Index

_

__call__() (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaFlatfield method) (zarrsmith.mosaic_manager.OperaFlatfield method) __commit_id__ (in module zarrsmith._version) __enter__() (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.MicroscopeManager method) (zarrsmith.mosaic_manager.mosaic.MosaicManager method) (zarrsmith.mosaic_manager.MosaicManager method) __exit__() (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.MicroscopeManager method) (zarrsmith.mosaic_manager.mosaic.MosaicManager method) (zarrsmith.mosaic_manager.MosaicManager method) __getattr__() (zarrsmith.microscope_manager.zarr_manager.AttrDict method) __getitem__() (zarrsmith.microscope_manager.evident_manager.VsiSceneArray method) (zarrsmith.microscope_manager.zarr_manager.ZarrDataset method) (zarrsmith.mosaic_manager.h5_array.H5Array method) (zarrsmith.mosaic_manager.H5Array method) (zarrsmith.mosaic_manager.PlaneStackArray method) (zarrsmith.mosaic_manager.tiff_array.PlaneStackArray method) __getstate__() (zarrsmith.microscope_manager.evident_manager.VsiSceneArray method) (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaFlatfield method) (zarrsmith.mosaic_manager.OperaFlatfield method) (zarrsmith.mosaic_manager.PlaneStackArray method) (zarrsmith.mosaic_manager.tiff_array.PlaneStackArray method) __iter__() (zarrsmith.microscope_manager.zarr_manager.ZarrDataset method) (zarrsmith.mosaic_manager.fusion._RegionSeries method) __len__() (zarrsmith.microscope_manager.evident_manager.VsiSceneArray method) (zarrsmith.microscope_manager.zarr_manager.ZarrDataset method) (zarrsmith.mosaic_manager.fusion._RegionSeries method) (zarrsmith.mosaic_manager.h5_array.H5Array method) (zarrsmith.mosaic_manager.H5Array method) (zarrsmith.mosaic_manager.PlaneStackArray method) (zarrsmith.mosaic_manager.tiff_array.PlaneStackArray method) __post_init__() (zarrsmith.mosaic_manager.Tile method) (zarrsmith.mosaic_manager.tile.Tile method) __repr__() (zarrsmith.microscope_manager.evident_manager.VsiSceneArray method) (zarrsmith.microscope_manager.zarr_manager.ZarrDataset method) (zarrsmith.mosaic_manager.czi_array.CziTileArray method) (zarrsmith.mosaic_manager.CziTileArray method) (zarrsmith.mosaic_manager.h5_array.H5Array method) (zarrsmith.mosaic_manager.H5Array method) (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaFlatfield method) (zarrsmith.mosaic_manager.OperaFlatfield method) (zarrsmith.mosaic_manager.tiff_array.TiffStackArray method) (zarrsmith.mosaic_manager.TiffStackArray method) __version__ (in module zarrsmith) (in module zarrsmith._version) __version_tuple__ (in module zarrsmith._version) _acquisitions() (zarrsmith.mosaic_manager.luxendo_mosaic_manager.LuxendoMosaicManager class method) (zarrsmith.mosaic_manager.LuxendoMosaicManager class method) _append_batch_csv() (in module zarrsmith.napari._convert_widget) _ARGB_PATTERN (in module zarrsmith.utils.colors) _array_create_kwargs() (in module zarrsmith.utils.ngff) _auto_coarse_level() (in module zarrsmith.utils.chromatic_shift) _auto_shard_for_level() (in module zarrsmith.utils.ngff) _available_memory_mb() (in module zarrsmith.utils.ngff) _axes_of() (in module zarrsmith.utils.dataset_ops) _axis_scale() (in module zarrsmith.utils.visualize) _axis_units() (in module zarrsmith.utils.visualize) _batch_row_kwargs() (in module zarrsmith.cli.zarrsmith) _BLOCKS (in module zarrsmith.mosaic_manager.opera_mosaic_manager) _blocks() (zarrsmith.mosaic_manager.fusion._RegionSeries method) _box() (in module zarrsmith.napari._mosaic_widget) _build_axes() (in module zarrsmith.utils.ngff) _build_coordinate_transformations() (in module zarrsmith.utils.ngff) _build_dask_array() (zarrsmith.microscope_manager.array_manager.ArrayManager method) (zarrsmith.microscope_manager.ArrayManager method) (zarrsmith.microscope_manager.evident_manager.EvidentManager method) (zarrsmith.microscope_manager.EvidentManager method) (zarrsmith.microscope_manager.luxendo_manager.LuxendoManager method) (zarrsmith.microscope_manager.LuxendoManager method) (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.opera_manager.OperaManager method) (zarrsmith.microscope_manager.OperaManager method) (zarrsmith.microscope_manager.scape_manager.ScapeManager method) (zarrsmith.microscope_manager.ScapeManager method) (zarrsmith.microscope_manager.viventis_manager.ViventisManager method) (zarrsmith.microscope_manager.ViventisManager method) (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) (zarrsmith.microscope_manager.zeiss_manager.ZeissManager method) (zarrsmith.microscope_manager.ZeissManager method) _build_frames() (in module zarrsmith.mosaic_manager.fusion) _build_multiscales() (in module zarrsmith.utils.ngff) _build_omero_metadata() (in module zarrsmith.utils.ngff) _build_own_frames() (in module zarrsmith.mosaic_manager.fusion) _build_ui() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _build_v2_compressor() (in module zarrsmith.utils.ngff) _build_v3_compressors() (in module zarrsmith.utils.ngff) _cache (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaFlatfield attribute) (zarrsmith.mosaic_manager.OperaFlatfield attribute) _canvas_size() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _cast() (in module zarrsmith.mosaic_manager.fusion) _cast_like() (in module zarrsmith.utils.chromatic_shift) _ceil_to_multiple() (in module zarrsmith.utils.chromatic_shift) _central_tiles() (in module zarrsmith.mosaic_manager.mosaic) _centre_block() (in module zarrsmith.mosaic_manager.mosaic) _channel_colors() (zarrsmith.microscope_manager.evident_manager.EvidentManager method) (zarrsmith.microscope_manager.EvidentManager method) _channel_colors_from_metadata() (in module zarrsmith.napari._convert_widget) _channel_index() (in module zarrsmith.cli.zarrsmith) _channel_names() (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaMosaicManager static method) (zarrsmith.mosaic_manager.OperaMosaicManager static method) _channel_volume() (in module zarrsmith.utils.chromatic_shift) _check_channel_values() (in module zarrsmith.utils.dataset_ops) _check_chunk_size() (in module zarrsmith.cli.zarrsmith) _check_data_type() (in module zarrsmith.utils.dataset_ops) _check_scales() (in module zarrsmith.utils.dataset_ops) _check_time_increment() (in module zarrsmith.utils.dataset_ops) _check_time_unit() (in module zarrsmith.utils.dataset_ops) _check_units() (in module zarrsmith.utils.dataset_ops) _check_write_options() (in module zarrsmith.mosaic_manager.fusion) _child_value() (zarrsmith.microscope_manager.evident_manager.EvidentManager static method) (zarrsmith.microscope_manager.EvidentManager static method) _choose_plot_features() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _chromatic_shift_kwargs() (in module zarrsmith.cli.zarrsmith) _chunk_shape_for_dataset() (in module zarrsmith.napari._convert_widget) _clear() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _clear_highlight() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _CLICK_TOLERANCE (in module zarrsmith.napari._mosaic_widget) _COLORMAPS (in module zarrsmith.mosaic_manager.mosaic) _combine() (in module zarrsmith.mosaic_manager.fusion) _compact_advanced_rows() (in module zarrsmith.napari._convert_widget) _connect_plotter() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _create_level_arrays() (in module zarrsmith.utils.ngff) _crop_bounds() (in module zarrsmith.mosaic_manager.fusion) _dataset_scale_vector() (in module zarrsmith.utils.downsampling) _dataset_size_mb() (in module zarrsmith.cli.zarrsmith) _default_window() (in module zarrsmith.utils.ngff) _DIM_IDS (zarrsmith.microscope_manager.scape_manager.ScapeManager attribute) (zarrsmith.microscope_manager.ScapeManager attribute) _display_windows() (in module zarrsmith.mosaic_manager.fusion) _downsample() (in module zarrsmith.mosaic_manager.fusion) _drop_axes_from_config_shapes() (in module zarrsmith.utils.to_zarr) _drop_singleton_axes() (in module zarrsmith.utils.to_zarr) _DROPPABLE_AXES (in module zarrsmith.utils.to_zarr) _ESTIMATE_OPTIONS (in module zarrsmith.cli.zarrsmith) _extract_metadata() (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) _fill_image_list() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _FILTER_MARGIN (in module zarrsmith.utils.chromatic_shift) _find_xlif_for_ome_tiff() (zarrsmith.microscope_manager.scape_manager.ScapeManager method) (zarrsmith.microscope_manager.ScapeManager method) _flips() (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaMosaicManager static method) (zarrsmith.mosaic_manager.OperaMosaicManager static method) _FOCUS (in module zarrsmith.mosaic_manager.zeiss_mosaic_manager) _focus_positions() (zarrsmith.mosaic_manager.zeiss_mosaic_manager.ZeissMosaicManager static method) (zarrsmith.mosaic_manager.ZeissMosaicManager static method) _form() (in module zarrsmith.napari._explorer_widget) _FRAME_Z_TAG (in module zarrsmith.microscope_manager.evident_manager) _fuse_level0() (in module zarrsmith.mosaic_manager.fusion) _fuse_region() (in module zarrsmith.mosaic_manager.fusion) _fuse_worker() (in module zarrsmith.napari._mosaic_widget) _generate_pyramid() (in module zarrsmith.utils.write_image_region) _get_group_multiscales() (in module zarrsmith.utils.ngff) _get_group_ome_attrs() (in module zarrsmith.utils.ngff) _get_image_meta() (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) _get_multiscales() (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) _get_nested_group() (in module zarrsmith.utils.write_image_region) _get_omero() (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) _group_extents() (in module zarrsmith.mosaic_manager.fusion) _group_log_weight() (in module zarrsmith.mosaic_manager.fusion) _guess_axes() (zarrsmith.microscope_manager.scape_manager.ScapeManager static method) (zarrsmith.microscope_manager.ScapeManager static method) _h5_handles (zarrsmith.microscope_manager.luxendo_manager.LuxendoManager attribute) (zarrsmith.microscope_manager.LuxendoManager attribute) _header() (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaMosaicManager static method) (zarrsmith.mosaic_manager.OperaMosaicManager static method) _HEX_COLOR_PATTERN (in module zarrsmith.utils.colors) _hide_popup() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _highlight (zarrsmith.napari._explorer_widget.ObjectsExplorer attribute) _hover_row (zarrsmith.napari._explorer_widget.ObjectsExplorer attribute) _hover_text() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _hover_timer (zarrsmith.napari._explorer_widget.ObjectsExplorer attribute) _image (zarrsmith.microscope_manager.zeiss_manager.ZeissManager attribute) (zarrsmith.microscope_manager.ZeissManager attribute) _image_read() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _image_size() (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaMosaicManager static method) (zarrsmith.mosaic_manager.OperaMosaicManager static method) _indices_to_expr() (in module zarrsmith.napari._convert_widget) _infer_data_type_from_group() (in module zarrsmith.utils.ngff) _infer_ngff_version() (in module zarrsmith.utils.ngff) _int_triplet() (in module zarrsmith.cli.zarrsmith) _invalidate_zarr_data() (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) _is_reciprocal_integer_shrink() (in module zarrsmith.utils.write_image_region) _isolate_toggled() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _iter_datasets() (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) _label_entry() (in module zarrsmith.utils.ngff) _label_wells() (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaMosaicManager static method) (zarrsmith.mosaic_manager.OperaMosaicManager static method) _labels_contains() (in module zarrsmith.utils.ngff) _layout_blocks() (in module zarrsmith.mosaic_manager.fusion) _lazy() (zarrsmith.mosaic_manager.mosaic.MosaicManager static method) (zarrsmith.mosaic_manager.MosaicManager static method) _lazy_series() (zarrsmith.mosaic_manager.mosaic.MosaicManager class method) (zarrsmith.mosaic_manager.MosaicManager class method) _level_chunks() (zarrsmith.microscope_manager.evident_manager.EvidentManager method) (zarrsmith.microscope_manager.EvidentManager method) _level_sizes() (zarrsmith.microscope_manager.evident_manager.EvidentManager method) (zarrsmith.microscope_manager.EvidentManager method) _link_layers() (in module zarrsmith.mosaic_manager.mosaic) _load_done() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _load_failed() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _load_group() (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) _load_labels() (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) _log_border_distance() (in module zarrsmith.mosaic_manager.fusion) _LUT_COLORS (zarrsmith.microscope_manager.scape_manager.ScapeManager attribute) (zarrsmith.microscope_manager.ScapeManager attribute) _MAP_COLORS (in module zarrsmith.napari._mosaic_widget) _mark_shown_image() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _merge_groups() (in module zarrsmith.mosaic_manager.fusion) _merge_sigmoid() (in module zarrsmith.mosaic_manager.fusion) _metadata_for_legacy_label() (in module zarrsmith.utils.create_empty_group) _metadata_for_write() (in module zarrsmith.utils.to_zarr) _micrometres() (in module zarrsmith.mosaic_manager.opera_mosaic_manager) _midline_ranges() (in module zarrsmith.mosaic_manager.fusion) _mirrored_array_kwargs() (in module zarrsmith.utils.chromatic_shift) _mosaic_manager_name_map() (in module zarrsmith.cli.zarrsmith)

