Index

_

_build_axes() (in module pymif.microscope_manager.utils.ngff) _build_coordinate_transformations() (in module pymif.microscope_manager.utils.ngff) _build_dask_array() (pymif.microscope_manager.luxendo_manager.LuxendoManager method) (pymif.microscope_manager.LuxendoManager method) (pymif.microscope_manager.opera_manager.OperaManager method) (pymif.microscope_manager.OperaManager method) (pymif.microscope_manager.scape_manager.ScapeManager method) (pymif.microscope_manager.ScapeManager method) (pymif.microscope_manager.viventis_manager.ViventisManager method) (pymif.microscope_manager.ViventisManager method) _build_omero_metadata() (in module pymif.microscope_manager.utils.ngff) _build_v2_compressor() (in module pymif.microscope_manager.utils.ngff) _build_v3_compressors() (in module pymif.microscope_manager.utils.ngff) _convert_spatial_units_to_micrometers() (pymif.microscope_manager.scape_manager.ScapeManager method) (pymif.microscope_manager.ScapeManager method) _default_window() (in module pymif.microscope_manager.utils.ngff) _extract_metadata() (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method) _find_xlif_for_ome_tiff() (pymif.microscope_manager.scape_manager.ScapeManager method) (pymif.microscope_manager.ScapeManager method) _generate_pyramid() (in module pymif.microscope_manager.utils.write_image_region) (in module pymif.microscope_manager.utils.write_label_region) _get_chunks() (in module pymif.microscope_manager.utils.ngff) _get_group_multiscales() (in module pymif.microscope_manager.utils.ngff) _get_group_ome_attrs() (in module pymif.microscope_manager.utils.ngff) _get_image_meta() (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method) _get_multiscales() (in module pymif.microscope_manager.utils.ngff) (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method) _get_nested_group() (in module pymif.microscope_manager.utils.write_label_region) _get_omero() (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method) _infer_ngff_version() (in module pymif.microscope_manager.utils.ngff) _load_group() (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.zarr_v04_manager.ZarrV04Manager method) (pymif.microscope_manager.ZarrManager method) (pymif.microscope_manager.ZarrV04Manager method) _load_labels() (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.zarr_v04_manager.ZarrV04Manager method) (pymif.microscope_manager.ZarrManager method) (pymif.microscope_manager.ZarrV04Manager method)

_normalize_color() (in module pymif.microscope_manager.utils.ngff) _normalize_unit() (in module pymif.microscope_manager.utils.ngff) _open_files (pymif.microscope_manager.luxendo_manager.LuxendoManager attribute) (pymif.microscope_manager.LuxendoManager attribute) (pymif.microscope_manager.microscope_manager.MicroscopeManager attribute) _parse_arguments() (in module pymif.cli.__arguments) _parse_color() (in module pymif.microscope_manager.utils.visualize) _parse_companion_file() (pymif.microscope_manager.viventis_manager.ViventisManager method) (pymif.microscope_manager.ViventisManager method) _parse_metadata() (pymif.microscope_manager.luxendo_manager.LuxendoManager method) (pymif.microscope_manager.LuxendoManager method) (pymif.microscope_manager.opera_manager.OperaManager method) (pymif.microscope_manager.OperaManager method) (pymif.microscope_manager.zeiss_manager.ZeissManager method) (pymif.microscope_manager.ZeissManager method) _parse_xlif_metadata() (pymif.microscope_manager.scape_manager.ScapeManager method) (pymif.microscope_manager.ScapeManager method) _read_h5_shape() (pymif.microscope_manager.luxendo_manager.LuxendoManager method) (pymif.microscope_manager.LuxendoManager method) _read_h5_stack() (pymif.microscope_manager.luxendo_manager.LuxendoManager method) (pymif.microscope_manager.LuxendoManager method) _read_multiscale_group() (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method) _register_label_on_root() (in module pymif.microscope_manager.utils.ngff) _resolve_format() (in module pymif.microscope_manager.utils.ngff) _run_conversion() (in module pymif.napari._convert_widget) _scale_index() (in module pymif.microscope_manager.utils.write_image_region) (in module pymif.microscope_manager.utils.write_label_region) _set_group_ngff_metadata() (in module pymif.microscope_manager.utils.ngff) _strip_ome_tiff_suffix() (pymif.microscope_manager.scape_manager.ScapeManager static method) (pymif.microscope_manager.ScapeManager static method) _validate_metadata() (in module pymif.microscope_manager.utils.ngff) _write_pyramid_v2() (in module pymif.microscope_manager.utils.ngff) _write_pyramid_v3() (in module pymif.microscope_manager.utils.ngff) _zoom_dask() (in module pymif.microscope_manager.utils.zoom) _zoom_numpy() (in module pymif.microscope_manager.utils.zoom)

