Index

_

__getattr__() (pymif.microscope_manager.zarr_manager.AttrDict method) __getitem__() (pymif.microscope_manager.zarr_manager.ZarrDataset method) __iter__() (pymif.microscope_manager.zarr_manager.ZarrDataset method) __len__() (pymif.microscope_manager.zarr_manager.ZarrDataset method) __repr__() (pymif.microscope_manager.zarr_manager.ZarrDataset method) _axes() (in module pymif.cli.pymif) _axis_index() (in module pymif.napari._convert_widget) (in module pymif.napari._overview_widget) _axis_scale() (in module pymif.microscope_manager.utils.visualize) _axis_size() (in module pymif.cli.pymif) (in module pymif.napari._convert_widget) (in module pymif.napari._overview_widget) _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_multiscales() (in module pymif.microscope_manager.utils.to_zarr) _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) _chunk_shape_for_dataset() (in module pymif.napari._convert_widget) _chunk_tuple() (in module pymif.microscope_manager.utils.pyramid) _convert_spatial_units_to_micrometers() (pymif.microscope_manager.scape_manager.ScapeManager method) (pymif.microscope_manager.ScapeManager method) _dataset_axes() (in module pymif.napari._convert_widget) (in module pymif.napari._overview_widget) _dataset_scale_vector() (in module pymif.microscope_manager.utils.downsampling) _dataset_size_mb() (in module pymif.cli.pymif) _default_window() (in module pymif.microscope_manager.utils.ngff) _downsample_nearest_exact_dask() (in module pymif.microscope_manager.utils.write_image_region) _downsample_nearest_exact_numpy() (in module pymif.microscope_manager.utils.write_image_region) _estimate_levels() (in module pymif.cli.pymif) _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) _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_image_region) _get_omero() (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method) _infer_data_type_from_group() (in module pymif.microscope_manager.utils.ngff) _infer_ngff_version() (in module pymif.microscope_manager.utils.ngff) _invalidate_zarr_data() (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method) _is_reciprocal_integer_shrink() (in module pymif.microscope_manager.utils.write_image_region) _iter_datasets() (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method) _label_entry() (in module pymif.microscope_manager.utils.ngff) _labels_contains() (in module pymif.microscope_manager.utils.ngff)

_load_group() (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method) _load_labels() (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method) _manager_name_map() (in module pymif.cli.pymif) _metadata_for_legacy_label() (in module pymif.microscope_manager.utils.create_empty_group) _metadata_for_write() (in module pymif.microscope_manager.utils.to_zarr) _normalize_chunks() (pymif.microscope_manager.array_manager.ArrayManager static method) (pymif.microscope_manager.ArrayManager static method) _normalize_color() (in module pymif.microscope_manager.utils.ngff) _normalize_downscale_factor() (in module pymif.cli.pymif) _normalize_unit() (in module pymif.microscope_manager.utils.ngff) _normalize_zoom_scale() (in module pymif.microscope_manager.utils.zoom) _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) _present() (in module pymif.cli.pymif) _present_range() (in module pymif.napari._convert_widget) _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) _rechunk_to_target() (in module pymif.microscope_manager.utils.pyramid) _register_label_on_root() (in module pymif.microscope_manager.utils.ngff) _resolve_format() (in module pymif.microscope_manager.utils.ngff) _resolve_zarr_manager() (in module pymif.cli.pymif) _run_conversion() (in module pymif.napari._convert_widget) _scale_for_axes() (in module pymif.napari._convert_widget) (in module pymif.napari._overview_widget) _scale_index() (in module pymif.microscope_manager.utils.write_image_region) (in module pymif.microscope_manager.utils.write_label_region) _select_chunk_size() (in module pymif.cli.pymif) _set_axis_labels() (in module pymif.microscope_manager.utils.visualize) _set_dimension_names() (in module pymif.microscope_manager.utils.ngff) _set_group_ngff_metadata() (in module pymif.microscope_manager.utils.ngff) _set_range_widget() (in module pymif.napari._convert_widget) _strip_ome_tiff_suffix() (pymif.microscope_manager.scape_manager.ScapeManager static method) (pymif.microscope_manager.ScapeManager static method) _subset_list() (in module pymif.microscope_manager.utils.subset) _sync_raw_aliases() (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method) _target_chunks() (in module pymif.microscope_manager.utils.pyramid) _validate_metadata() (in module pymif.microscope_manager.utils.ngff) _without_axis() (in module pymif.microscope_manager.utils.create_empty_group) _write_pyramid_v2() (in module pymif.microscope_manager.utils.ngff) _write_pyramid_v3() (in module pymif.microscope_manager.utils.ngff) _write_region() (in module pymif.microscope_manager.utils.write_image_region) _zoom_dask() (in module pymif.microscope_manager.utils.zoom) _zoom_numpy() (in module pymif.microscope_manager.utils.zoom)