_multi_table (zarrsmith.napari._explorer_widget.ObjectsExplorer attribute) _n_spatial() (in module zarrsmith.utils.dataset_ops) _ncc_curve() (in module zarrsmith.utils.chromatic_shift) _new_softmax_state() (in module zarrsmith.mosaic_manager.fusion) _nodes() (zarrsmith.microscope_manager.evident_manager.EvidentManager static method) (zarrsmith.microscope_manager.EvidentManager static method) _normalize_chunks() (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager static method) (zarrsmith.microscope_manager.MicroscopeManager static method) _normalize_downscale_factor() (in module zarrsmith.cli.zarrsmith) _normalize_shard_exclude_axes() (in module zarrsmith.cli.zarrsmith) _normalize_shards() (in module zarrsmith.cli.zarrsmith) _normalize_subset() (in module zarrsmith.cli.zarrsmith) _normalize_zoom_scale() (in module zarrsmith.utils.zoom) _NOT_CONVERSION_OPTIONS (in module zarrsmith.cli.zarrsmith) _NS (in module zarrsmith.utils.ome) _number() (zarrsmith.microscope_manager.evident_manager.EvidentManager static method) (zarrsmith.microscope_manager.EvidentManager static method) _ome_channel_color() (in module zarrsmith.utils.ome) _on_highlighted() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _on_label_selected() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _on_mouse_move() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _open_files (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager attribute) (zarrsmith.microscope_manager.MicroscopeManager attribute) (zarrsmith.mosaic_manager.mosaic.MosaicManager attribute) (zarrsmith.mosaic_manager.MosaicManager attribute) _open_scene() (in module zarrsmith.microscope_manager.evident_manager) _OPENING (in module zarrsmith.mosaic_manager.opera_mosaic_manager) _opening_done() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _orientation() (in module zarrsmith.mosaic_manager.opera_mosaic_manager) _overlap() (in module zarrsmith.mosaic_manager.fusion) _OVERWRITE_HINT (in module zarrsmith.cli.zarrsmith) _parse_arguments() (in module zarrsmith.cli.__arguments) _parse_color() (in module zarrsmith.utils.visualize) _parse_metadata() (zarrsmith.microscope_manager.array_manager.ArrayManager method) (zarrsmith.microscope_manager.ArrayManager method) (zarrsmith.microscope_manager.evident_manager.EvidentManager method) (zarrsmith.microscope_manager.EvidentManager method) (zarrsmith.microscope_manager.luxendo_manager.LuxendoManager method) (zarrsmith.microscope_manager.LuxendoManager method) (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.opera_manager.OperaManager method) (zarrsmith.microscope_manager.OperaManager method) (zarrsmith.microscope_manager.scape_manager.ScapeManager method) (zarrsmith.microscope_manager.ScapeManager method) (zarrsmith.microscope_manager.viventis_manager.ViventisManager method) (zarrsmith.microscope_manager.ViventisManager method) (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) (zarrsmith.microscope_manager.zeiss_manager.ZeissManager method) (zarrsmith.microscope_manager.ZeissManager method) _parse_shifts() (in module zarrsmith.cli.zarrsmith) _patch_plotter() (in module zarrsmith.napari._explorer_widget) _pixel_sizes() (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaMosaicManager static method) (zarrsmith.mosaic_manager.OperaMosaicManager static method) _PIXEL_TYPES (in module zarrsmith.mosaic_manager.zeiss_mosaic_manager) _place_tiles() (in module zarrsmith.mosaic_manager.fusion) _Placed (class in zarrsmith.mosaic_manager.fusion) _plane() (zarrsmith.mosaic_manager.PlaneStackArray method) (zarrsmith.mosaic_manager.tiff_array.PlaneStackArray method) _plane_files() (zarrsmith.microscope_manager.luxendo_manager.LuxendoManager method) (zarrsmith.microscope_manager.LuxendoManager method) (zarrsmith.microscope_manager.viventis_manager.ViventisManager static method) (zarrsmith.microscope_manager.ViventisManager static method) _PLATE (in module zarrsmith.mosaic_manager.opera_mosaic_manager) _plot_points() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _PLOTTER_IMPORT_ERROR (in module zarrsmith.napari._explorer_widget) _point_under() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _position() (in module zarrsmith.mosaic_manager.opera_mosaic_manager) _prefetch_planes() (in module zarrsmith.mosaic_manager.mosaic) _present() (in module zarrsmith.cli.zarrsmith) _present_range() (in module zarrsmith.napari._convert_widget) _print_shift_report() (in module zarrsmith.cli.zarrsmith) _profiles() (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaMosaicManager method) (zarrsmith.mosaic_manager.OperaMosaicManager method) _progress_bar() (in module zarrsmith.utils.ngff) _PROJECTIONS (in module zarrsmith.napari._mosaic_widget) _range_to_indices() (in module zarrsmith.napari._convert_widget) _raw_metadata (zarrsmith.microscope_manager.evident_manager.EvidentManager attribute) (zarrsmith.microscope_manager.EvidentManager attribute) _read() (zarrsmith.microscope_manager.evident_manager.VsiSceneArray method) (zarrsmith.mosaic_manager.czi_array.CziTileArray method) (zarrsmith.mosaic_manager.CziTileArray method) (zarrsmith.mosaic_manager.PlaneStackArray method) (zarrsmith.mosaic_manager.tiff_array.PlaneStackArray method) (zarrsmith.mosaic_manager.tiff_array.TiffStackArray method) (zarrsmith.mosaic_manager.TiffStackArray method) _READ_BLOCK (in module zarrsmith.mosaic_manager.opera_mosaic_manager) _read_block() (in module zarrsmith.mosaic_manager.fusion) _read_h5_stack() (zarrsmith.microscope_manager.luxendo_manager.LuxendoManager method) (zarrsmith.microscope_manager.LuxendoManager method) _read_info() (zarrsmith.mosaic_manager.luxendo_mosaic_manager.LuxendoMosaicManager static method) (zarrsmith.mosaic_manager.LuxendoMosaicManager static method) _read_multiscale_group() (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) _ready (zarrsmith.mosaic_manager.PlaneStackArray attribute) (zarrsmith.mosaic_manager.tiff_array.PlaneStackArray attribute) _refuse_output() (in module zarrsmith.cli.zarrsmith) _Region (class in zarrsmith.mosaic_manager.fusion) _REGION_2D (in module zarrsmith.mosaic_manager.fusion) _REGION_3D (in module zarrsmith.mosaic_manager.fusion) _REGION_MAX (in module zarrsmith.mosaic_manager.fusion) _region_shape() (in module zarrsmith.mosaic_manager.fusion) _REGION_VOXELS (in module zarrsmith.mosaic_manager.fusion) _RegionSeries (class in zarrsmith.mosaic_manager.fusion) _register_label_on_labels_group() (in module zarrsmith.utils.ngff) _request_thumbnail() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _require_axes() (in module zarrsmith.utils.chromatic_shift) _RESERVED_WRITE_OPTIONS (in module zarrsmith.mosaic_manager.fusion) _resolve_creation_shards() (in module zarrsmith.utils.ngff) _resolve_format() (in module zarrsmith.utils.ngff) _resolve_mosaic_manager() (in module zarrsmith.cli.zarrsmith) _resolve_num_workers() (in module zarrsmith.utils.ngff) _resolve_shards_for_levels() (in module zarrsmith.utils.ngff) _resolve_tiles() (zarrsmith.mosaic_manager.mosaic.MosaicManager method) (zarrsmith.mosaic_manager.MosaicManager method) _resolve_write_chunks() (in module zarrsmith.utils.ngff) _resolve_zarr_manager() (in module zarrsmith.cli.zarrsmith) _retake() (zarrsmith.mosaic_manager.luxendo_mosaic_manager.LuxendoMosaicManager static method) (zarrsmith.mosaic_manager.LuxendoMosaicManager static method) _run_conversion() (in module zarrsmith.napari._convert_widget) _run_stores() (in module zarrsmith.utils.ngff) _runs() (in module zarrsmith.mosaic_manager.fusion) _sample_mask() (in module zarrsmith.utils.chromatic_shift) _scale_index() (in module zarrsmith.utils.write_image_region) (in module zarrsmith.utils.write_label_region) _scan() (zarrsmith.mosaic_manager.luxendo_mosaic_manager.LuxendoMosaicManager method) (zarrsmith.mosaic_manager.LuxendoMosaicManager method) (zarrsmith.mosaic_manager.mosaic.MosaicManager method) (zarrsmith.mosaic_manager.MosaicManager method) (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaMosaicManager method) (zarrsmith.mosaic_manager.OperaMosaicManager method) (zarrsmith.mosaic_manager.zeiss_mosaic_manager.ZeissMosaicManager method) (zarrsmith.mosaic_manager.ZeissMosaicManager method) _scan_worker() (in module zarrsmith.napari._mosaic_widget) _scene (zarrsmith.microscope_manager.evident_manager.VsiSceneArray attribute) _scene_tag() (in module zarrsmith.napari._convert_widget) _scene_volume() (zarrsmith.microscope_manager.evident_manager.EvidentManager method) (zarrsmith.microscope_manager.EvidentManager method) _select_timepoints() (in module zarrsmith.mosaic_manager.fusion) _set_axis_labels() (in module zarrsmith.utils.visualize) _set_dimension_names() (in module zarrsmith.utils.ngff) _set_features() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _set_group_ngff_metadata() (in module zarrsmith.utils.ngff) _set_plot_features() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _set_range_widget() (in module zarrsmith.napari._convert_widget) _shape() (zarrsmith.mosaic_manager.luxendo_mosaic_manager.LuxendoMosaicManager static method) (zarrsmith.mosaic_manager.LuxendoMosaicManager static method) _show() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _show_dataset() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _show_image() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _sigmoid_add() (in module zarrsmith.mosaic_manager.fusion) _sigmoid_transitions() (in module zarrsmith.mosaic_manager.fusion) _SLAB_PLANES (in module zarrsmith.mosaic_manager.fusion) _slide (zarrsmith.microscope_manager.evident_manager.EvidentManager attribute) (zarrsmith.microscope_manager.EvidentManager attribute) _snap_shard_shape() (in module zarrsmith.utils.ngff) _softmax_add() (in module zarrsmith.mosaic_manager.fusion) _sorted_dataset_names() (zarrsmith.microscope_manager.luxendo_manager.LuxendoManager static method) (zarrsmith.microscope_manager.LuxendoManager static method) _source (zarrsmith.microscope_manager.array_manager.ArrayManager attribute) (zarrsmith.microscope_manager.ArrayManager attribute) _source_chunks() (in module zarrsmith.mosaic_manager.fusion) _spatial_factor() (in module zarrsmith.mosaic_manager.fusion) _spread_surface_points() (in module zarrsmith.utils.chromatic_shift) _stacks() (zarrsmith.mosaic_manager.zeiss_mosaic_manager.ZeissMosaicManager static method) (zarrsmith.mosaic_manager.ZeissMosaicManager static method) _strip_ome_tiff_suffix() (zarrsmith.microscope_manager.scape_manager.ScapeManager static method) (zarrsmith.microscope_manager.ScapeManager static method) _subpixel_peak() (in module zarrsmith.utils.chromatic_shift) _subset_list() (in module zarrsmith.utils.subset) _subset_string_from_widget() (in module zarrsmith.napari._convert_widget) _subset_to_crop() (in module zarrsmith.cli.zarrsmith) _sync_raw_aliases() (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) _syncing (zarrsmith.napari._explorer_widget.ObjectsExplorer attribute) _table_changed() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _TAG (in module zarrsmith.mosaic_manager.opera_mosaic_manager) _tags() (in module zarrsmith.mosaic_manager.opera_mosaic_manager) _target() (in module zarrsmith.mosaic_manager.fusion) _target_chunks() (in module zarrsmith.utils.pyramid) _TEMP_COMPRESSORS (in module zarrsmith.mosaic_manager.fusion) _thumbnail_failed() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _thumbnail_key() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _thumbnail_read() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _thumbnails (zarrsmith.napari._explorer_widget.ObjectsExplorer attribute) _tick() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _ticked (zarrsmith.napari._explorer_widget.ObjectsExplorer attribute) _ticks_changed() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _tile_from() (zarrsmith.mosaic_manager.luxendo_mosaic_manager.LuxendoMosaicManager class method) (zarrsmith.mosaic_manager.LuxendoMosaicManager class method) _tile_log_weight() (in module zarrsmith.mosaic_manager.fusion) _timepoint_cell() (in module zarrsmith.cli.zarrsmith) _TO_MICROMETER (in module zarrsmith.utils.units) _tp_ch() (zarrsmith.microscope_manager.luxendo_manager.LuxendoManager class method) (zarrsmith.microscope_manager.LuxendoManager class method) _UNIT (in module zarrsmith.mosaic_manager.opera_mosaic_manager) _UNIT_ALIASES (in module zarrsmith.utils.units) _UNITS (in module zarrsmith.mosaic_manager.opera_mosaic_manager) _user_metadata (zarrsmith.microscope_manager.array_manager.ArrayManager attribute) (zarrsmith.microscope_manager.ArrayManager attribute) _validate_metadata() (in module zarrsmith.utils.ngff) _VALIDATORS (in module zarrsmith.utils.dataset_ops) _warn_rows_skipped() (in module zarrsmith.cli.zarrsmith) _well_name() (in module zarrsmith.mosaic_manager.opera_mosaic_manager) _well_pitch() (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaMosaicManager static method) (zarrsmith.mosaic_manager.OperaMosaicManager static method) _WINDOW_SAMPLES (in module zarrsmith.mosaic_manager.fusion) _without_axis() (in module zarrsmith.utils.create_empty_group) _worker_done() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) _write_display_windows() (in module zarrsmith.mosaic_manager.fusion) _write_provenance() (in module zarrsmith.mosaic_manager.fusion) _write_pyramid_v2() (in module zarrsmith.utils.ngff) _write_pyramid_v3() (in module zarrsmith.utils.ngff) _write_region() (in module zarrsmith.utils.write_image_region) _xyz_to_zyx() (zarrsmith.microscope_manager.luxendo_manager.LuxendoManager static method) (zarrsmith.microscope_manager.LuxendoManager static method) _z_derivative() (in module zarrsmith.utils.chromatic_shift) _z_facing_surface() (in module zarrsmith.utils.chromatic_shift) _z_step() (zarrsmith.microscope_manager.evident_manager.EvidentManager method) (zarrsmith.microscope_manager.EvidentManager method) _z_unit() (in module zarrsmith.utils.chromatic_shift) _zoom_dask() (in module zarrsmith.utils.zoom) _zoom_numpy() (in module zarrsmith.utils.zoom) _zyx_spacings() (in module zarrsmith.utils.chromatic_shift)

