Index

_

__init__() (bioio.BioImage method) (bioio.writers.OmeTiffWriter method) (bioio.writers.OmeZarrWriter method) (bioio.writers.timeseries_writer.TimeseriesWriter method) (bioio.writers.two_d_writer.TwoDWriter method)

A

ArrayLikeReader (class in bioio.array_like_reader)

ArrayLikeReaderMetadata (class in bioio.array_like_reader)

B

BioImage (class in bioio), [1] (class in bioio.bio_image) bioio module bioio.array_like_reader module bioio.bio_image module bioio.ome_utils module bioio.plugins module bioio.writers module bioio.writers.ome_tiff_writer module

bioio.writers.ome_zarr_writer module bioio.writers.ome_zarr_writer_2 module bioio.writers.timeseries_writer module bioio.writers.two_d_writer module bioio.writers.writer module build_ome() (bioio.writers.ome_tiff_writer.OmeTiffWriter static method) (bioio.writers.ome_zarr_writer.OmeZarrWriter static method) (bioio.writers.OmeTiffWriter static method) (bioio.writers.OmeZarrWriter static method) (in module bioio.writers.ome_zarr_writer_2)

C

channel_names (bioio.bio_image.BioImage property) (bioio.BioImage property) check_type() (in module bioio.plugins) chunk_size (bioio.writers.ome_zarr_writer_2.ZarrLevel attribute) chunk_size_from_memory_target() (in module bioio.writers.ome_zarr_writer_2) compute_level_chunk_sizes_zslice() (in module bioio.writers.ome_zarr_writer_2)

compute_level_shapes() (in module bioio.writers.ome_zarr_writer_2) current_resolution_level (bioio.bio_image.BioImage property) (bioio.BioImage property) current_scene (bioio.bio_image.BioImage property) (bioio.BioImage property) current_scene_index (bioio.bio_image.BioImage property) (bioio.BioImage property)

D

dask_data (bioio.bio_image.BioImage property) (bioio.BioImage property) data (bioio.bio_image.BioImage property) (bioio.BioImage property) determine_plugin() (bioio.bio_image.BioImage static method) (bioio.BioImage static method) DIM_ORDERS (bioio.writers.timeseries_writer.TimeseriesWriter attribute) (bioio.writers.two_d_writer.TwoDWriter attribute)

dim_tuple_to_dict() (in module bioio.writers.ome_zarr_writer_2) dims (bioio.bio_image.BioImage property) (bioio.BioImage property) dtype (bioio.bio_image.BioImage property) (bioio.BioImage property) (bioio.writers.ome_zarr_writer_2.ZarrLevel attribute) dtype_to_ome_type() (in module bioio.ome_utils) dump_plugins() (in module bioio.plugins)

E

entrypoint (bioio.plugins.PluginEntry attribute)

error (bioio.plugins.PluginSupport attribute)

F

FFMPEG_FORMATS (bioio.writers.two_d_writer.TwoDWriter attribute)

G

generate_metadata() (bioio.writers.ome_zarr_writer_2.OmeZarrWriter method) generate_ome_channel_id() (in module bioio.ome_utils) generate_ome_image_id() (in module bioio.ome_utils) get_array_like_plugin() (in module bioio.plugins) get_dask_stack() (bioio.bio_image.BioImage method) (bioio.BioImage method) get_dependency_version_range_for_distribution() (in module bioio.plugins) get_extension_and_mode() (bioio.writers.two_d_writer.TwoDWriter static method) get_image_dask_data() (bioio.bio_image.BioImage method) (bioio.BioImage method) get_image_data() (bioio.bio_image.BioImage method) (bioio.BioImage method) get_mosaic_tile_position() (bioio.bio_image.BioImage method) (bioio.BioImage method)

get_mosaic_tile_positions() (bioio.bio_image.BioImage method) (bioio.BioImage method) get_plugins() (in module bioio.plugins) get_reader() (bioio.array_like_reader.ArrayLikeReaderMetadata static method) get_scale_ratio() (in module bioio.writers.ome_zarr_writer_2) get_stack() (bioio.bio_image.BioImage method) (bioio.BioImage method) get_supported_extensions() (bioio.array_like_reader.ArrayLikeReaderMetadata static method) get_xarray_dask_stack() (bioio.bio_image.BioImage method) (bioio.BioImage method) get_xarray_stack() (bioio.bio_image.BioImage method) (bioio.BioImage method)

