio.readers.array_like_reader.ArrayLikeReader property) (aicsimageio.readers.bfio_reader.BfioReader property) (aicsimageio.readers.bioformats_reader.BioformatsReader property) (aicsimageio.readers.czi_reader.CziReader property) (aicsimageio.readers.dv_reader.DVReader property) (aicsimageio.readers.lif_reader.LifReader property) (aicsimageio.readers.nd2_reader.ND2Reader property) (aicsimageio.readers.ome_tiff_reader.OmeTiffReader property) (aicsimageio.readers.ome_zarr_reader.OmeZarrReader property) (aicsimageio.readers.reader.Reader property) (aicsimageio.readers.sldy_reader.SldyReader property) (aicsimageio.readers.tiff_reader.TiffReader property)

physical_pixel_sizes() (in module aicsimageio.metadata.utils) PhysicalPixelSizes (class in aicsimageio.types)

R

reader (aicsimageio.aics_image.AICSImage property) Reader (class in aicsimageio.readers.reader), [1] reader_path (aicsimageio.aics_image.AICSImage attribute) reader_paths (aicsimageio.aics_image.AICSImage attribute)

ReaderClass (aicsimageio.aics_image.AICSImage attribute) reduce_to_slice() (in module aicsimageio.transforms) reshape_data() (in module aicsimageio.transforms) resolution_count (aicsimageio.readers.bioformats_reader.CoreMeta attribute)

S

Samples (aicsimageio.dimensions.DimensionNames attribute) save() (aicsimageio.aics_image.AICSImage method) (aicsimageio.writers.ome_tiff_writer.OmeTiffWriter static method) (aicsimageio.writers.timeseries_writer.TimeseriesWriter static method) (aicsimageio.writers.two_d_writer.TwoDWriter static method) (aicsimageio.writers.writer.Writer static method) scenes (aicsimageio.aics_image.AICSImage property) (aicsimageio.image_container.ImageContainer property) (aicsimageio.readers.array_like_reader.ArrayLikeReader property) (aicsimageio.readers.bfio_reader.BfioReader property) (aicsimageio.readers.bioformats_reader.BioformatsReader property) (aicsimageio.readers.czi_reader.CziReader property) (aicsimageio.readers.default_reader.DefaultReader property) (aicsimageio.readers.dv_reader.DVReader property) (aicsimageio.readers.lif_reader.LifReader property) (aicsimageio.readers.nd2_reader.ND2Reader property) (aicsimageio.readers.ome_tiff_reader.OmeTiffReader property) (aicsimageio.readers.ome_zarr_reader.OmeZarrReader property) (aicsimageio.readers.reader.Reader property) (aicsimageio.readers.sldy_reader.SldyReader property) (aicsimageio.readers.tiff_glob_reader.TiffGlobReader property) (aicsimageio.readers.tiff_reader.TiffReader property)

series_count (aicsimageio.readers.bioformats_reader.CoreMeta attribute) set_scene() (aicsimageio.aics_image.AICSImage method) (aicsimageio.image_container.ImageContainer method) (aicsimageio.readers.bfio_reader.BfioReader method) (aicsimageio.readers.reader.Reader method) set_series() (aicsimageio.readers.bioformats_reader.BioFile method) shape (aicsimageio.aics_image.AICSImage property) (aicsimageio.dimensions.Dimensions property) (aicsimageio.image_container.ImageContainer property) (aicsimageio.readers.bioformats_reader.CoreMeta attribute) (aicsimageio.readers.reader.Reader property) SldyImage (class in aicsimageio.readers.sldy_reader.sldy_image) SldyReader (class in aicsimageio.readers.sldy_reader) SpatialX (aicsimageio.dimensions.DimensionNames attribute) SpatialY (aicsimageio.dimensions.DimensionNames attribute) SpatialZ (aicsimageio.dimensions.DimensionNames attribute) SUPPORTED_READERS (aicsimageio.aics_image.AICSImage attribute)

T

TiffGlobReader (class in aicsimageio.readers.tiff_glob_reader) TiffReader (class in aicsimageio.readers.tiff_reader), [1] Time (aicsimageio.dimensions.DimensionNames attribute) TimeseriesWriter (class in aicsimageio.writers.timeseries_writer)

to_dask() (aicsimageio.readers.bioformats_reader.BioFile method) to_numpy() (aicsimageio.readers.bioformats_reader.BioFile method) transform_metadata_with_xslt() (in module aicsimageio.metadata.utils) transpose_to_dims() (in module aicsimageio.transforms) TwoDWriter (class in aicsimageio.writers.two_d_writer)

U

UnexpectedShapeError

UnsupportedFileFormatError

W

write_image() (aicsimageio.writers.ome_zarr_writer.OmeZarrWriter method)

Writer (class in aicsimageio.writers.writer)

X

X (aicsimageio.types.PhysicalPixelSizes attribute) xarray_dask_data (aicsimageio.aics_image.AICSImage property) (aicsimageio.image_container.ImageContainer property) (aicsimageio.readers.reader.Reader property)

xarray_data (aicsimageio.aics_image.AICSImage property) (aicsimageio.image_container.ImageContainer property) (aicsimageio.readers.reader.Reader property)

Y

Y (aicsimageio.types.PhysicalPixelSizes attribute)

Z

Z (aicsimageio.types.PhysicalPixelSizes attribute)