A

active (zarrsmith.napari._explorer_widget.Session attribute) add_image_layers() (in module zarrsmith.napari._explorer_widget) add_layers() (in module zarrsmith.utils.visualize) add_tile_map() (in module zarrsmith.napari._mosaic_widget) ALL_TIMEPOINTS (in module zarrsmith.mosaic_manager.fusion) ALLOWED_AXES (in module zarrsmith.utils.axes) ALLOWED_AXIS_SET (in module zarrsmith.utils.axes) append_batch_csv() (in module zarrsmith.napari._batch_csv) apply_chromatic_shift() (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) apply_display_windows() (in module zarrsmith.napari._mosaic_widget)

apply_metadata_updates() (in module zarrsmith.utils.dataset_ops) ArrayManager (class in zarrsmith.microscope_manager) (class in zarrsmith.microscope_manager.array_manager) as_labels() (in module zarrsmith.napari._explorer_widget) AttrDict (class in zarrsmith.microscope_manager.zarr_manager) attrs (zarrsmith.mosaic_manager.Tile attribute) (zarrsmith.mosaic_manager.tile.Tile attribute) axes (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) axis_index() (in module zarrsmith.napari._dataset_helpers) axis_names_from_multiscales() (in module zarrsmith.utils.downsampling) axis_size() (in module zarrsmith.napari._dataset_helpers)