A

add_label() (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method) add_roi_layer() (in module pymif.napari._overview_widget)

add_zrange_layer() (in module pymif.napari._overview_widget) ArrayManager (class in pymif.microscope_manager) (class in pymif.microscope_manager.array_manager)

B

build_pyramid() (in module pymif.microscope_manager.utils.pyramid) (pymif.microscope_manager.microscope_manager.MicroscopeManager method)

C

chunks (pymif.microscope_manager.array_manager.ArrayManager attribute) (pymif.microscope_manager.ArrayManager attribute) (pymif.microscope_manager.luxendo_manager.LuxendoManager attribute) (pymif.microscope_manager.LuxendoManager attribute) (pymif.microscope_manager.opera_manager.OperaManager attribute) (pymif.microscope_manager.OperaManager attribute) (pymif.microscope_manager.scape_manager.ScapeManager attribute) (pymif.microscope_manager.ScapeManager attribute) (pymif.microscope_manager.viventis_manager.ViventisManager attribute) (pymif.microscope_manager.ViventisManager attribute) (pymif.microscope_manager.zarr_manager.ZarrManager attribute) (pymif.microscope_manager.zarr_v04_manager.ZarrV04Manager attribute) (pymif.microscope_manager.ZarrManager attribute) (pymif.microscope_manager.ZarrV04Manager attribute) (pymif.microscope_manager.zeiss_manager.ZeissManager attribute) (pymif.microscope_manager.ZeissManager attribute)

close() (pymif.microscope_manager.microscope_manager.MicroscopeManager method) compressor (pymif.microscope_manager.utils.ngff.ZarrWriteConfig attribute) compressor_level (pymif.microscope_manager.utils.ngff.ZarrWriteConfig attribute) compute (pymif.microscope_manager.utils.ngff.ZarrWriteConfig attribute) convert_batch() (in module pymif.cli.pymif) convert_single() (in module pymif.cli.pymif) convert_widget() (in module pymif.napari._convert_widget) convert_worker() (in module pymif.napari._convert_widget) create_empty_dataset() (in module pymif.microscope_manager.utils.create_empty_dataset) create_empty_group() (in module pymif.microscope_manager.utils.create_empty_group) (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method)

D

data (pymif.microscope_manager.array_manager.ArrayManager attribute) (pymif.microscope_manager.ArrayManager attribute) (pymif.microscope_manager.microscope_manager.MicroscopeManager attribute) dataset_reader() (in module pymif.napari._convert_widget)

DEFAULT_COLORS (in module pymif.microscope_manager.utils.ngff) (in module pymif.microscope_manager.utils.to_zarr) downsample_nn() (in module pymif.microscope_manager.utils.pyramid) draw_3d_polygon() (in module pymif.napari._overview_widget)

E

EmittingStream (class in pymif.napari._convert_widget)

F

flush() (pymif.napari._convert_widget.EmittingStream method)

G

get_available_datasets() (pymif.microscope_manager.luxendo_manager.LuxendoManager method) (pymif.microscope_manager.LuxendoManager method)

get_chunk_size() (in module pymif.napari._convert_widget) get_n_levels() (in module pymif.napari._convert_widget)

I

isatty() (pymif.napari._convert_widget.EmittingStream method)

L

LuxendoManager (class in pymif.microscope_manager) (class in pymif.microscope_manager.luxendo_manager)