A

add_roi_layer() (in module pymif.napari._overview_widget) add_zrange_layer() (in module pymif.napari._overview_widget) ALLOWED_AXES (in module pymif.microscope_manager.utils.axes) ALLOWED_AXIS_SET (in module pymif.microscope_manager.utils.axes)

ArrayManager (class in pymif.microscope_manager) (class in pymif.microscope_manager.array_manager) AttrDict (class in pymif.microscope_manager.zarr_manager) axes_to_string() (in module pymif.microscope_manager.utils.axes) axis_names_from_multiscales() (in module pymif.microscope_manager.utils.downsampling)

B

build_pyramid() (in module pymif.microscope_manager.utils.pyramid) (pymif.microscope_manager.microscope_manager.MicroscopeManager method) (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager 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.ZarrManager 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) (pymif.microscope_manager.zarr_manager.ZarrDataset attribute) data_type (pymif.microscope_manager.utils.ngff.ZarrWriteConfig attribute)

DATA_TYPES (in module pymif.microscope_manager.utils.axes) dataset_reader() (in module pymif.napari._convert_widget) DEFAULT_COLORS (in module pymif.microscope_manager.utils.ngff) 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

factor_power() (in module pymif.microscope_manager.utils.pyramid)

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) get_spatial_axes() (in module pymif.microscope_manager.utils.pyramid)

I

index_list_from_selection() (in module pymif.microscope_manager.utils.axes)

infer_axes_from_ndim() (in module pymif.microscope_manager.utils.axes) isatty() (pymif.napari._convert_widget.EmittingStream method)

L

level_scale_ratios_from_multiscales() (in module pymif.microscope_manager.utils.downsampling)

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.ZarrDataset attribute) (pymif.microscope_manager.zarr_manager.ZarrManager attribute) (pymif.microscope_manager.ZarrManager attribute) MicroscopeManager (class in pymif.microscope_manager.microscope_manager) mode (pymif.microscope_manager.zarr_manager.ZarrManager attribute) (pymif.microscope_manager.ZarrManager 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.axes pymif.microscope_manager.utils.create_empty_dataset pymif.microscope_manager.utils.create_empty_group pymif.microscope_manager.utils.downsampling 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

multiply_scales() (in module pymif.microscope_manager.utils.pyramid) multiply_spatial_scales() (in module pymif.microscope_manager.utils.downsampling)

N

name (pymif.microscope_manager.zarr_manager.ZarrDataset attribute) 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)

normalize_axes() (in module pymif.microscope_manager.utils.axes) normalize_data_type() (in module pymif.microscope_manager.utils.axes) normalize_spatial_factor() (in module pymif.microscope_manager.utils.downsampling) normalize_spatial_factor_for_axes() (in module pymif.microscope_manager.utils.downsampling)

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.ZarrDataset attribute) (pymif.microscope_manager.zarr_manager.ZarrManager attribute) (pymif.microscope_manager.ZarrManager 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.axes module

pymif.microscope_manager.utils.create_empty_dataset module pymif.microscope_manager.utils.create_empty_group module pymif.microscope_manager.utils.downsampling 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.ZarrManager method) (pymif.microscope_manager.zeiss_manager.ZeissManager method) (pymif.microscope_manager.ZeissManager method)

relative_level_factors() (in module pymif.microscope_manager.utils.downsampling) relative_level_factors_for_axes() (in module pymif.microscope_manager.utils.downsampling) reorder_channels() (pymif.microscope_manager.microscope_manager.MicroscopeManager method) (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method)

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) Selection (in module pymif.microscope_manager.utils.subset) selection_length_and_spacing() (in module pymif.microscope_manager.utils.axes) SPATIAL_AXES (in module pymif.microscope_manager.utils.axes) (in module pymif.microscope_manager.utils.downsampling) (in module pymif.microscope_manager.utils.ngff) spatial_axes_in_order() (in module pymif.microscope_manager.utils.axes) spatial_axis_indices() (in module pymif.microscope_manager.utils.axes) SPATIAL_AXIS_SET (in module pymif.microscope_manager.utils.axes)

spatial_factor_power() (in module pymif.microscope_manager.utils.downsampling) spatial_factor_power_for_axes() (in module pymif.microscope_manager.utils.downsampling) spatial_values_for_axes() (in module pymif.microscope_manager.utils.axes) SpatialFactor (in module pymif.microscope_manager.utils.downsampling) (in module pymif.microscope_manager.utils.pyramid) SpatialIntFactor (in module pymif.microscope_manager.utils.downsampling) SpatialScale (in module pymif.microscope_manager.utils.downsampling) 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) (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager 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) (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method)

U

update_metadata() (pymif.microscope_manager.microscope_manager.MicroscopeManager method) (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager 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.ZarrManager 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) write_multiscale_to_group() (in module pymif.microscope_manager.utils.to_zarr)

Z

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

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)