B

BATCH_CSV_COLUMNS (in module zarrsmith.napari._convert_widget) batch_row() (in module zarrsmith.napari._mosaic_widget) blend (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) BLENDS (in module zarrsmith.mosaic_manager.fusion) blocks (zarrsmith.mosaic_manager.fusion._RegionSeries attribute) bounding_box() (zarrsmith.mosaic_manager.mosaic.MosaicManager method) (zarrsmith.mosaic_manager.MosaicManager method)

bounds (zarrsmith.mosaic_manager.fusion._Region attribute) box() (in module zarrsmith.napari._explorer_widget) boxed_picks() (in module zarrsmith.napari._mosaic_widget) build_metadata() (in module zarrsmith.utils.metadata) build_pyramid() (in module zarrsmith.utils.pyramid) (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method)

C

centroid_columns() (in module zarrsmith.napari._explorer_widget) centroids_from_labels() (in module zarrsmith.napari._explorer_widget) channel (zarrsmith.mosaic_manager.Tile attribute) (zarrsmith.mosaic_manager.tile.Tile attribute) channel_count() (in module zarrsmith.utils.dataset_ops) channel_index (zarrsmith.mosaic_manager.fusion._Region attribute) channel_names() (in module zarrsmith.mosaic_manager.zeiss_mosaic_manager) (in module zarrsmith.utils.visualize) ChannelInfo (class in zarrsmith.utils.metadata) channels (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) (zarrsmith.mosaic_manager.mosaic.MosaicManager property) (zarrsmith.mosaic_manager.MosaicManager property) (zarrsmith.utils.ome.OmePixels attribute) check_output_path() (in module zarrsmith.utils.output_path) check_reader() (in module zarrsmith.mosaic_manager) (in module zarrsmith.mosaic_manager.readers) check_single_field() (in module zarrsmith.mosaic_manager.fields) chromatic_shift_batch() (in module zarrsmith.cli.zarrsmith) chromatic_shift_correct() (in module zarrsmith.cli.zarrsmith) chromatic_shift_single() (in module zarrsmith.cli.zarrsmith) chunks (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager attribute) (zarrsmith.microscope_manager.MicroscopeManager attribute) (zarrsmith.microscope_manager.zarr_manager.ZarrManager attribute) (zarrsmith.microscope_manager.ZarrManager attribute) (zarrsmith.mosaic_manager.PlaneStackArray attribute) (zarrsmith.mosaic_manager.tiff_array.PlaneStackArray attribute) (zarrsmith.utils.ngff.ZarrWriteConfig attribute) clean_table() (in module zarrsmith.napari._explorer_widget) close() (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.MicroscopeManager method) (zarrsmith.mosaic_manager.mosaic.MosaicManager method) (zarrsmith.mosaic_manager.MosaicManager method)

coefficients (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaFlatfield attribute) (zarrsmith.mosaic_manager.OperaFlatfield attribute) color (zarrsmith.utils.metadata.ChannelInfo attribute) commit_id (in module zarrsmith._version) compose_dock() (in module zarrsmith.napari._layout) compressor (zarrsmith.utils.ngff.ZarrWriteConfig attribute) compressor_level (zarrsmith.utils.ngff.ZarrWriteConfig attribute) compute (zarrsmith.utils.ngff.ZarrWriteConfig attribute) connected_components() (in module zarrsmith.mosaic_manager) (in module zarrsmith.mosaic_manager.fields) conservative_compute_multiscale_level() (in module zarrsmith.napari._convert_widget) contrast_limits() (in module zarrsmith.napari._explorer_widget) (zarrsmith.mosaic_manager.mosaic.MosaicManager method) (zarrsmith.mosaic_manager.MosaicManager method) convert_batch() (in module zarrsmith.cli.zarrsmith) convert_mosaic_batch() (in module zarrsmith.cli.zarrsmith) convert_mosaic_single() (in module zarrsmith.cli.zarrsmith) convert_single() (in module zarrsmith.cli.zarrsmith) convert_widget() (in module zarrsmith.napari._convert_widget) convert_worker() (in module zarrsmith.napari._convert_widget) coords (zarrsmith.mosaic_manager.czi_array.CziTileArray attribute) (zarrsmith.mosaic_manager.CziTileArray attribute) correct_chromatic_shift() (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) create_empty_dataset() (in module zarrsmith.utils.create_empty_dataset) create_empty_group() (in module zarrsmith.utils.create_empty_group) (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) czi_distance() (in module zarrsmith.utils.czi) CziTileArray (class in zarrsmith.mosaic_manager) (class in zarrsmith.mosaic_manager.czi_array)

D

data (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager attribute) (zarrsmith.microscope_manager.MicroscopeManager attribute) (zarrsmith.microscope_manager.zarr_manager.ZarrDataset attribute) (zarrsmith.mosaic_manager.Tile attribute) (zarrsmith.mosaic_manager.tile.Tile attribute) data() (zarrsmith.napari._explorer_widget.Session method) data_type (zarrsmith.utils.ngff.ZarrWriteConfig attribute) DATA_TYPES (in module zarrsmith.utils.axes) dataset (zarrsmith.mosaic_manager.h5_array.H5Array attribute) (zarrsmith.mosaic_manager.H5Array attribute) dataset_axes() (in module zarrsmith.napari._dataset_helpers) dataset_reader() (in module zarrsmith.napari._convert_widget) default_channel_color() (in module zarrsmith.utils.colors) DEFAULT_CHANNEL_PALETTE (in module zarrsmith.utils.colors) default_chunk_size() (in module zarrsmith.utils.chunks) DEFAULT_CHUNKS (zarrsmith.microscope_manager.array_manager.ArrayManager attribute) (zarrsmith.microscope_manager.ArrayManager attribute) (zarrsmith.microscope_manager.evident_manager.EvidentManager attribute) (zarrsmith.microscope_manager.EvidentManager attribute) (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager attribute) (zarrsmith.microscope_manager.MicroscopeManager attribute) (zarrsmith.microscope_manager.scape_manager.ScapeManager attribute) (zarrsmith.microscope_manager.ScapeManager attribute) (zarrsmith.microscope_manager.zeiss_manager.ZeissManager attribute) (zarrsmith.microscope_manager.ZeissManager attribute) DEFAULT_MAX_WORKERS (in module zarrsmith.utils.ngff) DEFAULT_MEMORY_FRACTION (in module zarrsmith.utils.ngff) default_num_levels() (in module zarrsmith.utils.chunks) default_output() (in module zarrsmith.napari._mosaic_widget)

DEFAULT_SHARD_EXCLUDE_AXES (in module zarrsmith.utils.ngff) DEFAULT_WORKER_FRACTION (in module zarrsmith.utils.ngff) detect_microscope() (in module zarrsmith.mosaic_manager) (in module zarrsmith.mosaic_manager.readers) detect_reader() (in module zarrsmith.microscope_manager) (in module zarrsmith.microscope_manager.readers) detected (zarrsmith.mosaic_manager.readers.WrongReaderError attribute) (zarrsmith.mosaic_manager.WrongReaderError attribute) dims (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaFlatfield attribute) (zarrsmith.mosaic_manager.OperaFlatfield attribute) DISPLAY_PERCENTILES (in module zarrsmith.mosaic_manager.fusion) display_windows() (in module zarrsmith.mosaic_manager) (in module zarrsmith.mosaic_manager.fusion) downsample_nearest() (in module zarrsmith.utils.downsampling) dragEnterEvent() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) drop_singleton (zarrsmith.utils.ngff.ZarrWriteConfig attribute) dropEvent() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) ds (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) dtype (zarrsmith.microscope_manager.evident_manager.VsiSceneArray attribute) (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) (zarrsmith.mosaic_manager.h5_array.H5Array attribute) (zarrsmith.mosaic_manager.H5Array attribute) (zarrsmith.mosaic_manager.PlaneStackArray attribute) (zarrsmith.mosaic_manager.tiff_array.PlaneStackArray attribute) (zarrsmith.mosaic_manager.Tile property) (zarrsmith.mosaic_manager.tile.Tile property) (zarrsmith.utils.ome.OmePixels attribute)