M

main() (in module pymif.cli.pymif) make_overview() (in module pymif.napari._overview_widget) metadata (pymif.microscope_manager.array_manager.ArrayManager attribute) (pymif.microscope_manager.ArrayManager attribute) (pymif.microscope_manager.microscope_manager.MicroscopeManager attribute) (pymif.microscope_manager.zarr_manager.ZarrManager attribute) (pymif.microscope_manager.zarr_v04_manager.ZarrV04Manager attribute) (pymif.microscope_manager.ZarrManager attribute) (pymif.microscope_manager.ZarrV04Manager attribute) MicroscopeManager (class in pymif.microscope_manager.microscope_manager) mode (pymif.microscope_manager.zarr_manager.ZarrManager attribute) (pymif.microscope_manager.zarr_v04_manager.ZarrV04Manager attribute) (pymif.microscope_manager.ZarrManager attribute) (pymif.microscope_manager.ZarrV04Manager attribute) module pymif pymif.cli pymif.cli.__arguments pymif.cli.pymif pymif.microscope_manager pymif.microscope_manager.array_manager pymif.microscope_manager.luxendo_manager pymif.microscope_manager.microscope_manager pymif.microscope_manager.opera_manager pymif.microscope_manager.scape_manager pymif.microscope_manager.utils pymif.microscope_manager.utils.create_empty_dataset pymif.microscope_manager.utils.create_empty_group pymif.microscope_manager.utils.ngff pymif.microscope_manager.utils.pyramid pymif.microscope_manager.utils.subset pymif.microscope_manager.utils.to_zarr pymif.microscope_manager.utils.visualize pymif.microscope_manager.utils.write_image_region pymif.microscope_manager.utils.write_label_region pymif.microscope_manager.utils.zoom pymif.microscope_manager.viventis_manager pymif.microscope_manager.zarr_manager pymif.microscope_manager.zarr_v04_manager pymif.microscope_manager.zeiss_manager pymif.napari pymif.napari._convert_widget pymif.napari._overview_widget

N

ngff_version (pymif.microscope_manager.utils.ngff.ZarrWriteConfig attribute) (pymif.microscope_manager.zarr_manager.ZarrManager attribute) (pymif.microscope_manager.ZarrManager attribute)

ngff_version_override (pymif.microscope_manager.zarr_manager.ZarrManager attribute) (pymif.microscope_manager.ZarrManager attribute)

O

ome_tiff_path (pymif.microscope_manager.scape_manager.ScapeManager attribute) (pymif.microscope_manager.ScapeManager attribute) OperaManager (class in pymif.microscope_manager) (class in pymif.microscope_manager.opera_manager)

overview_widget() (in module pymif.napari._overview_widget) overwrite (pymif.microscope_manager.utils.ngff.ZarrWriteConfig attribute)

P

pad_to_divisible() (in module pymif.microscope_manager.utils.pyramid) path (pymif.microscope_manager.luxendo_manager.LuxendoManager attribute) (pymif.microscope_manager.LuxendoManager attribute) (pymif.microscope_manager.opera_manager.OperaManager attribute) (pymif.microscope_manager.OperaManager attribute) (pymif.microscope_manager.viventis_manager.ViventisManager attribute) (pymif.microscope_manager.ViventisManager attribute) (pymif.microscope_manager.zarr_manager.ZarrManager attribute) (pymif.microscope_manager.zarr_v04_manager.ZarrV04Manager attribute) (pymif.microscope_manager.ZarrManager attribute) (pymif.microscope_manager.ZarrV04Manager attribute) (pymif.microscope_manager.zeiss_manager.ZeissManager attribute) (pymif.microscope_manager.ZeissManager attribute) pymif module pymif.cli module pymif.cli.__arguments module pymif.cli.pymif module pymif.microscope_manager module pymif.microscope_manager.array_manager module pymif.microscope_manager.luxendo_manager module pymif.microscope_manager.microscope_manager module pymif.microscope_manager.opera_manager module pymif.microscope_manager.scape_manager module pymif.microscope_manager.utils module

pymif.microscope_manager.utils.create_empty_dataset module pymif.microscope_manager.utils.create_empty_group module pymif.microscope_manager.utils.ngff module pymif.microscope_manager.utils.pyramid module pymif.microscope_manager.utils.subset module pymif.microscope_manager.utils.to_zarr module pymif.microscope_manager.utils.visualize module pymif.microscope_manager.utils.write_image_region module pymif.microscope_manager.utils.write_label_region module pymif.microscope_manager.utils.zoom module pymif.microscope_manager.viventis_manager module pymif.microscope_manager.zarr_manager module pymif.microscope_manager.zarr_v04_manager module pymif.microscope_manager.zeiss_manager module pymif.napari module pymif.napari._convert_widget module pymif.napari._overview_widget module