I

imread() (in module bioio.bio_image) imread_dask() (in module bioio.bio_image) imread_xarray() (in module bioio.bio_image)

imread_xarray_dask() (in module bioio.bio_image) init_store() (bioio.writers.ome_zarr_writer_2.OmeZarrWriter method) insert_sorted_by_timestamp() (in module bioio.plugins)

M

metadata (bioio.bio_image.BioImage property) (bioio.BioImage property) (bioio.plugins.PluginEntry attribute) module bioio bioio.array_like_reader bioio.bio_image bioio.ome_utils bioio.plugins bioio.writers bioio.writers.ome_tiff_writer bioio.writers.ome_zarr_writer bioio.writers.ome_zarr_writer_2 bioio.writers.timeseries_writer bioio.writers.two_d_writer bioio.writers.writer

mosaic_tile_dims (bioio.bio_image.BioImage property) (bioio.BioImage property)

O

ome_metadata (bioio.bio_image.BioImage property) (bioio.BioImage property) ome_to_numpy_dtype() (in module bioio.ome_utils) OmeTiffWriter (class in bioio.writers), [1] (class in bioio.writers.ome_tiff_writer)

OmeZarrWriter (class in bioio.writers), [1] (class in bioio.writers.ome_zarr_writer) (class in bioio.writers.ome_zarr_writer_2) OmeZarrWriter2 (in module bioio.writers)

P

physical_pixel_sizes (bioio.array_like_reader.ArrayLikeReader property) (bioio.bio_image.BioImage property) (bioio.BioImage property)

plugin_feasibility_report() (in module bioio) (in module bioio.plugins) PluginEntry (class in bioio.plugins) PluginSupport (class in bioio.plugins)

R

reader (bioio.bio_image.BioImage property) (bioio.BioImage property) resize() (in module bioio.writers.ome_zarr_writer_2)

resolution_level_dims (bioio.bio_image.BioImage property) (bioio.BioImage property) resolution_levels (bioio.bio_image.BioImage property) (bioio.BioImage property)

S

save() (bioio.bio_image.BioImage method) (bioio.BioImage method) (bioio.writers.ome_tiff_writer.OmeTiffWriter static method) (bioio.writers.OmeTiffWriter static method) (bioio.writers.timeseries_writer.TimeseriesWriter static method) (bioio.writers.two_d_writer.TwoDWriter static method) (bioio.writers.writer.Writer static method) scenes (bioio.array_like_reader.ArrayLikeReader property) (bioio.bio_image.BioImage property) (bioio.BioImage property)

set_resolution_level() (bioio.bio_image.BioImage method) (bioio.BioImage method) set_scene() (bioio.bio_image.BioImage method) (bioio.BioImage method) shape (bioio.bio_image.BioImage property) (bioio.BioImage property) (bioio.writers.ome_zarr_writer_2.ZarrLevel attribute) supported (bioio.plugins.PluginSupport attribute)

T

TimeseriesWriter (class in bioio.writers.timeseries_writer), [1]

timestamp (bioio.plugins.PluginEntry attribute) TwoDWriter (class in bioio.writers.two_d_writer), [1]

W

write_image() (bioio.writers.ome_zarr_writer.OmeZarrWriter method) (bioio.writers.OmeZarrWriter method) write_metadata() (bioio.writers.ome_zarr_writer_2.OmeZarrWriter method)

write_t_batches() (bioio.writers.ome_zarr_writer_2.OmeZarrWriter method) write_t_batches_array() (bioio.writers.ome_zarr_writer_2.OmeZarrWriter method) write_t_batches_image_sequence() (bioio.writers.ome_zarr_writer_2.OmeZarrWriter method) Writer (class in bioio.writers.writer)

X

xarray_dask_data (bioio.bio_image.BioImage property) (bioio.BioImage property)

xarray_data (bioio.bio_image.BioImage property) (bioio.BioImage property)

Z

zarray (bioio.writers.ome_zarr_writer_2.ZarrLevel attribute)

ZarrLevel (class in bioio.writers.ome_zarr_writer_2)