E

EmittingStream (class in zarrsmith.napari._log) enable_drag_and_drop() (in module zarrsmith.napari._layout) error (zarrsmith.mosaic_manager.fusion.FusionPlan property) (zarrsmith.mosaic_manager.FusionPlan property) estimate_chromatic_shift() (in module zarrsmith.utils.chromatic_shift) (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) EvidentManager (class in zarrsmith.microscope_manager) (class in zarrsmith.microscope_manager.evident_manager)

exact_factors (zarrsmith.microscope_manager.evident_manager.VsiSceneArray property) explorer_widget() (in module zarrsmith.napari._explorer_widget) export_contrast_settings() (in module zarrsmith.napari._export_widget) export_files() (in module zarrsmith.napari._export_widget) export_stem() (in module zarrsmith.napari._export_widget) export_widget() (in module zarrsmith.napari._export_widget) Extent (in module zarrsmith.utils.chromatic_shift) extent (zarrsmith.mosaic_manager.Tile property) (zarrsmith.mosaic_manager.tile.Tile property) extra (zarrsmith.napari._explorer_widget.Session attribute)

F

factor_power() (in module zarrsmith.utils.pyramid) FALLBACK_MEMORY_BUDGET_MB (in module zarrsmith.utils.ngff) feature_rows (zarrsmith.napari._explorer_widget.Session attribute) features() (zarrsmith.napari._explorer_widget.Session method) field (zarrsmith.mosaic_manager.Tile attribute) (zarrsmith.mosaic_manager.tile.Tile attribute) field_name() (in module zarrsmith.mosaic_manager.zeiss_mosaic_manager) field_path() (in module zarrsmith.napari._explorer_widget) FIELD_PREFIX (in module zarrsmith.mosaic_manager.fields) field_summary() (in module zarrsmith.napari._mosaic_widget) field_tiles() (zarrsmith.mosaic_manager.mosaic.MosaicManager method) (zarrsmith.mosaic_manager.MosaicManager method) fields (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) (zarrsmith.mosaic_manager.mosaic.MosaicManager property) (zarrsmith.mosaic_manager.MosaicManager property) fields_of() (in module zarrsmith.mosaic_manager.fields) find_index() (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaMosaicManager static method) (zarrsmith.mosaic_manager.OperaMosaicManager static method) find_tile_map() (in module zarrsmith.napari._mosaic_widget) first_of_series() (in module zarrsmith.mosaic_manager.tile)

flatfield (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaMosaicManager attribute) (zarrsmith.mosaic_manager.OperaMosaicManager attribute) flatfields (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaMosaicManager attribute) (zarrsmith.mosaic_manager.OperaMosaicManager attribute) flush() (zarrsmith.napari._log.EmittingStream method) folder (zarrsmith.mosaic_manager.tiff_array.TiffStackArray attribute) (zarrsmith.mosaic_manager.TiffStackArray attribute) folder_of() (in module zarrsmith.napari._mosaic_widget) frames (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) from_profile() (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaFlatfield class method) (zarrsmith.mosaic_manager.OperaFlatfield class method) full_size (zarrsmith.microscope_manager.evident_manager.VsiSceneArray attribute) fuse() (zarrsmith.mosaic_manager.mosaic.MosaicManager method) (zarrsmith.mosaic_manager.MosaicManager method) fuse_kwargs() (in module zarrsmith.napari._mosaic_widget) fuse_tiles() (in module zarrsmith.mosaic_manager) (in module zarrsmith.mosaic_manager.fusion) fusion_tiles() (zarrsmith.mosaic_manager.mosaic.MosaicManager method) (zarrsmith.mosaic_manager.MosaicManager method) FusionPlan (class in zarrsmith.mosaic_manager) (class in zarrsmith.mosaic_manager.fusion)

G

get_available_datasets() (zarrsmith.microscope_manager.luxendo_manager.LuxendoManager class method) (zarrsmith.microscope_manager.LuxendoManager class method) get_channel_adjustment() (in module zarrsmith.napari._export_widget) get_chunks() (in module zarrsmith.utils.chunks) go_to() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) grid_shape (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute)

group (zarrsmith.mosaic_manager.Tile attribute) (zarrsmith.mosaic_manager.tile.Tile attribute) group_labels() (in module zarrsmith.napari._mosaic_widget) groups (zarrsmith.mosaic_manager.mosaic.MosaicManager property) (zarrsmith.mosaic_manager.MosaicManager property) guess_label_column() (in module zarrsmith.napari._explorer_widget)

H

H5Array (class in zarrsmith.mosaic_manager) (class in zarrsmith.mosaic_manager.h5_array) has_content() (in module zarrsmith.utils.output_path) has_path_columns() (in module zarrsmith.napari._explorer_widget)

has_zarr_name() (in module zarrsmith.utils.output_path) hex_to_rgb() (in module zarrsmith.utils.colors) hide_layers() (in module zarrsmith.napari._export_widget) HOVER_DELAY_MS (in module zarrsmith.napari._explorer_widget) HOVER_RADIUS_PX (in module zarrsmith.napari._explorer_widget)

I

image_channel_names() (in module zarrsmith.napari._explorer_widget) image_contrast_limits() (in module zarrsmith.napari._explorer_widget) IMAGE_INDEX (in module zarrsmith.napari._explorer_widget) image_sources() (in module zarrsmith.napari._explorer_widget) ImageSource (class in zarrsmith.napari._explorer_widget) index_list_from_selection() (in module zarrsmith.utils.axes) INDEX_NAMES (in module zarrsmith.mosaic_manager.opera_mosaic_manager)

infer_axes_from_ndim() (in module zarrsmith.utils.axes) infer_downscale_factors() (in module zarrsmith.utils.dataset_ops) is_czi() (in module zarrsmith.napari._mosaic_widget) is_full_resolution (zarrsmith.microscope_manager.evident_manager.VsiSceneArray property) is_read (zarrsmith.napari._explorer_widget.ImageSource property) is_zarr_store() (in module zarrsmith.utils.output_path) isatty() (zarrsmith.napari._log.EmittingStream method)

J

JUMP_CONTEXT (in module zarrsmith.napari._explorer_widget)

K

keep_plotter_columns() (zarrsmith.napari._explorer_widget.Session method)

known_updates() (in module zarrsmith.utils.dataset_ops)

L

LABEL_COLUMNS (in module zarrsmith.napari._explorer_widget) label_fields() (in module zarrsmith.mosaic_manager) (in module zarrsmith.mosaic_manager.fields) LABEL_IDS_KEY (in module zarrsmith.napari._explorer_widget) labels (zarrsmith.napari._explorer_widget.Session attribute) LABELS_LAYER (in module zarrsmith.napari._explorer_widget) layer_geometry() (in module zarrsmith.utils.visualize) layout (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) layouts (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) level_scale_ratios_from_multiscales() (in module zarrsmith.utils.downsampling) load() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) logger (in module zarrsmith.microscope_manager.evident_manager) (in module zarrsmith.microscope_manager.microscope_manager) (in module zarrsmith.microscope_manager.zarr_manager) (in module zarrsmith.microscope_manager.zeiss_manager) (in module zarrsmith.mosaic_manager.fields) (in module zarrsmith.mosaic_manager.fusion) (in module zarrsmith.mosaic_manager.luxendo_mosaic_manager) (in module zarrsmith.mosaic_manager.mosaic) (in module zarrsmith.mosaic_manager.opera_mosaic_manager) (in module zarrsmith.mosaic_manager.zeiss_mosaic_manager) (in module zarrsmith.utils.chromatic_shift) (in module zarrsmith.utils.dataset_ops)

LOGO_PATH (in module zarrsmith.napari._layout) LOGO_SIZE (in module zarrsmith.napari._layout) LuxendoManager (class in zarrsmith.microscope_manager) (class in zarrsmith.microscope_manager.luxendo_manager) LuxendoMosaicManager (class in zarrsmith.mosaic_manager) (class in zarrsmith.mosaic_manager.luxendo_mosaic_manager)