R

read() (pymif.microscope_manager.array_manager.ArrayManager method) (pymif.microscope_manager.ArrayManager method) (pymif.microscope_manager.luxendo_manager.LuxendoManager method) (pymif.microscope_manager.LuxendoManager method) (pymif.microscope_manager.microscope_manager.MicroscopeManager method) (pymif.microscope_manager.opera_manager.OperaManager method) (pymif.microscope_manager.OperaManager method) (pymif.microscope_manager.scape_manager.ScapeManager method) (pymif.microscope_manager.ScapeManager method) (pymif.microscope_manager.viventis_manager.ViventisManager method) (pymif.microscope_manager.ViventisManager method) (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.zarr_v04_manager.ZarrV04Manager method) (pymif.microscope_manager.ZarrManager method) (pymif.microscope_manager.ZarrV04Manager method) (pymif.microscope_manager.zeiss_manager.ZeissManager method) (pymif.microscope_manager.ZeissManager method)

reorder_channels() (pymif.microscope_manager.microscope_manager.MicroscopeManager method) root (pymif.microscope_manager.zarr_v04_manager.ZarrV04Manager attribute) (pymif.microscope_manager.ZarrV04Manager attribute)

S

ScapeManager (class in pymif.microscope_manager) (class in pymif.microscope_manager.scape_manager) scenes (pymif.microscope_manager.zeiss_manager.ZeissManager attribute) (pymif.microscope_manager.ZeissManager attribute) SPATIAL_AXES (in module pymif.microscope_manager.utils.ngff) (in module pymif.microscope_manager.utils.to_zarr)

storage_options (pymif.microscope_manager.utils.ngff.ZarrWriteConfig attribute) subset_dask_array() (in module pymif.microscope_manager.utils.subset) subset_dataset() (pymif.microscope_manager.microscope_manager.MicroscopeManager method) subset_metadata() (in module pymif.microscope_manager.utils.subset)

T

text_written (pymif.napari._convert_widget.EmittingStream attribute)

to_zarr() (in module pymif.microscope_manager.utils.to_zarr) (pymif.microscope_manager.microscope_manager.MicroscopeManager method)

U

update_metadata() (pymif.microscope_manager.microscope_manager.MicroscopeManager method)

V

validate_uniform_spacing() (in module pymif.microscope_manager.utils.subset) visualize() (in module pymif.microscope_manager.utils.visualize) (pymif.microscope_manager.microscope_manager.MicroscopeManager method) visualize_zarr() (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.zarr_v04_manager.ZarrV04Manager method) (pymif.microscope_manager.ZarrManager method) (pymif.microscope_manager.ZarrV04Manager method)

ViventisManager (class in pymif.microscope_manager) (class in pymif.microscope_manager.viventis_manager)

W

write() (pymif.napari._convert_widget.EmittingStream method) write_image_region() (in module pymif.microscope_manager.utils.write_image_region) (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method)

write_label_region() (in module pymif.microscope_manager.utils.write_label_region) (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method)

Z

zarr_convert() (in module pymif.cli.pymif) zarr_format (pymif.microscope_manager.utils.ngff.ZarrWriteConfig attribute) zarr_format_override (pymif.microscope_manager.zarr_manager.ZarrManager attribute) (pymif.microscope_manager.ZarrManager attribute) ZarrManager (class in pymif.microscope_manager) (class in pymif.microscope_manager.zarr_manager)

ZarrV04Manager (class in pymif.microscope_manager) (class in pymif.microscope_manager.zarr_v04_manager) ZarrWriteConfig (class in pymif.microscope_manager.utils.ngff) ZeissManager (class in pymif.microscope_manager) (class in pymif.microscope_manager.zeiss_manager)