M

main() (in module zarrsmith.cli.zarrsmith) make_button_holder() (in module zarrsmith.napari._layout) make_log_appender() (in module zarrsmith.napari._log) make_log_pane() (in module zarrsmith.napari._layout) make_logo_header() (in module zarrsmith.napari._layout) make_section() (in module zarrsmith.napari._layout) make_title() (in module zarrsmith.napari._layout) MAX_BOX_PX (in module zarrsmith.napari._explorer_widget) MAX_COARSEST_SIZE (in module zarrsmith.utils.chunks) MAX_PLANE_CHUNK_BYTES (zarrsmith.microscope_manager.evident_manager.EvidentManager attribute) (zarrsmith.microscope_manager.EvidentManager attribute) MAX_THUMBNAILS (in module zarrsmith.napari._explorer_widget) mean (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaFlatfield attribute) (zarrsmith.mosaic_manager.OperaFlatfield attribute) metadata (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager attribute) (zarrsmith.microscope_manager.MicroscopeManager attribute) (zarrsmith.microscope_manager.zarr_manager.ZarrDataset attribute) (zarrsmith.microscope_manager.zarr_manager.ZarrManager attribute) (zarrsmith.microscope_manager.ZarrManager attribute) metadata_axes() (in module zarrsmith.utils.axes) metadata_axis_size() (in module zarrsmith.utils.axes) MicroscopeManager (class in zarrsmith.microscope_manager) (class in zarrsmith.microscope_manager.microscope_manager) midline (zarrsmith.mosaic_manager.fusion._Region attribute) MIN_CONTENT_HEIGHT (in module zarrsmith.napari._layout) MIN_LOG_HEIGHT (in module zarrsmith.napari._layout) MIN_POINT_SIZE (in module zarrsmith.napari._explorer_widget) MIN_WIDTH (in module zarrsmith.napari._layout) mode (zarrsmith.microscope_manager.zarr_manager.ZarrManager attribute) (zarrsmith.microscope_manager.ZarrManager attribute) module zarrsmith zarrsmith._version zarrsmith.cli zarrsmith.cli.__arguments zarrsmith.cli.zarrsmith zarrsmith.microscope_manager zarrsmith.microscope_manager.array_manager zarrsmith.microscope_manager.evident_manager zarrsmith.microscope_manager.luxendo_manager zarrsmith.microscope_manager.microscope_manager zarrsmith.microscope_manager.opera_manager zarrsmith.microscope_manager.readers zarrsmith.microscope_manager.scape_manager zarrsmith.microscope_manager.viventis_manager zarrsmith.microscope_manager.zarr_manager zarrsmith.microscope_manager.zarr_v04_manager zarrsmith.microscope_manager.zeiss_manager zarrsmith.mosaic_manager zarrsmith.mosaic_manager.czi_array zarrsmith.mosaic_manager.fields zarrsmith.mosaic_manager.fusion zarrsmith.mosaic_manager.h5_array zarrsmith.mosaic_manager.luxendo_mosaic_manager zarrsmith.mosaic_manager.mosaic zarrsmith.mosaic_manager.opera_mosaic_manager zarrsmith.mosaic_manager.readers zarrsmith.mosaic_manager.tiff_array zarrsmith.mosaic_manager.tile zarrsmith.mosaic_manager.zeiss_mosaic_manager zarrsmith.napari zarrsmith.napari._batch_csv zarrsmith.napari._convert_widget zarrsmith.napari._dataset_helpers zarrsmith.napari._explorer_widget zarrsmith.napari._export_widget zarrsmith.napari._layout zarrsmith.napari._log zarrsmith.napari._mosaic_widget zarrsmith.napari._output_check zarrsmith.utils zarrsmith.utils.axes zarrsmith.utils.chromatic_shift zarrsmith.utils.chunks zarrsmith.utils.colors zarrsmith.utils.create_empty_dataset zarrsmith.utils.create_empty_group zarrsmith.utils.czi zarrsmith.utils.dataset_ops zarrsmith.utils.downsampling zarrsmith.utils.metadata zarrsmith.utils.ngff zarrsmith.utils.ome zarrsmith.utils.output_path zarrsmith.utils.pyramid zarrsmith.utils.subset zarrsmith.utils.to_zarr zarrsmith.utils.units zarrsmith.utils.visualize zarrsmith.utils.write_image_region zarrsmith.utils.write_label_region zarrsmith.utils.zoom

MOSAIC_BATCH_COLUMNS (in module zarrsmith.napari._mosaic_widget) mosaic_convert() (in module zarrsmith.cli.zarrsmith) MOSAIC_READERS (in module zarrsmith.mosaic_manager) (in module zarrsmith.mosaic_manager.readers) (in module zarrsmith.napari._mosaic_widget) mosaic_widget() (in module zarrsmith.napari._mosaic_widget) MosaicManager (class in zarrsmith.mosaic_manager) (class in zarrsmith.mosaic_manager.mosaic) move_near_mouse() (zarrsmith.napari._explorer_widget.ThumbnailPopup method) multiple_fields (zarrsmith.mosaic_manager.fusion.FusionPlan property) (zarrsmith.mosaic_manager.FusionPlan property) multiple_fields_message() (in module zarrsmith.mosaic_manager.fields) MultipleFieldsError, [1] multiply_scales() (in module zarrsmith.utils.pyramid)

N

n_available (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) n_missing (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) n_skipped (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) name (zarrsmith.microscope_manager.zarr_manager.ZarrDataset attribute) (zarrsmith.napari._explorer_widget.ImageSource property) (zarrsmith.utils.metadata.ChannelInfo attribute) native_levels (zarrsmith.microscope_manager.evident_manager.EvidentManager attribute) (zarrsmith.microscope_manager.EvidentManager attribute) natural_key() (in module zarrsmith.mosaic_manager.fields) nbytes (zarrsmith.mosaic_manager.fusion.FusionPlan property) (zarrsmith.mosaic_manager.FusionPlan property) ndim (zarrsmith.microscope_manager.evident_manager.VsiSceneArray attribute) (zarrsmith.mosaic_manager.h5_array.H5Array attribute) (zarrsmith.mosaic_manager.H5Array attribute) (zarrsmith.mosaic_manager.PlaneStackArray attribute) (zarrsmith.mosaic_manager.tiff_array.PlaneStackArray attribute)

ngff_version (zarrsmith.microscope_manager.zarr_manager.ZarrManager attribute) (zarrsmith.microscope_manager.ZarrManager attribute) (zarrsmith.utils.ngff.ZarrWriteConfig attribute) ngff_version_override (zarrsmith.microscope_manager.zarr_manager.ZarrManager attribute) (zarrsmith.microscope_manager.ZarrManager attribute) NO_GROUP (in module zarrsmith.napari._mosaic_widget) normalize_axes() (in module zarrsmith.utils.axes) normalize_data_type() (in module zarrsmith.utils.axes) normalize_shifts() (in module zarrsmith.utils.chromatic_shift) normalize_spatial_factor() (in module zarrsmith.utils.downsampling) normalize_spatial_factor_for_axes() (in module zarrsmith.utils.downsampling) normalize_unit() (in module zarrsmith.utils.units) num_workers (zarrsmith.utils.ngff.ZarrWriteConfig attribute)

O

object_radius_um() (in module zarrsmith.napari._explorer_widget) OBJECT_RGB (in module zarrsmith.napari._explorer_widget) ObjectsExplorer (class in zarrsmith.napari._explorer_widget) offset (zarrsmith.mosaic_manager.fusion._Placed attribute) ome_color_to_hex() (in module zarrsmith.utils.colors) ome_tiff_path (zarrsmith.microscope_manager.scape_manager.ScapeManager attribute) (zarrsmith.microscope_manager.ScapeManager attribute) OmePixels (class in zarrsmith.utils.ome) open_labels() (in module zarrsmith.napari._explorer_widget) OperaFlatfield (class in zarrsmith.mosaic_manager) (class in zarrsmith.mosaic_manager.opera_mosaic_manager) OperaManager (class in zarrsmith.microscope_manager) (class in zarrsmith.microscope_manager.opera_manager) OperaMosaicManager (class in zarrsmith.mosaic_manager) (class in zarrsmith.mosaic_manager.opera_mosaic_manager)

origin (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaFlatfield attribute) (zarrsmith.mosaic_manager.OperaFlatfield attribute) (zarrsmith.mosaic_manager.Tile attribute) (zarrsmith.mosaic_manager.tile.Tile attribute) OTHER_RGB (in module zarrsmith.napari._explorer_widget) output_allowed() (in module zarrsmith.napari._output_check) output_for_drop() (in module zarrsmith.napari._mosaic_widget) output_problem() (in module zarrsmith.napari._output_check) output_refusal() (in module zarrsmith.utils.output_path) output_summary() (in module zarrsmith.napari._convert_widget) overwrite (zarrsmith.utils.ngff.ZarrWriteConfig attribute)

P

parse_acapella() (in module zarrsmith.mosaic_manager.opera_mosaic_manager) parse_channel_color() (in module zarrsmith.utils.colors) parse_color() (in module zarrsmith.utils.colors) parse_ome_xml() (in module zarrsmith.utils.ome) path (zarrsmith.microscope_manager.evident_manager.VsiSceneArray attribute) (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager attribute) (zarrsmith.microscope_manager.MicroscopeManager attribute) (zarrsmith.microscope_manager.zarr_manager.ZarrDataset attribute) (zarrsmith.microscope_manager.zarr_manager.ZarrManager attribute) (zarrsmith.microscope_manager.ZarrManager attribute) (zarrsmith.mosaic_manager.czi_array.CziTileArray attribute) (zarrsmith.mosaic_manager.CziTileArray attribute) (zarrsmith.mosaic_manager.h5_array.H5Array attribute) (zarrsmith.mosaic_manager.H5Array attribute) (zarrsmith.mosaic_manager.mosaic.MosaicManager attribute) (zarrsmith.mosaic_manager.MosaicManager attribute) path() (zarrsmith.mosaic_manager.tiff_array.TiffStackArray method) (zarrsmith.mosaic_manager.TiffStackArray method) PATH_COLUMNS (in module zarrsmith.napari._explorer_widget) path_field() (in module zarrsmith.napari._explorer_widget) path_text() (in module zarrsmith.napari._explorer_widget) paths (zarrsmith.mosaic_manager.tiff_array.TiffStackArray attribute) (zarrsmith.mosaic_manager.TiffStackArray attribute) per_timepoint (zarrsmith.mosaic_manager.fusion.FusionPlan property) (zarrsmith.mosaic_manager.FusionPlan property) picked_stack_ids() (in module zarrsmith.napari._mosaic_widget) picked_tiles() (in module zarrsmith.napari._mosaic_widget) picklable (zarrsmith.mosaic_manager.h5_array.H5Array attribute) (zarrsmith.mosaic_manager.H5Array attribute) (zarrsmith.mosaic_manager.PlaneStackArray attribute) (zarrsmith.mosaic_manager.tiff_array.PlaneStackArray attribute)

placed (zarrsmith.mosaic_manager.fusion._Region attribute) (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) plan (zarrsmith.mosaic_manager.fusion._RegionSeries attribute) plan_fusion() (in module zarrsmith.mosaic_manager) (in module zarrsmith.mosaic_manager.fusion) plan_z_extent() (in module zarrsmith.utils.chromatic_shift) planes (zarrsmith.mosaic_manager.czi_array.CziTileArray attribute) (zarrsmith.mosaic_manager.CziTileArray attribute) PlaneStackArray (class in zarrsmith.mosaic_manager) (class in zarrsmith.mosaic_manager.tiff_array) points_projection_kwargs() (in module zarrsmith.napari._dataset_helpers) popup (zarrsmith.napari._explorer_widget.ObjectsExplorer attribute) position() (zarrsmith.napari._explorer_widget.Session method) positions (zarrsmith.mosaic_manager.mosaic.MosaicManager property) (zarrsmith.mosaic_manager.MosaicManager property) prefetch() (zarrsmith.mosaic_manager.PlaneStackArray method) (zarrsmith.mosaic_manager.tiff_array.PlaneStackArray method) problem (zarrsmith.napari._explorer_widget.ImageSource attribute) profile() (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaFlatfield method) (zarrsmith.mosaic_manager.OperaFlatfield method) progress (zarrsmith.mosaic_manager.luxendo_mosaic_manager.LuxendoMosaicManager attribute) (zarrsmith.mosaic_manager.LuxendoMosaicManager attribute) (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaMosaicManager attribute) (zarrsmith.mosaic_manager.OperaMosaicManager attribute) (zarrsmith.utils.ngff.ZarrWriteConfig attribute) PROJECTIONS (in module zarrsmith.mosaic_manager.fusion) PROVENANCE_KEY (in module zarrsmith.mosaic_manager.fusion) (in module zarrsmith.utils.chromatic_shift)

R

raw_metadata (zarrsmith.microscope_manager.evident_manager.EvidentManager property) (zarrsmith.microscope_manager.EvidentManager property) read() (zarrsmith.microscope_manager.array_manager.ArrayManager method) (zarrsmith.microscope_manager.ArrayManager method) (zarrsmith.microscope_manager.evident_manager.EvidentManager method) (zarrsmith.microscope_manager.EvidentManager method) (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) (zarrsmith.microscope_manager.zeiss_manager.ZeissManager method) (zarrsmith.microscope_manager.ZeissManager method) (zarrsmith.napari._explorer_widget.ImageSource method) read_dataset() (in module zarrsmith.napari._explorer_widget) read_image() (in module zarrsmith.napari._explorer_widget) read_index() (in module zarrsmith.mosaic_manager.opera_mosaic_manager) read_plate() (in module zarrsmith.mosaic_manager.opera_mosaic_manager) read_table() (in module zarrsmith.napari._explorer_widget)

reader_options() (in module zarrsmith.mosaic_manager) (in module zarrsmith.mosaic_manager.mosaic) READERS (in module zarrsmith.microscope_manager) (in module zarrsmith.microscope_manager.readers) rechunk_to_shape() (in module zarrsmith.utils.chunks) reference_timepoint (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) refresh_tile_map() (in module zarrsmith.napari._mosaic_widget) relative_level_factors_for_axes() (in module zarrsmith.utils.downsampling) reorder_channels() (in module zarrsmith.utils.dataset_ops) (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) repeated_labels_message() (in module zarrsmith.napari._explorer_widget) RepeatedLabelsError resample() (in module zarrsmith.napari._explorer_widget) resolve_path() (in module zarrsmith.napari._explorer_widget) rows (zarrsmith.napari._explorer_widget.ImageSource attribute)

S

samples (zarrsmith.mosaic_manager.fusion._Region attribute) (zarrsmith.mosaic_manager.fusion._RegionSeries attribute) scale (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) (zarrsmith.mosaic_manager.opera_mosaic_manager.OperaFlatfield attribute) (zarrsmith.mosaic_manager.OperaFlatfield attribute) scale_for_axes() (in module zarrsmith.napari._dataset_helpers) scale_for_level() (in module zarrsmith.utils.metadata) scale_zyx (zarrsmith.utils.ome.OmePixels attribute) scan_workers (zarrsmith.mosaic_manager.luxendo_mosaic_manager.LuxendoMosaicManager attribute) (zarrsmith.mosaic_manager.LuxendoMosaicManager attribute) ScapeManager (class in zarrsmith.microscope_manager) (class in zarrsmith.microscope_manager.scape_manager) scene (zarrsmith.microscope_manager.evident_manager.VsiSceneArray property) scene_index (zarrsmith.microscope_manager.evident_manager.VsiSceneArray attribute) (zarrsmith.mosaic_manager.zeiss_mosaic_manager.ZeissMosaicManager attribute) (zarrsmith.mosaic_manager.ZeissMosaicManager attribute) scene_names() (in module zarrsmith.mosaic_manager.zeiss_mosaic_manager) scenes (zarrsmith.microscope_manager.evident_manager.EvidentManager attribute) (zarrsmith.microscope_manager.EvidentManager attribute) (zarrsmith.microscope_manager.zeiss_manager.ZeissManager attribute) (zarrsmith.microscope_manager.ZeissManager attribute) select() (zarrsmith.mosaic_manager.mosaic.MosaicManager method) (zarrsmith.mosaic_manager.MosaicManager method) select_tiles() (in module zarrsmith.napari._mosaic_widget) Selection (in module zarrsmith.utils.subset) selection_length_and_spacing() (in module zarrsmith.utils.axes) series_keys() (in module zarrsmith.mosaic_manager.tile) Session (class in zarrsmith.napari._explorer_widget) session (zarrsmith.napari._explorer_widget.ObjectsExplorer attribute) set_picked() (in module zarrsmith.napari._mosaic_widget) set_settings() (in module zarrsmith.napari._export_widget) shape (zarrsmith.microscope_manager.evident_manager.VsiSceneArray attribute) (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) (zarrsmith.mosaic_manager.h5_array.H5Array attribute) (zarrsmith.mosaic_manager.H5Array attribute) (zarrsmith.mosaic_manager.PlaneStackArray attribute) (zarrsmith.mosaic_manager.tiff_array.PlaneStackArray attribute) (zarrsmith.mosaic_manager.Tile property) (zarrsmith.mosaic_manager.tile.Tile property) shape_tuple() (in module zarrsmith.utils.chunks) shard_exclude_axes (zarrsmith.utils.ngff.ZarrWriteConfig attribute) shard_target_mb (zarrsmith.utils.ngff.ZarrWriteConfig attribute) shards (zarrsmith.utils.ngff.ZarrWriteConfig attribute) shift_along_axis() (in module zarrsmith.utils.chromatic_shift)

shift_levels() (in module zarrsmith.utils.chromatic_shift) short_name() (in module zarrsmith.napari._explorer_widget) show_drag_box() (in module zarrsmith.napari._mosaic_widget) show_first_timepoint() (in module zarrsmith.napari._mosaic_widget) show_image() (zarrsmith.napari._explorer_widget.ObjectsExplorer method) show_layers() (in module zarrsmith.napari._export_widget) show_views() (zarrsmith.napari._explorer_widget.ThumbnailPopup method) shown_contrast_limits() (in module zarrsmith.napari._mosaic_widget) SIGMOID_STEEPNESS (in module zarrsmith.mosaic_manager.fusion) size (zarrsmith.mosaic_manager.fusion._Placed attribute) size_c (zarrsmith.utils.ome.OmePixels attribute) SIZE_COLUMNS (in module zarrsmith.napari._explorer_widget) size_t (zarrsmith.utils.ome.OmePixels attribute) size_x (zarrsmith.utils.ome.OmePixels attribute) size_y (zarrsmith.utils.ome.OmePixels attribute) size_z (zarrsmith.utils.ome.OmePixels attribute) skipped_tile_ids() (in module zarrsmith.napari._mosaic_widget) sort_dropped() (in module zarrsmith.napari._explorer_widget) source_of_row (zarrsmith.napari._explorer_widget.Session attribute) SPATIAL_AXES (in module zarrsmith.utils.axes) (in module zarrsmith.utils.downsampling) (in module zarrsmith.utils.ngff) spatial_axes() (in module zarrsmith.napari._explorer_widget) spatial_axes_in_order() (in module zarrsmith.utils.axes) spatial_axis_indices() (in module zarrsmith.utils.axes) SPATIAL_AXIS_SET (in module zarrsmith.utils.axes) spatial_factor_power() (in module zarrsmith.utils.downsampling) spatial_factor_power_for_axes() (in module zarrsmith.utils.downsampling) spatial_values_for_axes() (in module zarrsmith.utils.axes) SpatialFactor (in module zarrsmith.utils.downsampling) (in module zarrsmith.utils.pyramid) SpatialIntFactor (in module zarrsmith.utils.downsampling) SpatialScale (in module zarrsmith.utils.downsampling) stack_fields() (in module zarrsmith.napari._mosaic_widget) stack_id() (in module zarrsmith.napari._mosaic_widget) stacked (zarrsmith.mosaic_manager.fusion._RegionSeries attribute) storage_options (zarrsmith.utils.ngff.ZarrWriteConfig attribute) subset_dask_array() (in module zarrsmith.utils.subset) subset_dataset() (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) subset_levels() (in module zarrsmith.utils.dataset_ops) subset_metadata() (in module zarrsmith.utils.subset) summary() (zarrsmith.mosaic_manager.fusion.FusionPlan method) (zarrsmith.mosaic_manager.FusionPlan method)

T

T (in module zarrsmith.utils.ome) TABLE_SUFFIXES (in module zarrsmith.napari._explorer_widget) text (zarrsmith.napari._explorer_widget.ThumbnailPopup attribute) text_written (zarrsmith.napari._log.EmittingStream attribute) thumbnail() (zarrsmith.napari._explorer_widget.Session method) THUMBNAIL_CONTEXT (in module zarrsmith.napari._explorer_widget) THUMBNAIL_PX (in module zarrsmith.napari._explorer_widget) thumbnail_views() (in module zarrsmith.napari._explorer_widget) ThumbnailPopup (class in zarrsmith.napari._explorer_widget) tiffdata (zarrsmith.utils.ome.OmePixels attribute) TiffStackArray (class in zarrsmith.mosaic_manager) (class in zarrsmith.mosaic_manager.tiff_array) Tile (class in zarrsmith.mosaic_manager) (class in zarrsmith.mosaic_manager.tile) tile (zarrsmith.mosaic_manager.fusion._Placed attribute) tile() (zarrsmith.mosaic_manager.mosaic.MosaicManager method) (zarrsmith.mosaic_manager.MosaicManager method) tile_at() (in module zarrsmith.napari._mosaic_widget) tile_footprints() (in module zarrsmith.napari._mosaic_widget) tile_id() (zarrsmith.mosaic_manager.mosaic.MosaicManager method) (zarrsmith.mosaic_manager.MosaicManager method) tile_layers() (in module zarrsmith.napari._mosaic_widget) TILE_MAP (in module zarrsmith.napari._mosaic_widget) TILE_MODES (in module zarrsmith.napari._mosaic_widget) tiles (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) (zarrsmith.mosaic_manager.mosaic.MosaicManager attribute) (zarrsmith.mosaic_manager.MosaicManager attribute)

tiles_by_ids() (zarrsmith.mosaic_manager.mosaic.MosaicManager method) (zarrsmith.mosaic_manager.MosaicManager method) tiles_in_box() (in module zarrsmith.napari._mosaic_widget) time_column (zarrsmith.napari._explorer_widget.Session attribute) TIME_COLUMNS (in module zarrsmith.napari._explorer_widget) time_increment (zarrsmith.utils.ome.OmePixels attribute) time_increment_unit (zarrsmith.utils.ome.OmePixels attribute) time_index (zarrsmith.mosaic_manager.fusion._Region attribute) timepoint (zarrsmith.mosaic_manager.Tile attribute) (zarrsmith.mosaic_manager.tile.Tile attribute) timepoints (zarrsmith.mosaic_manager.fusion.FusionPlan attribute) (zarrsmith.mosaic_manager.FusionPlan attribute) (zarrsmith.mosaic_manager.mosaic.MosaicManager property) (zarrsmith.mosaic_manager.MosaicManager property) TITLE_STYLE (in module zarrsmith.napari._layout) to_micrometers() (in module zarrsmith.utils.units) to_tczyx() (in module zarrsmith.utils.axes) to_zarr() (in module zarrsmith.utils.to_zarr) (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) toggle_tile_at() (in module zarrsmith.napari._mosaic_widget) total (zarrsmith.mosaic_manager.fusion._RegionSeries attribute) transform (zarrsmith.mosaic_manager.tiff_array.TiffStackArray attribute) (zarrsmith.mosaic_manager.TiffStackArray attribute) transitions (zarrsmith.mosaic_manager.fusion._Region attribute)

U

units (zarrsmith.mosaic_manager.Tile attribute) (zarrsmith.mosaic_manager.tile.Tile attribute) units_for_axes() (in module zarrsmith.utils.visualize) units_kwargs() (in module zarrsmith.napari._dataset_helpers)

units_zyx (zarrsmith.utils.ome.OmePixels attribute) update_metadata() (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method)

V

VALID_UPDATE_KEYS (in module zarrsmith.utils.dataset_ops) version (in module zarrsmith._version) version_tuple (in module zarrsmith._version) views (zarrsmith.napari._explorer_widget.ThumbnailPopup attribute) visualize() (in module zarrsmith.utils.visualize) (zarrsmith.microscope_manager.microscope_manager.MicroscopeManager method) (zarrsmith.microscope_manager.MicroscopeManager method) (zarrsmith.mosaic_manager.mosaic.MosaicManager method) (zarrsmith.mosaic_manager.MosaicManager method)

visualize_zarr() (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) ViventisManager (class in zarrsmith.microscope_manager) (class in zarrsmith.microscope_manager.viventis_manager) voxel_size (zarrsmith.mosaic_manager.Tile attribute) (zarrsmith.mosaic_manager.tile.Tile attribute) voxel_sizes() (in module zarrsmith.napari._explorer_widget) VsiSceneArray (class in zarrsmith.microscope_manager.evident_manager)

W

warn_user() (in module zarrsmith.napari._output_check) WELL_PITCH (in module zarrsmith.mosaic_manager.opera_mosaic_manager) write() (zarrsmith.napari._log.EmittingStream method) write_chromatic_shift_corrected() (in module zarrsmith.utils.chromatic_shift) write_empty_pyramid() (in module zarrsmith.utils.create_empty_dataset) write_image_region() (in module zarrsmith.utils.write_image_region) (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method)

write_label_region() (in module zarrsmith.utils.write_label_region) (zarrsmith.microscope_manager.zarr_manager.ZarrManager method) (zarrsmith.microscope_manager.ZarrManager method) write_multiscale_to_group() (in module zarrsmith.utils.to_zarr) WrongReaderError, [1]

X

xml_attr() (in module zarrsmith.utils.ome)

Z

zarr_convert() (in module zarrsmith.cli.zarrsmith) zarr_data (zarrsmith.microscope_manager.zarr_manager.ZarrDataset attribute) zarr_format (zarrsmith.utils.ngff.ZarrWriteConfig attribute) zarr_format_override (zarrsmith.microscope_manager.zarr_manager.ZarrManager attribute) (zarrsmith.microscope_manager.ZarrManager attribute) ZARR_METADATA_FILES (in module zarrsmith.utils.output_path) zarr_path() (in module zarrsmith.napari._explorer_widget) ZarrDataset (class in zarrsmith.microscope_manager.zarr_manager) ZarrManager (class in zarrsmith.microscope_manager) (class in zarrsmith.microscope_manager.zarr_manager) zarrsmith module zarrsmith._version module zarrsmith.cli module zarrsmith.cli.__arguments module zarrsmith.cli.zarrsmith module zarrsmith.microscope_manager module zarrsmith.microscope_manager.array_manager module zarrsmith.microscope_manager.evident_manager module zarrsmith.microscope_manager.luxendo_manager module zarrsmith.microscope_manager.microscope_manager module zarrsmith.microscope_manager.opera_manager module zarrsmith.microscope_manager.readers module zarrsmith.microscope_manager.scape_manager module zarrsmith.microscope_manager.viventis_manager module zarrsmith.microscope_manager.zarr_manager module zarrsmith.microscope_manager.zarr_v04_manager module zarrsmith.microscope_manager.zeiss_manager module zarrsmith.mosaic_manager module zarrsmith.mosaic_manager.czi_array module zarrsmith.mosaic_manager.fields module zarrsmith.mosaic_manager.fusion module zarrsmith.mosaic_manager.h5_array module zarrsmith.mosaic_manager.luxendo_mosaic_manager module zarrsmith.mosaic_manager.mosaic module zarrsmith.mosaic_manager.opera_mosaic_manager module zarrsmith.mosaic_manager.readers module zarrsmith.mosaic_manager.tiff_array module zarrsmith.mosaic_manager.tile module zarrsmith.mosaic_manager.zeiss_mosaic_manager module zarrsmith.napari module

zarrsmith.napari._batch_csv module zarrsmith.napari._convert_widget module zarrsmith.napari._dataset_helpers module zarrsmith.napari._explorer_widget module zarrsmith.napari._export_widget module zarrsmith.napari._layout module zarrsmith.napari._log module zarrsmith.napari._mosaic_widget module zarrsmith.napari._output_check module zarrsmith.utils module zarrsmith.utils.axes module zarrsmith.utils.chromatic_shift module zarrsmith.utils.chunks module zarrsmith.utils.colors module zarrsmith.utils.create_empty_dataset module zarrsmith.utils.create_empty_group module zarrsmith.utils.czi module zarrsmith.utils.dataset_ops module zarrsmith.utils.downsampling module zarrsmith.utils.metadata module zarrsmith.utils.ngff module zarrsmith.utils.ome module zarrsmith.utils.output_path module zarrsmith.utils.pyramid module zarrsmith.utils.subset module zarrsmith.utils.to_zarr module zarrsmith.utils.units module zarrsmith.utils.visualize module zarrsmith.utils.write_image_region module zarrsmith.utils.write_label_region module zarrsmith.utils.zoom module ZarrV04Manager (class in zarrsmith.microscope_manager) (class in zarrsmith.microscope_manager.zarr_v04_manager) ZarrWriteConfig (class in zarrsmith.utils.ngff) ZeissManager (class in zarrsmith.microscope_manager) (class in zarrsmith.microscope_manager.zeiss_manager) ZeissMosaicManager (class in zarrsmith.mosaic_manager) (class in zarrsmith.mosaic_manager.zeiss_mosaic_manager) zrange (zarrsmith.mosaic_manager.fusion._Region attribute)